[0001] This application claims priority to U.S. Provisional Application No.62/180,042, filed June 15, 2015, the contents of which are hereby incorporated by reference in the entirety for all purposes.

BACKGROUND OF THE INVENTION

[0002] The oil palm (E. guineensis and E. oleifera) can be classified into separate groups based on its fruit characteristics, and has three naturally occurring fruit types which vary in shell thickness and oil yield. Dura type palms are homozygous for a wild type allele of the shell gene (sh+/sh+), have a thick seed coat or shell (2-8mm) and produce approximately 5.3 tons of oil per hectare per year. Tenera type palms are heterozygous for a wild type and mutant allele of the shell gene (sh+/sh-), have a relatively thin shell surrounded by a distinct fiber ring, and produce approximately 7.4 tons of oil per hectare per year. Finally, pisifera type palms are homozygous for a mutant allele of the shell gene (sh-/sh-), have no seed coat or shell, and are usually female sterile (Hartley, 1988) (Table 1). Therefore, the inheritance of the single gene controlling shell phenotype is a major contributor to palm oil yield.

[0003] Tenera palms are hybrids between the dura and pisifera palms. Whitmore (1973) described the various fruit forms as different varieties of oil palm. However, Latiff (2000) was in agreement with Purseglove (1972) that varieties or cultivars as proposed by Whitmore (1973), do not occur in the strict sense in this species. As such, Latiff (2000) proposed the term“race” to differentiate dura, pisifera and tenera. Race was considered an appropriate term as it reflects a permanent microspecies, where the different races are capable of exchanging genes with one another, which has been adequately demonstrated in the different fruit forms observed in oil palm (Latiff, 2000). In fact, the characteristics of the three different races turn out to be controlled simply by the inheritance of a single gene. Genetic studies revealed that the shell gene shows co-dominant monogenic inheritance, which is exploitable in breeding programmes (Beirnaert and Vanderweyen, 1941).

[0004] The shell gene responsible for this phenotype was first reported in the Belgian Congo in the 1940’s (Beirnaert and Venderweyan, 1941). However, tenera fruit forms were recognized and exploited in Africa well before then (Devuyst, 1953; Godding, 1930; Sousa et al., 2011). Given the central role played by the shell gene, oil palm breeding utilizes reciprocal recurrent selection of maternal (dura) and paternal (pisifera) pools using the North Carolina Model 1 maize breeding design (Rajanaidu el al., 2000). The Deli dura population, direct descendants of the four original African palms planted in Bogor Botanical Garden, Indonesia (1848), has excellent combining ability with the AVROS (Algemene Vereniging van Rubberplanters ter Oostkust van Sumatra) and other pisifera parental palms. AVROS pisifera palms were derived from the famous“Djongo” palm from Congo, but more recently several different accessions of dura and pisifera have also been sourced from Africa (Rajanaidu el al., 2000).

[0005] Tenera fruit types have a higher mesocarp to fruit ratio, which directly translates to significantly higher oil yield than either the dura or pisifera palm (as illustrated in Table 1).

[0006] Since the crux of the breeding programmes in oil palm is to produce planting materials with higher oil yield, the tenera palm is the preferred choice for commercial planting. It is for this reason that substantial resources are invested by commercial seed producers to cross selected dura and pisifera palms in hybrid seed production. And despite

the many advances which have been made in the production of hybrid oil palm seeds, two significant problems remain in the seed production process. First, batches of tenera seeds, which will produce the high oil yield tenera type palm, are often contaminated with dura seeds (Donough and Law, 1995). Today, it is estimated that dura contamination of tenera seeds can reach rates of approximately 5% (reduced from as high as 20-30% in the early 1990’s as the result of improved quality control practices). Seed contamination is due in part to the difficulties of producing pure tenera seeds in open plantation conditions, where workers use ladders to manually pollinate tall trees, and where palm flowers for a given bunch mature over a period time, making it difficult to pollinate all flowers in a bunch with a single manual pollination event. Some flowers of the bunch may have matured prior to manual pollination and therefore may have had the opportunity to be wind pollinated from an unknown tree, thereby producing contaminant seeds in the bunch. Alternatively premature flowers may exist in the bunch at the time of manual pollination, and may mature after the pollination occurred allowing them to be wind pollinated from an unknown tree thereby producing contaminant seeds in the bunch. Prior to the invention described herein, it was not possible to identify the fruit type of a given seed or a given plant arising from a seed until the plant matured enough to produce a first batch of fruit, which typically takes approximately six years after germination. Notably, in the four to five years interval from germination to fruit production, significant land, labor, financial and energy resources are invested into what are believed to be tenera trees, some of which will ultimately be of the unwanted low yielding contaminant fruit types. By the time these suboptimal trees are identified, it is impractical to remove them from the field and replace them with tenera trees, and thus growers achieve lower palm oil yields for the 25 to 30 year production life of the contaminant trees. Therefore, the issue of contamination of batches of tenera seeds with dura or pisifera seeds is a problem for oil palm breeding, underscoring the need for a method to predict the fruit type of seeds and nursery plantlets with high accuracy.

[0007] A second problem in the seed production process is the investment seed producers make in maintaining dura and pisifera lines, and in the other expenses incurred in the hybrid seed production process. Traditionally, there was no know way to produce a tree with an optimal shell phenotype which when crossed to itself or to another tree with optimal shell phenotype would produce seeds which would only generate optimal shell phenotypes.

Therefore, there is a need to engineer trees to breed true from one generation to the next for optimal shell phenotype. There is also a need to separate predicted tenera plants (e.g., seeds or seedlings) from any contaminating dura and/or pisifera plants produced during the the

hybrid production process. Similarly, there is a need to separate predicted dura plants from pisifera and/or tenera plants and predicted pisifera plants from dura and/or tenera plants to maintain breeding stocks for hybrid production.

[0008] The genetic mapping of the SHELL gene was initially attempted by Mayes et al. (1997). A second group in Brazil, using a combination of bulked segregation analysis (BSA) and genetic mapping, reported two random amplified polymorphic DNA (RAPD) markers flanking the shell locus (Moretzsohn et al., 2000). More recently, Billotte et al., (2005) reported a simple sequence repeat (SSR)–based high density linkage map for oil palm, involving a cross between a thin shelled E. guineensis (tenera) palm and a thick shelled E. guineensis (dura) palm. A patent application filed by the Malaysian Palm Oil Board (MPOB) describes the identification of a marker using restriction fragment technology, in particular a Restriction Fragment Length Polymorphism (RFLP) marker linked to the shell gene for plant identification and breeding purposes (RAJINDER SINGH, LESLIE OOI CHENG-LI, RAHIMAH A. RAHMAN AND LESLIE LOW ENG TI.2008. Method for identification of a molecular marker linked to the shell gene of oil palm. Patent Application No. PI 20084563. Patent Filed on 13 Nov 2008). The RFLP marker (SFB 83) was identified by way of generation or construction of a genetic map for a tenera fruit type palm. The patent application publications U.S.2013/024729 and U.S.2015/0037793, filed by MPOB, describe the identification of the SHELL gene, two pisifera alleles (shAVROS and shMPOB) and methods for predicting fruit form phenotype by detecting wild-type and pisifera alleles of the SHELL gene.

BRIEF SUMMARY OF THE INVENTION

[0009] Here we describe the identification of novel alleles of the SHELL gene responsible for different fruit form phenotypes and methods for predicting or determining the shell phenotype of a palm plant (including but not limited to a whole palm plant or palm seed). The SHELL gene is an oil palm MADS-box gene substantially similar to Arabidopsis SEEDSTICK (STK), also referred to as AGAMOUS-like 11 (AGL11), as well as to

Arabidopsis SHATTERPROOF (SHP1), also referred to as AGAMOUS-like 1 (AGL1).

[0010] Two SHELL alleles, shMPOB and shAVROS, have been previously identified either of which result in the preferred tenera fruit form when present in an oil palm having one copy of a mutant allele and one wild-type allele. For example, heterozygous oil palms including the wildtype SHELL allele, ShDeliDura, on one chromosome and either of the two mutant SHELL alleles on the other chromosome exhibit a tenera phenotype.

[0011] Described herein are nine additional mutations in exon one of the SHELL gene, referred to as SHELL alleles three (3), four (4), five (5), six (6), seven (7), eight (8), nine (9), ten (10), and eleven (11). The amino acid sequences of the SHELL gene product resulting from alleles 3-11 are depicted in SEQ ID NOs:3-11 respectively. The nucleotide sequences for exon 1 of the SHELL gene for alleles 3-11 are depicted in SEQ ID NOs:13-21 respectively. As with the shMPOB and shAVROS alleles, the presence of these SHELL alleles can result in a tenera phenotype when heterozygous with a wild-type allele or a pisifera phenotype when either homozygous, or heterozygous with another non-functional SHELL allele.

[0012] In reference to the wild-type SHELL (ShDeliDura) gene, the allele 3 polymorphism is an adenosine to cytosine (AÆC) mutation at nucleotide position 67 of exon 1 of the SHELL gene. Allele 3 results in a lysine to glutamine substitution within the conserved MADS box domain of SHELL. As diagrammed in FIG.1, the entire MADS box domain of SHELL is encoded by exon 1 of the SHELL gene. The variant amino acid occurs 6 amino acids N-terminal to the amino acid substitution arising from the shMPOB allele, 8 amino acids N-terminal to the amino acid substitution arising from the shAVROS allele, and at position 23 of the translated open reading frame of exon 1 (FIG.2 and 3).

[0013] Similarly, the allele 4 polymorphism is a cytosine to adenosine (CÆA) mutation at nucleotide position 122 of exon 1 of the SHELL gene. Allele 4 results in an alanine to aspartate substitution within the conserved MADS box domain of SHELL. The variant amino acid occurs at position 41 of the translated open reading frame of exon 1 (FIG.2 and 3).

[0014] The allele 5 polymorphism is an adenosine to thymine (AÆT) mutation at nucleotide position 69 of exon 1 of the SHELL gene. Allele 5 results in a lysine to asparagine mutation at postion 23 of the translated open reading frame of exon 1 (FIG.2 and 3). The allele 6 polymorphism is a guanosine to cytosine (GÆC) mutation at position 34 of exon 1 of the SHELL gene. Allele 6 results in a glutamate to glutamine mutation at position 12 of the translated open reading frame of exon 1 (FIG.2 and 3). The allele 7 polymorphism is a deletion of fifteen nucleotides at positions 23-37 of exon 1 of the SHELL gene (or nucleotides 22-36 because alignment of the gap is ambiguous). Allele 7 results in an in frame deletion of five amino acids at positions 8 to 12 of the translated open reading frame of exon 1 (FIG.2 and 3). Amino acid positions 8 to 12 of the SHELL gene are encoded by nucleotides 22-36. The allele 8 polymorphism is a guanosine to adenosine (GÆA) mutation

at position 71 of exon 1 of the SHELL gene. Allele 8 results in an arginine to histidine mutation at position 24 of the translated open reading frame of exon 1 (FIG.2 and 3).

[0015] The allele 9 polymorphism is a cytosine to guanosine (CÆG) mutation at position 70 of exon 1 of the SHELL gene. Allele 9 results in an arginine to glycine mutation at position 24 of the translated open reading frame of exon 1. The allele 10 polymorphism is a thymine to adenosine (TÆA) mutation at position 110 of exon 1 of the SHELL gene. Allele 10 results in a valine to aspartate mutation at position 37 of the translated open reading frame of exon 1 (FIG.2 and 3).

[0016] The allele 11 polymorphism is a thymine to cytosine (TÆC) mutation at position 114 of exon 1 of the SHELL gene. Allele 11 is a silent mutation in that it does not affect the resulting amino acid sequence of the SHELL gene product (FIG.2 and 3). This mutation can be detected to confirm or predict the presence or absence of a wildtype SHELL gene product and therefore predict a dura phenotype when homozygous or heterozygous with another wildtype allele in a palm plant and a tenera phenotype when heterozygous with an inactive SHELL allele. Alternatively, in some embodiments this mutation can affect gene expression and/or transcriptional or translational regulation of the SHELL gene. Accordingly in such embodiments, the mutation can correlate with a pisifera when homozygous or heterozygous with an inactive SHELL allele in a palm plant or tenera when heterozygous with a wildtype allele.

[0017] Also described herein is a mutation in intron 1 of the SHELL gene that has been discovered in a subset of oil palm plants having the allele 3 mutation. This mutation is referred to herein as allele 12 and depicted in SEQ ID NO:12. The mutation results in deletion of four nucleotides at positions 43-46 of intron 1 of the wild-type SHELL (ShDeliDura) gene. The mutation may be silent in that it may not by itself contribute to the presence or absence of a SHELL fruit form phenotype (e.g., dura, tenera, or pisifera). However, due to the close physical distance (i.e., genetic linkage) between the intron 1 mutation and exon 1, the contribution of parental germ plasm known to have a particular SHELL allele (wild-type or mutant) within exon 1 and the intron 1 marker can be tracked with a high degree of confidence in progeny by detection of the allele 12 mutation rather than a mutation in exon 1. Moreover, in some cases, the mutation in intron 1 may be in linkage disequilibrium with exon 1 or a portion thereof. Alternatively, allele 12 may alter transcriptional regulation or splicing and thus exhibit a pisifera SHELL phenotype when homozygous or a tenera phenotype when heterozygous with a wildtype SHELL allele.

[0018] Nuclear proteins, such as transcription factors, must be actively transported into and retained within the nucleus to be functional. The nuclear localization mechanism involves the binding of nuclear localization protein signals in the nuclear protein to importin α and importin β subunits in the cytoplasm. Importin α binds to the nuclear localization signal (NLS), while importin β interacts with importin α as well as the nuclear pore. In plant MADS box proteins, the prominent NLS amino acid motif is KR[K or R]X4KK (SEQ ID NO:29), where X can be any amino acid (Gramzow and Theissen, 2010). The SHELL MADS box domain includes this motif (KRRNGLLKK; SEQ ID NO:30) at amino acids 23-31. MADS box proteins may also have a bipartite NLS which that involves additional upstream amino acids. An example is the bipartite NLS of petunia FLORAL BINDING PROTEIN 11 (FBP11) which includes the sequence

MGRGKIEIKRIENNTNRQVTFCKRRNGLLKK (SEQ ID NO:31). The bipartite NLS is made up of NLS amino acids (underlined), as well as conserved basic amino acids

(italicized), all of which contribute to the nuclear localization mechanism (Immink et al., 2002).

[0019] The SHELL MADS box domain includes a very similar bipartite NLS including amino acids 3, 5, 9-10, and 21-31 (MGRGKIEIKRIENTTSRQVTFCKRRNGLLKK; SEQ ID NO:32) (FIG.2 and 3). It is noteworthy that of the ten sequence changes resulting in amino acid substitutions or deletions reported here (shAVROS, shMPOB, and alleles 3-10), six change one or more of these highly conserved NLS amino acids (shAVROS, shMPOB, allele 3, allele 5, allele 7, allele 8 and allele 9), and a 7th (shMPOB) introduces a proline substitution at a variable position within the prominent NLS that would be expected to significantly alter the secondary structure of the protein within the NLS domain (FIG.2 and 3). These findings suggest that a common mechanism imparting the pisifera (when homozygous or heterozygous with another nonfunctional SHELL allele) or tenera (when heterozygous with a wildtype SHELL allele) phenotype may be the reduction or prevention of the nuclear localization of nonfunctional SHELL proteins or dimers of SHELL proteins with other MADS box transcription factors. Therefore, it is likely that mutation of any of the conserved NLS amino acids (boxed in FIG. 2 and 3), or any mutation that disrupted SHELL NLS function, can be associated with the pisifera or tenera phenotype.

[0020] Accordingly in one aspect, methods for determining or predicting the shell phenotype of a palm (e.g., oil palm) plant (including but not limited to a whole palm plant or palm seed) are provided. In some embodiments, the method comprises, providing a sample from the plant or seed; and determining from the sample the genotype of a polymorphic

marker at a position in exon 1 of the SHELL gene selected from the group consisting of nucleotides:

(i) 7, 8, 9, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 109, 110, 111, 114, 121, 122, and 123;

(ii) 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 67, 69, 70, 71, 110, 114, and 122; or

(iii) 7-9, 13-15, 25-30, 61-75 and 88-92. In some cases, heterozygosity at one or more of the polymorphic markers for a pisifera and a dura allele predicts the presence of the tenera shell phenotype. In some cases, homozygosity for a genotype of a predicted pisifera allele at one or more of the polymorphic markers predicts the presence of the pisifera shell phenotype. In some cases, the genotype of the polymorphic marker can comprise one or more of the predicted pisifera allele genotypes depicted in SEQ ID NOs:13-21.

[0021] In some cases, a mutation with respect to the wild-type SHELL (ShDeliDura) gene at one or more of the nucleotide positions that results in an amino acid substitution (e.g., non-conservative substitution), deletion, insertion, or frameshift can predict a pisifera phenotype when homozygous or heterozygous with a different mutation with respect to the wild-type SHELL (ShDeliDura) gene, or a tenera phenotype when heterozygous with respect to the wild-type allele. For example, a mutation with respect to the wild-type SHELL (ShDeliDura) gene at one or more of the nucleotide positions that results in an amino acid substitution (e.g., non-conservative substitution), deletion, insertion, or frameshift can predict a pisifera phenotype when heterozygous with a different mutation that results in a non-functional SHELL gene, such as a mutation that results in a different substitution (e.g., non-conservative substitution), deletion, insertion, or frameshift.

[0022] In some embodiments, the genotype of the polymorphic marker comprises a deletion or mutation of one or more nucleotides selected from the group consisting of nucleotides: (i) 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, and 37; (ii) 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, and 36; or (iii) 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, and 37, of exon 1 of the SHELL gene. In some embodiments, the genotype of the polymorphic marker comprises a deletion of one or more, or all, of nucleotides 23-37 (or 22-36) of exon 1 of the SHELL gene. In some embodiments, the genotype of the polymorphic marker comprises a mutation of nucleotide 34 of exon 1 of the SHELL gene (e.g., a mutation relative to ShDeliDura). In some embodiments, the mutation

comprises a missense (e.g., non-conservative substitution), nonsense, insertion, deletion, or frameshift mutation. In some embodiments, the genotype of the polymorphic marker comprises a cytosine (C) at nucleotide 34 of exon 1 of the SHELL gene.

[0023] In some embodiments, the genotype of the polymorphic marker comprises a mutation of nucleotide 67 of exon 1 of the SHELL gene (e.g., a mutation relative to

ShDeliDura). In some embodiments, the mutation comprises a missense (e.g., non-conservative substitution), nonsense, insertion, deletion, or frameshift mutation. In some embodiments, the genotype of the polymorphic marker comprises a cytosine (C) at nucleotide 67 of exon 1 of the SHELL gene. In some embodiments, the genotype of the polymorphic marker comprises a mutation of nucleotide 69 of exon 1 of the SHELL gene (e.g., a mutation relative to ShDeliDura). In some embodiments, the mutation comprises a missense (e.g., non-conservative substitution), nonsense, insertion, deletion, or frameshift mutation. In some embodiments, the genotype of the polymorphic marker comprises a thymine (T) at nucleotide 69 of exon 1 of the SHELL gene.

[0024] In some embodiments, the genotype of the polymorphic marker comprises a mutation of nucleotide 70 of exon 1 of the SHELL gene (e.g., a mutation relative to

ShDeliDura). In some embodiments, the mutation comprises a missense (e.g., non-conservative substitution), nonsense, insertion, deletion, or frameshift mutation. In some embodiments, the genotype of the polymorphic marker comprises a guanosine (G) at nucleotide 70 of exon 1 of the SHELL gene. In some embodiments, the genotype of the polymorphic marker comprises a mutation of nucleotide 71 of exon 1 of the SHELL gene (e.g., a mutation relative to ShDeliDura). In some embodiments, the mutation comprises a missense (e.g., non-conservative substitution), nonsense, insertion, deletion, or frameshift mutation. In some embodiments, the genotype of the polymorphic marker comprises an adenosine (A) at nucleotide 71 of exon 1 of the SHELL gene. In some embodiments, the genotype of the polymorphic marker comprises a mutation of nucleotide 110 of exon 1 of the SHELL gene (e.g., a mutation relative to ShDeliDura). In some embodiments, the mutation comprises a missense (e.g., non-conservative substitution), nonsense, insertion, deletion, or frameshift mutation. In some embodiments, the genotype of the polymorphic marker comprises an adenosine (A) at nucleotide 110 of exon 1 of the SHELL gene.

[0025] In some embodiments, the genotype of the polymorphic marker comprises a mutation of nucleotide 114 of exon 1 of the SHELL gene (e.g., a mutation relative to ShDeliDura). In some embodiments, the mutation comprises a missense (e.g., non-conservative substitution), nonsense, insertion, deletion, or frameshift mutation. In some embodiments, the genotype of the polymorphic marker comprises a cytosine (C) at nucleotide 114 of exon 1 of the SHELL gene. In some embodiments, the genotype of the polymorphic marker comprises a mutation of nucleotide 122 of exon 1 of the SHELL gene (e.g., a mutation relative to ShDeliDura). In some embodiments, the mutation comprises a missense (e.g., non-conservative substitution), nonsense, insertion, deletion, or frameshift mutation. In some embodiments, the genotype of the polymorphic marker comprises an adenosine (A) at nucleotide 122 of exon 1 of the SHELL gene.

[0026] In any one of the foregoing embodiments, the method can comprise, providing a sample from the plant or seed; and determining from the sample the genotype of a polymorphic marker at a position in exon 1 of the SHELL gene selected from the group consisting of nucleotides:

(i) 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 110, 114, and 122;

(ii) 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 67, 69, 70, 71, 110, 114, and 122 ; or

(iii) 67, 69, 70, and 71. In some cases, heterozygosity at one or more of the polymorphic markers for a pisifera and a dura allele predicts the presence of the tenera shell phenotype. In some cases, homozygosity for a genotype of a predicted pisifera allele at one or more of the polymorphic markers predicts the presence of the pisifera shell phenotype. In some cases, heterozygosity for a genotype of a first predicted pisifera allele at one or more of the polymorphic markers and a second predicted pisifera allele at one or more of the polymorphic markers predicts the presence of the pisifera shell phenotype. In some cases, the genotype of the polymorphic marker can comprise one or more of the predicted pisifera allele genotypes depicted in SEQ ID NOs:13, 15, 17, 18, and 19.

[0027] In some embodiments, the method comprises, providing a sample from the plant or seed; and determining from the sample the genotype of a polymorphic marker at a position in intron 1 of the SHELL gene selected from the group consisting of nucleotides 43, 44, 45, and 46. In some cases, heterozygosity at one or more of the polymorphic markers for a pisifera and a dura allele predicts the presence of the tenera shell phenotype. In some cases, homozygosity for a genotype of a predicted pisifera allele at one or more of the polymorphic markers predicts the presence of the pisifera shell phenotype. In some cases, heterozygosity for a genotype of a first predicted pisifera allele at one or more of the polymorphic markers and a genotype of a second predicted pisifera allele at one or more of the polymorphic

markers predicts the presence of the pisifera shell phenotype. In some cases, the genotype of the polymorphic marker can comprise one or more, or all, of the deleted of the nucleotides of intron 1 depicted in SEQ ID NO:12.

[0028] In some embodiments, the method comprises, providing a sample from the plant or seed; and detecting in the sample a genotype of a polymorphic marker that encodes for a mutation in the SHELL gene product at one or more amino acid positions selected from the group consisting of amino acid positions 3, 5, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 30, 37, and 4,1 selected from the group consisting of amino acid positions 3, 5, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 37, and 41, selected from the group consisting of amino acid positions 8, 9, 10, 11, 12, 23, 24, 37, and 41 or selected from the group consisting of amino acid positions 8, 9, 10, 11, 12, 23, 24, 31, 37, and 41. In some cases, the genotype of the polymorphic marker comprises a deletion of one or more, or all, of the amino acids at positions 8-12 of the wildtype SHELL gene product. In some cases, heterozygosity at one or more of the polymorphic markers for a pisifera and a dura allele predicts the presence of the tenera shell phenotype. In some cases, homozygosity for a genotype of a predicted pisifera allele at one or more of the polymorphic markers predicts the presence of the pisifera shell phenotype. In some cases, heterozygosity for a genotype of a first predicted pisifera allele at one or more of the polymorphic markers and a second predicted pisifera allele at one or more of the polymorphic markers predicts the presence of the pisifera shell phenotype. In some cases, the genotype of the polymorphic marker can comprise one or more of the predicted pisifera allele SHELL gene products depicted in SEQ ID NOs:3-10, or one or more of the predicted pisifera allele SHELL gene products depicted in SEQ ID NOs:3, 5, 7, 8, and 9.

[0029] In some embodiments, the genotype of the polymorphic marker comprises a mutation at amino acid position 23 as compared to the wildtype SHELL gene product. In some cases, the mutation comprises a lysine to glutamine or a lysine to asparagine mutation at amino acid position 23. In some embodiments, the genotype of the polymorphic marker comprises a mutation at amino acid position 24 as compared to the wildtype SHELL gene product. In some cases, the mutation comprises an arginine to histidine or an arginine to glycine mutation at amino acid position 24. In some embodiments, the genotype of the polymorphic maker comprises a mutation at amino acid position 37 of the wildtype SHELL gene product. In some cases, the mutation comprises a valine to aspartate mutation at amino acid 37. In some embodiments, the genotype of the polymorphic marker comprises a mutation at amino acid position 41 of the wildtype SHELL gene product. In some cases, the mutation comprises an alanine to aspartate mutation at amino acid 41.

[0030] In some embodiments, the method comprises, providing a sample from the plant or seed; and detecting in the sample a genotype of a polymorphic marker that encodes for a mutation in the SHELL gene product at a position in the nuclear localization signal (NLS) of the SHELL gene product, wherein the mutation at the position in the NLS comprises a mutation at an amino acid position selected from the group consisting of amino acid position 3, 5, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, and 30; or amino acid position 23, 24, 25, 26, 27, 28, and 30 of the SHELL gene product. In some cases, the mutation is at an amino acid position selected from the group consisting of amino acid position 23 and 24 of the SHELL gene product. In some cases, the mutation at amino acid position 23 comprises a lysine to glutamine mutation. In some cases, the mutation at amino acid position 23 comprises a lysine to asparagine mutation. In some cases, the mutation at amino acid position 24 comprises an arginine to histidine mutation. In some cases, the mutation at amino acid position 24 comprises an arginine to glycine mutation.

[0031] In some embodiments, the plant or seed is generated from i) a cross between a plant having the dura shell phenotype and a plant having the pisifera shell phenotype, ii) the selfing of a tenera palm, iii) a cross between two plants having the tenera shell phenotype, iv) a cross between a plant having the dura shell phenotype and a plant having the tenera shell phenotype, or v) a cross between a plant having the tenera shell phenotype and a plant having the pisifera shell phenotype. In some embodiments, the plant is less than 5 years old. In some embodiments, the plant is less than one year old. In some embodiments, the polymorphic marker is, or is at least, 86, 88, 90, 92, 94, 96, 97, 98, or 99% predictive of the tenera phenotype.

[0032] In some embodiments, the method further comprises selecting the seed or plant for cultivation if the plant is heterozygous for the polymorphic marker (e.g., heterozygous for a dura and a pisifera marker predicting a tenera phenotype). In some embodiments, the method further comprises selecting the seed or plant for cultivation if the plant is

homozygous for a polymorphic marker (e.g., indicating a dura or a pisifera phenotype). In some embodiments, plants or seeds are discarded, stored (e.g., stored separately from tenera plants or seeds) or cultivated (e.g., cultivated separately from tenera plants or seeds) if the plants or seeds do not have a genotype predictive of the tenera shell phenotype, such as if the plants or seeds have a genotype predictive of a pisifera phenotype or have a genotype predictive of a dura phenotype.

[0033] Also provided is a method for segregating a plurality of palm (e.g., oil palm) plants into different categories based on predicted shell phenotype. In some embodiments, the

method comprises, providing a sample from each plant in the plurality of plants; determining from the samples the genotype of at least one polymorphic marker at a position in exon 1 of the SHELL gene selected from the group consisting of: (i) nucleotides 7, 8, 9, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 109, 110, 111, 114, 121, 122, and 123; (ii) nucleotides 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, and 37; (iii) nucleotide 34; (iv) nucleotides 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, and 92; (v) nucleotides 67, 69, 70, and 71; (vi) nucleotide 67; (vii) nucleotide 69; (viii) nucleotide 70; (ix) nucleotide 71; (x) nucleotide 110; (xi) nucleotide 114; or (xii) nucleotide 122; and segregating the plants into groups based on the genotype of the polymorphic marker, wherein the groups correspond to plants predicted to have the tenera shell phenotype, plants predicted to have the dura shell phenotype, and plants predicted to have the pisifera shell phenotype.

[0034] Also provided are kits for determining the shell phenotype of a palm seed or plant. In some embodiments, the kit comprises, one or more oligonucleotide primers or probes that independently comprise:

a sequence of at least, e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 (or 20, 22, 24, 30, or more) consecutive nucleotides of SEQ ID NO:27; or;

a sequence 100% complementary to at least e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 (or 20, 22, 24, 30, or more) consecutive nucleotides of SEQ ID NO:27, wherein the one or more primers or probes independently hybridize to a sequence that is within, or within about, 5,000; 2,500; 1,000; 750; 500; 250; 200; 150; 100; 75; 50; 25, or 1 bp of a position in exon 1 of the SHELL gene selected from the group consisting of:

(i) nucleotides 7, 8, 9, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 109, 110, 111, 114, 121, 122, and 123;

(ii) nucleotides 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, and 37;

(iii) nucleotide 34;

(iv) nucleotides 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, and 92

(v) nucleotides 67, 69, 70, and 71;

(vi) nucleotide 67;

(vii) nucleotide 69;

(viii) nucleotide 70;

(ix) nucleotide 71;

(x) nucleotide 110;

(xi) nucleotide 114; or

(xii) nucleotide 122.

[0035] In some embodiments, the one or more primers or probes independently hybridize to a sequence that is adjacent to, or contains, a position in exon 1 of the SHELL gene selected from the group consisting of one or more of the foregoing groups of nucleotides (i)-(xii).

[0036] In some embodiments, the one or more primers or probes specifically hybridize to palm plant DNA or RNA.

[0037] In some embodiments, a detectable label is linked (e.g., covalently linked) to the oligonucleotide. In some embodiments, the detectable label is fluorescent.

[0038] In some embodiments, the kit further comprises a polynucleotide encoding a polypeptide comprising a sequence substantially (e.g., a least 80, 85, 90, 95, 97, 98, 99%) identical or identical to at least 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 consecutive nucleotides of SEQ ID NO:13, 14, 15, 16, 17, 18, 19, 20, or 21, wherein the polynucleotide comprises a mutation depicted in SEQ ID NO:13, 14, 15, 16, 17, 18, 19, 20, or 21 relative to wild-type, shAVROS, or shMPOB SHELL.

[0039] Also provided is an isolated nucleic acid comprising a polynucleotide encoding a polypeptide comprising a sequence substantially (e.g., a least 80, 85, 90, 95, 97, 98, 99%) identical or identical to at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 consecutive amino acids of SEQ ID NO:3, 4, 5, 6, 7, 8, 9, 10, or 11, wherein the polynucleotide comprises a mutation depicted in SEQ ID NO:13, 14, 15, 16, 17, 18, 19, 20, or 21 relative to wild-type, shAVROS, or shMPOB SHELL.

[0040] Also provided is a cell or seed or plant comprising a heterologous expression cassette, the expression cassette comprising a heterologous promoter operably linked to a

polynucleotide encoding a polypeptide comprising a sequence substantially (e.g., a least 80, 85, 90, 95, 97, 98, 99%) identical or identical to SEQ ID NO:3, 4, 5, 6, 7, 8, 9, 10, or 11, e.g., wherein the polynucleotide comprises a mutation depicted in SEQ ID NO:13, 14, 15, 16, 17, 18, 19, 20, or 21 relative to wild-type, shAVROS, or shMPOB SHELL. In some embodiments, the seed or plant is a palm (e.g., oil palm) seed or palm (e.g., oil palm) plant. In some embodiments, the polypeptide comprises the amino acid sequence of SEQ ID NO:3, 4, 5, 6, 7, 8, 9, 10, or 11. In some embodiments, the heterologous promoter results in expression level of an RNA encoding the polypeptide in the seed or plant that is less than, equal to, or more than expression of an endogenous SHELL RNA in the seed or plant. In some embodiments, the seed or plant comprises two dura alleles of an endogenous SHELL gene. In some embodiments, the seed or plant produces fruit having mature shells that are on average less than 2 mm thick, less than 3 mm thick, or are between 0.5 and 3 mm thick.

[0041] Also provided is a cell or seed or plant comprising a heterologous expression cassette, the expression cassette comprising a promoter operably linked to a polynucleotide having at least 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 consecutive nucleotides of SEQ ID NO:13, 14, 15, 16, 17, 18, 19, 20, or 21, or a complement thereof, which polynucleotide, when expressed in the seed or plant, reduces expression of an endogenous SHELL polypeptide in the seed or plant (compared to a control plant lacking the expression cassette), wherein reduced expression of the SHELL polypeptide results in reduced shell thickness of the future seeds produced by the plant. In some embodiments, the polynucleotide encodes an siRNA, antisense polynucleotide, a microRNA, or a sense suppression nucleic acid, thereby suppressing expression of an endogenous SHELL gene. In some embodiments, the seed or plant makes mature shells that are on average less than 2 mm thick, less than about 3 mm thick, or are between 0.5 and 3 mm thick.

[0042] Also provided is a method of making a plant as described above or elsewhere herein, comprising introducing the expression cassette into a plant.

[0043] Also provided is a method of cultivating the plants described herein.

[0044] Other embodiments will be evident from reading the rest of the disclosure.

DEFINITIONS

[0045] A "shell phenotype" refers to the three fruit forms of E. guineensis– dura, tenera and pisifera. The dura (wild-type) fruit form is exemplified by the presence of a shell having an average thickness of at least 2-8 mm and is typically found in palm plants having a homozygous wild-type SHELL genotype. The pisifera fruit form is exemplified by the absence of a shell and is typically found in palm plants that lack a functional SHELL gene. For example, a pisifera palm plant can have two non-functional SHELL genes (e.g., homozygous for a non-functional SHELL genotype or heterozygous for two different non-functional SHELL genotypes). The tenera fruit form is exemplified by the presence of a thin shell having an average thickness of less than about 3 mm (e.g., approximately 0.5-3 mm) and is typically found in palm plants that are heterozygous for a functional and a non-functional SHELL gene. Heterologous palm plants that overexpress or underexpress the SHELL gene or gene product or partially or completely interfere with the activity of an endogenous SHELL gene product can also exhibit a dura, tenera, or pisifera fruit form phenotype.

[0046] A "polymorphic marker" refers to a genetic marker that distinguishes between two alleles. The polymorphic marker can be a nucleotide substitution, insertion, deletion, or rearrangement, or a combination thereof.

[0047] As used herein,“detecting a genotype” refers to: (i) analyzing a nucleic acid to determine a genotype by performing a sequencing, hybridization, polymerization, or sequence specific endonuclease digestion reaction or by detecting the mass of the nucleic acid, or a portion thereof; or (ii) analyzing a polypeptide, or portion thereof, encoded by the nucleic acid by performing a sequencing, detection (e.g., ELISA), or sequence specific proteolytic digestion reaction, or by detecting the mass of the polypeptide, or a portion thereof.

[0048] As used herein, the terms“nucleic acid,”“polynucleotide” and“oligonucleotide” refer to nucleic acid regions, nucleic acid segments, primers, probes, amplicons and oligomer fragments. The terms are not limited by length and are generic to linear polymers of polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), and any other N-glycoside of a purine or pyrimidine base, or modified purine or pyrimidine bases. These terms include double- and single-stranded DNA, as well as double-and single-stranded RNA.

[0049] A nucleic acid, polynucleotide or oligonucleotide can comprise, for example, phosphodiester linkages or modified linkages including, but not limited to phosphotriester, phosphoramidate, siloxane, carbonate, carboxymethylester, acetamidate, carbamate, thioether, bridged phosphoramidate, bridged methylene phosphonate, phosphorothioate,

methylphosphonate, phosphorodithioate, bridged phosphorothioate or sulfone linkages, and combinations of such linkages.

[0050] A nucleic acid, polynucleotide or oligonucleotide can comprise the five biologically occurring bases (adenine, guanine, thymine, cytosine and uracil) and/or bases other than the five biologically occurring bases.

[0051] Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Add. APL. Math.2:482 (1981), by the homology alignment algorithm of Needle man and Wunsch J. Mol. Biol.48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (U.S.A.) 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, WI), or by inspection.

[0052] "Percentage of sequence identity" is determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.

[0053] The term "substantial identity" of polypeptide sequences means that a polypeptide comprises a sequence that has at least 75% sequence identity. Alternatively, percent identity can be any integer from 75% to 100%. Exemplary embodiments include at least: 75%, 80%, 85%, 90%, 95%, or 99% compared to a reference sequence using the programs described herein; preferably BLAST using standard or default parameters, as described below. One of skill will recognize that these values can be appropriately adjusted to determine

corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning and the like. Polypeptides which are "substantially similar" share sequences as noted above except that residue positions which are not identical may differ by conservative amino acid changes. Conservative amino acid substitutions refer to the interchangeability of residues having similar side chains. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; a group of amino acids having acidic side chains is aspartic acid and glutamic acid; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Preferred conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine.

[0054] One indication that nucleotide sequences are substantially identical is if two molecules hybridize to each other, or a third nucleic acid, under stringent conditions.

Stringent conditions are sequence dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5oC lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Typically, stringent conditions will be those in which the salt concentration is about 0.02 molar at pH 7 and the temperature is at least about 60oC.

[0055] The term "promoter" or“regulatory element” refers to a region or sequence determinants located upstream or downstream from the start of transcription and which are involved in recognition and binding of RNA polymerase and other proteins to initiate transcription. Promoters need not be of plant origin, for example, promoters derived from plant viruses, such as the CaMV35S promoter, can be used.

[0056] The term "plant" includes whole plants, shoots, vegetative organs/structures (e.g. leaves, stems and tubers), roots, flowers and floral organs/structures (e.g. bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (e.g. vascular tissue, seed tissue, ground tissue, and the like) and cells (e.g. guard cells, egg cells, trichomes and the like), and progeny of same. The class of plants that can be used in the method of the invention is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), gymnosperms, ferns, and multicellular algae. It includes plants of a variety of ploidy levels, including aneuploid, polyploid, diploid, haploid and hemizygous. In an exemplary embodiment, the plant is an oil

palm plant (E. guineensis or E. oleifera, or a hybrid thereof). In some cases, the plant is E. guineensis.

[0057] An“expression cassette” refers to a nucleic acid construct, which when introduced into a host cell, results in transcription and/or translation of a RNA or polypeptide, respectively. Antisense constructs or sense constructs that are not or cannot be translated are expressly included by this definition. The expression cassette can contain a heterologous promoter.

[0058] The term "operably linked" refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.

[0059] A polynucleotide sequence or amino acid sequence is“heterologous to” an organism or a second polynucleotide sequence if it originates from a foreign species, or, if from the same species, is modified from its original form. For example, a heterologous promoter operably linked to a coding sequence refers to a promoter from a species different from that from which the coding sequence was derived, or, if from the same species, a promoter that is different from any naturally occurring allelic variants, or a promoter that is not naturally found to be operably linked to the specified coding sequence in the specified plant.

[0060] As used herein, the term“nucleotide position” and the like, in the context of a nucleotide position of exon 1 of the SHELL gene refers to the position of a nucleotide relative to the adenosine of the wild-type SHELL gene initiator (i.e., amino terminal) methionine triplet codon (“ATG”). Thus, e.g., nucleotide position 1 refers to the adenosine of the ATG initator methionine triplet codon of the wild-type SHELL gene; and, position 2 refers to the next nucleotide (i.e.,“T” of the ATG initiator methionine triplet codon), and so on. Similarly, in the context of a nucleotide position of intron 1 of the SHELL gene, the term “nucleotide position” and the like refers to the position of a nucleotide relative to the first nucleotide of intron 1 of the wild-type SHELL gene. Thus, the first nucleotide of intron 1 of the SHELL gene is at position 1, the second at position 2, and so on.

[0061] Similarly, the term“amino acid position” in the context of a particular amino acid, or group of amino acids, of the SHELL gene refers to an amino acid position relative to the initiator (i.e., amino terminal) methionine of the SHELL gene. Thus, for example, amino acid position 1 refers to the amino terminal methionine, amino acid position 2 refers to the adjacent glycine of the wild-type SHELL or an alternative amino acid or deletion found in a mutatnt SHELL allele at the same position. It will be appreciated that these positions are independent of any N-terminal degradation or conjugation or other post-translational processing. For example, in a SHELL polypeptide in which the N-terminal methionine amino acid is removed post-translationally, position 2 still refers to the previously adjacent glycine amino acid and position 3 refers to the adjacent arginine amino acid of the wild-type SHELL or an alternative amino acid or deletion found in a mutant SHELL allele at the same position.

BRIEF DESCRIPTION OF THE DRAWINGS

[0062] FIG.1. SHELL gene model. Exons (boxes) and introns (horizontal lines) were validated by RNA-seq. A diagram of protein domains encoded by the indicated exons is provided below the gene diagram. MADS box, I, K and C domains of the SHELL protein are indicated.

[0063] FIG.2. Nucleotide variants in the SHELL gene. The DNA sequence of the wildtype (ShDeliDura) exon 1 encoding the MADS box domain of SHELL (SEQ ID NO: 25) is shown in the top line of the DNA sequence alignment. Sequences of the AVROS, MPOB, Allele 3, Allele 4, Allele 5, Allele 6, Allele 7, Allele 8, Allele 9, Allele 10 and Allele 11 (SEQ ID NO: 22, 23, 13-21, respectively) alleles are shown aligned to the dura sequence. Single nucleotide variants are indicated by boxes. Deleted bases (Allele 7) are indicated by dashes.

[0064] FIG.3. Amino acid variants in the SHELL gene. The peptide sequence of the wildtype (ShDeliDura) MADS box domain (SEQ ID NO: 24) is shown in the top line of the peptide alignment. Sequences of the AVROS, MPOB, Allele 3, Allele 4, Allele 5, Allele 6, Allele 7, Allele 8, Allele 9, Allele 10 and Allele 11 (SEQ ID NO: 1-11, respectively) peptides are shown aligned to the dura peptide sequence. Variant amino acids caused by missense single nucleotide variants are indicated by the appropriate single letter amino acid code. Deleted amino acids (Allele 7) are indicated by astericks. Amino acids that are unchanged relative to dura peptide sequence are indicated by dashes.

DETAILED DESCRIPTION OF THE INVENTION

I. Introduction

[0065] The present disclosure describes the discovery of alleles 3-10 of the SHELL gene that are predicted to modulate the fruit form phenotype of palm (e.g., oil palm) plants.

Similarly, alleles 11 (depicted in SEQ ID NOs:11 and 21) and 12 (depicted in SEQ ID NO:12) are either predicted to modulate the fruit form phenotype directly or can be used to infer the genotype of the SHELL gene due to their close physical linkage to the allele 3-10 polymorphisms. A polymorphic marker closely linked to the SHELL gene, or the identification of the presence, absence, or number of copies of alleles 3-11 in an oil palm plant can be used by seed producers as a quality control tool to i) reduce or eliminate dura or pisifera contamination of tenera seed or plantlets, ii) reduce or eliminate dura or tenera contamination of pisifera seed or plantlets, iii) reduce or eliminate pisifera or tenera contamination of dura seed or plantlets, iv) positively identify tenera seeds or plantlets which are then selected as suitable planting material for commercial palm oil production, v) positively identify dura seeds or plantlets which can then be selected as suitable planting material for commercial production of dura germplasm, or vi) positively identify pisifera seeds or plantlets which can then be selected as suitable planting material for commercial production of pisifera germplasm.

[0066] The identification of the SHELL gene or a marker genetically linked to shell trait is also of importance in breeding programmes. The marker or the alleles of the gene responsible for the trait can be used to separate the dura, tenera and pisifera plants in the nursery; the advantage here being that they could be planted separately based on shell fruit form phenotype. This is of interest as the pisifera palms usually show very vigorous vegetative growth, so in a trial consisting of all three types, distortion of results could occur due to intra-cross competition. Furthermore, separating out the pisifera palms and planting them in high density encourages male inflorescence and this facilitates pollen production which is used in breeding programmes (Jack et al., 1998). Accordingly, following detection of the presence or absence of a SHELL genotype predicted to result in a dura, pisifera, or tenera phenotype, or a linked marker as described below, a further step of: (1) reduction elimination of dura or pisifera contamination of tenera seed or plantlets, (2) positive identification of tenera seeds or plantlets which are then selected as suitable planting material for commercial palm oil production, or (3) separating dura, tenera and pisifera plants into two or more groups (e.g., plants predicted to be tenera in one group and plants predicted to be dura or pisifera in a second group; plants predicted to be dura in one group and plants predicted to be tenera or pisifera in a second group; plants predicted to be pisifera in one group and plants predicted to be dura or tenera in a second group, or separating into three groups: dura, pisifera, and tenera) can be achieved.

[0067] Any marker that exists that is polymorphic between the parent dura and pisifera trees in a cross and is linked to the shell locus has the potential to serve as a molecular signal to identify tenera trees in a cross. For example, if a dura tree, which is homozygous for“T” (i.e., T/T) at a given SNP position near the shell locus is crossed with a pisifera tree that is homozygous for“A” (i.e., A/A) at the same SNP position, then one could genotype seeds of the cross, or one could genotype plantlets arising from seeds of the cross, at the SNP position to track and identify contaminant seeds or plantlets. Seeds that are determined to be heterozygous at the SNP position, (i.e., A/T) are very likely to be tenera, unless a recombination between the marker and the shell gene had occurred in the individual being genotyped. Similarly, seeds which are homozygous at the SNP position for“A” or“T”, (i.e., A/A or T/T), are pisifera or dura contaminant trees respectively, and when these trees become sexually mature in several years, they will produce suboptimal fruit types.

Additionally, seeds or plantlets which have a“C” or“G” in the SNP position, neither of which is present in paternal palm of the cross, are likely trees arising from a different pollen donor than the one intended in the cross, and therefore can be discarded as contaminant seeds or plantlets. Markers that are in closer proximity to the SHELL locus would have higher predictive accuracy than markers that are farther away from the shell locus, because the closer the marker is to the shell gene, the less likely a recombination could occur which would break the linkage between the marker and the shell gene. Consequently, polymorphic markers within the shell gene itself are expected to have the strongest predictive power, and analysis of multiple markers closely linked to or within the shell gene may be advantageous.

II. Determination of shell phenotype based on nucleic acid detection

[0068] In view of the discovery that the SHELL genotype segregates with the

tenera/pisifera/dura shell phenotype, genotyping a plant or seed at the SHELL locus or at adjacent genomic regions can be used to predict the shell phenotype of a palm plant.

[0069] SEQ ID NO:24 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the dura fruit type (ShDeliDura). The endogenous protein includes additional C-terminal amino acids not included in SEQ ID NO:24. In oil palm of the dura fruit type, the proteins derived from both alleles of the gene include: (i) an isoleucine (I), lysine (K), arginine (R), isoleucine (I), and glutamate (E) at positions 8-12 respectively, which are deleted in predicted pisifera allele 7; (ii) a glutamate (E) at position 12, which is mutated to a glutamine (Q) in predicted pisifera allele 6; (iii) a lysine (K) at position 23 which is mutated to a glutamine (Q) in predicted pisifera allele 3 and an asparagine (N) in predicted pisifera allele 5; (iv) an arginine (R), which is mutated to a histidine (H) in predicted pisifera allele 8 and a glycine (G) in predicted pisifera allele 9; (v) a leucine (L) at position 29, which is mutated to a proline in the pisifera allele shMPOB; (vi) a lysine (K) at position 31, which is mutated to an asparagine in the pisifera allele shAVROS; (vii) a valine (V) at position 37, which is mutated to an aspartate (D) in predicted pisifera allele 10; and (viii) an alanine (A) at position 41, which is mutated to an aspartate (D) in predicted pisifera allele 4.

[0070] SEQ ID NO:1 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the pisifera fruit type that is derived from the Zaire line (shAVROS). The endogenous protein includes additional C-terminal amino acids not included in SEQ ID NO:1. This polypeptide includes an asparagine (N) amino acid at the 31st amino acid position. A nucleotide sequence encoding exon 1 of the shAVROS allele is provided in SEQ ID NO:22.

[0071] SEQ ID NO:2 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the pisifera fruit type that is derived from the Nigerian line (shMPOB). The endogenous protein includes additional C-terminal amino acids not included here. This polypeptide includes a proline (P) amino acid at the 29th amino acid position. A nucleotide sequence encoding exon 1 of the shMPOB allele is provided in SEQ ID NO:23.

[0072] SEQ ID NO:3 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the predicted pisifera fruit type SHELL allele 3. The endogenous protein includes additional C-terminal amino acids not included here. This polypeptide includes a glutamine (Q) amino acid at the 23rd amino acid position. A nucleotide sequence encoding exon 1 of allele 3 is provided in SEQ ID NO:13.

[0073] SEQ ID NO:4 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the predicted pisifera fruit type SHELL allele 4. The endogenous protein includes additional C-terminal amino acids not included here. This polypeptide includes an aspartate (D) amino acid at the 41st amino acid position. A nucleotide sequence encoding exon 1 of allele 4 is provided in SEQ ID NO:14.

[0074] SEQ ID NO:5 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the predicted pisifera fruit type SHELL allele 5. The endogenous protein includes additional C-terminal amino acids not included

here. This polypeptide includes an asparagine (N) amino acid at the 23rd amino acid position. A nucleotide sequence encoding exon 1 of allele 5 is provided in SEQ ID NO:15.

[0075] SEQ ID NO:6 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the predicted pisifera fruit type SHELL allele 6. The endogenous protein includes additional C-terminal amino acids not included here. This polypeptide includes a glutamine (E) amino acid at the 12th amino acid position. A nucleotide sequence encoding exon 1 of allele 6 is provided in SEQ ID NO:16.

[0076] SEQ ID NO:7 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the predicted pisifera fruit type SHELL allele 7. The endogenous protein includes additional C-terminal amino acids not included here. This polypeptide has a deletion of amino acids lysine (K), arginine (R), isoleucine (I), and glutamate (E), at positions 8-12 respectively in comparison to wildtype allele ShDeliDura. A nucleotide sequence encoding exon 1 of allele 7 is provided in SEQ ID NO:17.

[0077] SEQ ID NO:8 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the predicted pisifera fruit type SHELL allele 8. The endogenous protein includes additional C-terminal amino acids not included here. This polypeptide includes a histidine (H) amino acid at the 24th amino acid position. A nucleotide sequence encoding exon 1 of allele 8 is provided in SEQ ID NO:18.

[0078] SEQ ID NO:9 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the predicted pisifera fruit type SHELL allele 9. The endogenous protein includes additional C-terminal amino acids not included here. This polypeptide includes a glycine (G) amino acid at the 24th amino acid position. A nucleotide sequence encoding exon 1 of allele 9 is provided in SEQ ID NO:19.

[0079] SEQ ID NO:10 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the predicted pisifera fruit type SHELL allele 10. The endogenous protein includes additional C-terminal amino acids not included here. This polypeptide includes an aspartate (D) amino acid at the 37th amino acid position. A nucleotide sequence encoding exon 1 of allele 10 is provided in SEQ ID NO:20.

[0080] SEQ ID NO:11 represents the predicted amino acid sequence of the N-terminal 181 amino acids of the protein expressed in oil palm of the predicted pisifera fruit type SHELL allele 11. The endogenous protein includes additional C-terminal amino acids not included here. The allele encodes a silent mutation with respect to a wild-type SHELL gene

(ShDeliDura). A nucleotide sequence encoding exon 1 of allele 11 is provided in SEQ ID NO:21. As described herein, this silent mutation may affect transcriptional or translational regulation and therefore provide a pisifera phenotype despite encoding for a wild-type protein sequence. Alternatively, the nucleotide sequence encoding for this silent mutation can be used to infer the presence or absence of a genotype at one or more of the foregoing polymorphic nucleotide (e.g., one or more of the polymorphic markers relative to wild-type exemplified in SEQ ID Nos: 13-20, 13-20 and 23, 13-20 and 22, or 13-20 and 22-23) or amino acid markers (e.g., one or more of the polymorphic markers relative to wild-type exemplified in SEQ ID Nos: 3-10, 2-10, 1 and 3-10, or 1-10).

[0081] SEQ ID NO:12 represents the nucleotide sequence of the first 56 nucleotides of intron 1 of SHELL allele 12 in which nucleotides 43, 44, 45, and 46 are deleted relative to intron 1 of a wild-type SHELL allele (ShDeliDura). As this polymorphism is within a non-coding region of the SHELL gene, it is a silent mutation. As described herein, this silent mutation may affect transcriptional or translational regulation, or splicing, and therefore provide a pisifera phenotype. Alternatively, the presence or absence of allele 12 can be used to infer the presence or absence of a genotype at one or more of the foregoing polymorphic nucleotide (e.g., one or more of the polymorphic markers relative to wild-type exemplified in SEQ ID Nos: 13-20, 13-21, 13-20 and 22, 13-20 and 23, or 13-23) or amino acid markers (e.g., one or more of the polymorphic markers relative to wild-type exemplified in SEQ ID Nos: 3-10, 3-11, 2-10, 2-11, 1-10, 1 and 3-10, 1 and 3-11, or 1-11).

[0082] Oil palm trees of the pisifera fruit type are the result of one of at least four possibilities: i) two homozygous SHELL alleles having a nucleotide sequence coding for one of the following protein sequences: SEQ ID NOs:3-10; ii) two heterozygous SHELL alleles having two different nucleotide sequences independently coding for one of following protein sequences: SEQ ID NOs:3-10, or iii) one SHELL allele coding for the ShAVROS or ShMPOB protein sequence and the other allele coding for a mutation relative to wild-type represented in one or more of the following protein sequences: SEQ ID NOs:3-10. In some cases, nucleotide sequences comprising SEQ ID NO:12 and/or 21 are similarly, predicted pisifera alleles. In such cases, a pisifera fruit type can result in plants homozygous for SEQ ID NO:12 or 21 or heterozygous for SEQ ID NO:12 or 21 and a different allele selected from the group consisting of any one of SEQ ID NOs:13-23 (e.g., any one of SEQ ID NOs:13-20) or encoding any one of SEQ ID NOs:1-10 (e.g., any one of SEQ ID NOs:3-10).

[0083] Oil palm trees of the tenera fruit type are the result of one allele coding for one or more of the pisifera alleles described herein and one allele coding for a wild-type (ShDeliDura) SHELL protein. It will be appreciated that SEQ ID NOs:1-11 and 24 are representative sequences and that different individual palms may have an amino acid sequence having one, two, three, four, or more amino acid changes relative to SEQ ID NOS:1-11 and 24, due, for example, to natural variation. Similarly SEQ ID NOs:12-23 and 25 are representative sequences and different individual palms may have a nucleotide sequence having one, two, three, four, or more nucleotide changes relative to SEQ ID NOs:12-23 and 25 due to, for example, natural variation.

[0084] One or more polymorphism(s) between pisifera and dura SHELL alleles can be used to determine the shell phenotype of a palm or other plant. For example, when the polymorphism is co-dominant (detectable independent of the other allele) then:

the presence of only a dura SHELL allele indicates that the plant has or will have a dura shell phenotype;

the presence of only a pisifera SHELL allele indicates that the plant has or will have a pisifera shell phenotype; and

the presence of a pisifera SHELL allele and a dura SHELL allele indicates that the plant has or will have a tenera shell phenotype.

[0085] However, genomic regions adjacent to the SHELL gene are also useful to determining whether a palm plant will likely manifest a particular shell phenotype. Because of genetic linkage to the SHELL gene, polymorphisms adjacent to the SHELL locus are predictive of shell phenotype, albeit with reduced accuracy as a function of increased distance from the SHELL locus. SEQ ID NO:27 provides an approximately 3.4 MB genomic region of the palm genome that comprises the SHELL gene. Table A of U.S. Patent Application Publication No.2013/0247249 discloses 8217 SNPs identified within SEQ ID NO:27. A selection of these SNPs have been genetically mapped relative to the SHELL locus. The estimated predictive values of these SNPs are also described in Table A of U.S.

2013/0247249. Thus, as an example, the SNP listed in row 1 of U.S.2013/0247249, Table A as having a estimated prediction success of 83, represents an SNP that is accurate in predicting shell phenotype 83% of the time. Said another way, by using this SNP as a genetic marker, one can correctly predict shell phenotype of palm plants 83 out of 100 times. Thus, even at a significant physical distance from the SHELL locus on the palm chromosome, polymorphic markers allow for relatively accurate prediction of shell phenotype of plants. In some embodiments, the polymorphic marker is within 1, 10, 20, 50, 100, 200, 500, 1000 kb from the SHELL gene (e.g., the gene corresponding to SEQ ID NO:28).

[0086] Accordingly, methods of detecting one or more polymorphic marker within a region of the palm genome corresponding to SEQ ID NO:27 are provided. Such methods are useful for predicting shell phenotype of palm plants for example. While over 8200 specific polymorphisms are provided in U.S.2013/0247249, it should be appreciated that the polymorphisms represented are merely an example of polymorphisms within the genomic region corresponding to SEQ ID NO:27. Additional polymorphisms can be identified as desired and also be used to predict shell phenotype of a palm plant. Such additional polymorphisms are intended to be encompassed in the methods described herein. Moreover, it will be appreciated that SEQ ID NO:27 is a representative sequence and that different individual palms may have a corresponding genomic region having one or more nucleotide changes relative to SEQ ID NO:27 due, for example, to natural variation. As noted elsewhere herein, nevertheless, identifying the region of a genome corresponding to SEQ ID NO:27 can be readily determined using alignment programs, etc.

[0087] The nucleic acid sequences provided herein were generated by nucleotide sequencing and on occasion, include one or more stretches of "N's." These stretches of N's represent gaps in assembly of sequences of an estimated size. The precise number of N's in a sequence is an estimate (for example, 100 N's may only represent 30 bases). N's can be any base, and are likely repetitive sequence in the genome.

[0088] Detecting specific polymorphic markers can be accomplished by methods known in the art for detecting sequences at polymorphic sites. For example, standard techniques for genotyping for the presence of SNPs and/or microsatellite markers can be used, such as fluorescence-based techniques (Chen, X. et al., Genome Res.9(5): 492-98 (1999)), utilizing PCR, LCR, Nested PCR and other techniques for nucleic acid amplification. Specific commercial methodologies available for SNP genotyping include, but are not limited to, TaqMan™ genotyping assays and SNPlex platforms (Applied Biosystems), gel

electrophoresis (Applied Biosystems), mass spectrometry (e.g., MassARRAY system from Sequenom), minisequencing methods, real-time PCR, Bio-Plex system (BioRad), CEQ and SNPstream systems (Beckman), array hybridization technology (e.g., Affymetrix GeneChip; Perlegen), BeadArray Technologies (e.g., Illumina GoldenGate and Infinium assays), array tag technology (e.g., Parallele), and endonuclease-based fluorescence hybridization technology (Invader; Third Wave). Some of the available array platforms, including Affymetrix SNP Array 6.0 and Illumina CNV370-Duo and 1M BeadChips, include SNPs that tag certain copy number variants.

WHAT IS CLAIMED IS:

1. A method for predicting the shell phenotype of a palm plant or seed, the method comprising:

(a) determining from a nucleic acid sample from the palm plant or seed the presence, absence, or number of pisifera or dura alleles by

(i) detecting a genotype of at least one polymorphic marker corresponding to nucleotide 7, 8, 9, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 109, 110, 111, 114, 121, 122, or 123 of exon 1 of a SHELL gene; or

(ii) detecting a genotype of a polymorphic marker selected from the group consisting of those depicted in SEQ ID NOs:12 and 29-8245 to thereby predict the genotype of at least one polymorphic marker corresponding to nucleotide 7, 8, 9, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 109, 110, 111, 114, 121, 122, or 123 of exon 1 of a SHELL gene; and (b) predicting the shell phenotype of the palm plant based on the presence, absence, or number of pisifera or dura alleles.

2. A method for segregating a plurality of palm plants into different categories based on predicted shell phenotype, the method comprising:

(a) predicting the shell phenotype of the palm plant based on the presence, absence, or number of pisifera or dura alleles by:

(i) detecting a genotype of at least one polymorphic marker corresponding to nucleotide 7, 8, 9, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 109, 110, 111, 114, 121, 122, or 123 of exon 1 of a SHELL gene; or

(ii) detecting a genotype of a linked marker selected from the group consisting of those depicted in SEQ ID NOs:12 and 29-8245 to thereby predict the genotype of at least one polymorphic marker corresponding to nucleotide 7, 8, 9, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 109, 110, 111, 114, 121, 122, or 123 of exon 1 of a SHELL gene; and

(c) segregating the plants into groups based on the genotype of the polymorphic marker, wherein at least one group only contains one of (i) plants predicted to have the tenera shell phenotype, (i) plants predicted to have the dura shell phenotype, or (iii) plants predicted to have the pisifera shell phenotype.

3. The method of claim 1 or 2, wherein the presence, absence, or number of pisifera or dura alleles is determined by detecting the genotype of at least one polymorphic marker corresponding to nucleotide 7, 8, 9, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 109, 110, 111, 114, 121, 122, or 123 of exon 1 of the SHELL gene.

4. The method of any one of claims 1 - 3, wherein the presence of one predicted pisifera allele and one predicted dura allele predicts a tenera shell phenotype.

5. The method of any one of claims 1 - 4, wherein the plant or seed is generated from (i) an attempted cross between a plant having the dura shell phenotype and a plant having the pisifera shell phenotype, (ii) selfing of a tenera palm, (iii) a cross between two plants having the tenera shell phenotype, (iv) a cross between dura and tenera palms, or (v) a cross between tenera and pisifera palms.

6. The method of any one of claims 1 - 4, wherein the plant is less than 5 years old.

7. The method of any one of claims 1 - 4, wherein the plant is less than one year old.

8. The method of any one of claims 1 - 4, further comprising selecting the plant for cultivation if the plant is heterozygous for the polymorphic marker.

9. The method of any one of claims 1 - 4, further comprising selecting the plant for cultivation if the plant has a dura genotype.

10. The method of any one of claims 1 - 4, further comprising selecting the plant for cultivation if the plant has a pisafera genotype.

11. The method of any one of claims 1 - 4, wherein the plants or seeds are discarded if the plants or seeds do not have a genotype predictive of the tenera shell phenotype.

12. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of the polymorphic marker corresponding to nucleotide 67 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wild-type of the polymorphic marker indicates the presence of a pisifera allele.

13. The method of claim 12, wherein detecting an AÆC mutation of the polymorphic marker corresponding to nucleotide 67 of exon 1 of the SHELL gene indicates the presence of a pisifera allele.

14. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of the polymorphic marker corresponding to nucleotide 69 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wild-type of the polymorphic marker indicates the presence of a pisifera allele.

15. The method of claim 14, wherein detecting an AÆT mutation of the polymorphic marker corresponding to nucleotide 69 of exon 1 of the SHELL gene indicates the presence of a pisifera allele.

16. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of the polymorphic marker corresponding to nucleotide 70 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wild-type of the polymorphic marker indicates the presence of a pisifera allele.

17. The method of claim 16, wherein detecting a CÆG mutation of the polymorphic marker corresponding to nucleotide 70 of exon 1 of the SHELL gene indicates the presence of a pisifera allele.

18. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of the polymorphic marker corresponding to nucleotide 71 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wild-type of the polymorphic marker indicates the presence of a pisifera allele.

19. The method of claim 18, wherein detecting a GÆA mutation of the polymorphic marker corresponding to nucleotide 71 of exon 1 of the SHELL gene indicates the presence of a pisifera allele.

20. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of one or more polymorphic markers corresponding to nucleotides 23-37 or 22-36 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wid-type of the one or more polymorphic markers indicates the presence of a pisifera allele.

21. The method of claim 20, wherein detecting a deletion mutation of one or more of nucleotides 23-37 or one or more of nucleotides 22-36 of exon 1 of the SHELL gene indicates the presence of a pisifera allele.

22. The method of claim 21, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the presence or absence of a deletion relative to wild-type of nucleotides 23-37 or 22-36 of exon 1 of the SHELL gene, and wherein detecting the presence of the deletion indicates the presence of a pisifera allele.

23. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of at least one polymorphic marker corresponding to nucleotide 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 67, 69, 70, or 71 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wild-type of the at least one polymorphic marker indicates the presence of a pisifera allele.

24. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of at least one polymorphic marker corresponding to nucleotide 7, 8, 9, 13, 14, 15, 25, 26, 27, 28, 29, 30, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, or 92 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wild-type of the at least one polymorphic marker indicates the presence of a pisifera allele.

25. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of the polymorphic marker corresponding to nucleotide 110 of exon 1 of the SHELL gene, and

wherein detecting a mutation relative to wild-type of the polymorphic marker indicates the presence of a pisifera allele.

26. The method of claim 25, wherein detecting a TÆA mutation of the polymorphic marker corresponding to nucleotide 110 of exon 1 of the SHELL gene indicates the presence of a pisifera allele.

27. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of the polymorphic marker corresponding to nucleotide 122 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wild-type of the polymorphic marker indicates the presence of a pisifera allele.

28. The method of claim 27, wherein detecting a CÆA mutation of the polymorphic marker corresponding to nucleotide 122 of exon 1 of the SHELL gene indicates the presence of a pisifera allele.

29. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of the polymorphic marker corresponding to nucleotide 34 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wild-type of the polymorphic marker indicates the presence of a pisifera allele.

30. The method of claim 29, wherein detecting a GÆC mutation of the polymorphic marker corresponding to nucleotide 34 of exon 1 of the SHELL gene indicates the presence of a pisifera allele.

31. The method of any one of claims 1 - 11, wherein determining the presence, absence, or number of pisifera or dura alleles comprises detecting the genotype of the polymorphic marker corresponding to nucleotide 114 of exon 1 of the SHELL gene, and wherein detecting a mutation relative to wild-type of the polymorphic marker indicates the presence of a pisifera allele.

32. The method of claim 31, wherein detecting a TÆC mutation of the polymorphic marker corresponding to nucleotide 114 of exon 1 of the SHELL gene indicates the presence of a pisifera allele.

33. A method for predicting the shell phenotype of a palm plant or seed, the method comprising,

(a) determining from a nucleic acid sample from the palm plant or seed the presence, absence, or number of pisifera or dura alleles by detecting the genotype of at least one polymorphic marker encoding one or more amino acids selected from the group consisting of amino acids 3, 5, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 30, 37, and 41 of a SHELL polypeptide; and

(b) predicting the shell phenotype of the palm plant based on the presence, absence, or number of pisifera or dura alleles.

34. A method for segregating a plurality of palm plants into different categories based on predicted shell phenotype, the method comprising,

(a) predicting the shell phenotype of the palm plant based on the presence, absence, or number of pisifera or dura alleles by detecting the genotype of at least one polymorphic marker encoding one or more amino acids selected from the group consisting of amino acids 3, 5, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 30, 37, and 41 of a SHELL polypeptide; and

(b) segregating the plants into groups based on the genotype of the polymorphic marker, wherein at least one group only contains one of (i) plants predicted to have the tenera shell phenotype, (i) plants predicted to have the dura shell phenotype, or (iii) plants predicted to have the pisifera shell phenotype.

35. The method of claim 33 or 34, wherein predicting the shell phenotype of the palm plant based on the presence, absence, or number of pisifera or dura alleles comprises detecting the presence or absence of a deletion or mutation relative to wild-type of one or more amino acids selected from the group consisting of amino acids 8, 9, 10, 11, and 12 of the SHELL polypeptide, and wherein detecting a deletion or mutation relative to ShDeliDura indicates the presence of a pisifera allele.

36. The method of claim 35, wherein detecting a deletion of amino acids 8-12 of the SHELL polypeptide relative to wild-type indicates the presence of a pisifera allele.

37. The method of claim 35, wherein detecting a mutation of amino acid 12 of the SHELL polypeptide relative to wild-type indicates the presence of a pisifera allele.

38. The method of claim 37, wherein the mutation is an EÆQ mutation.

39. The method of claim 33 or 34, wherein detecting a mutation in the polymorphic marker encoding amino acid 23 of the SHELL polypeptide relative to wild-type indicates the presence of a pisifera allele.

40. The method of claim 39, wherein the mutation is a KÆQ mutation.

41. The method of claim 39, wherein the mutation is a KÆN mutation.

42. The method of claim 33 or 34, wherein detecting a mutation in the polymorphic marker encoding amino acid 24 of the SHELL polypeptide relative to wild-type indicates the presence of a pisifera allele.

43. The method of claim 42, wherein the mutation is an RÆG mutation.

44. The method of claim 42, wherein the mutation is an RÆH mutation.

45. The method of claim 33 or 34, wherein detecting a mutation in the polymorphic marker encoding amino acid 37 of the SHELL polypeptide relative to wild-type indicates the presence of a pisifera allele.

46. The method of claim 45, wherein the mutation is a VÆD mutation.

47. The method of claim 33 or 34, wherein detecting a mutation in the polymorphic marker encoding amino acid 41 of the SHELL polypeptide relative to wild-type indicates the presence of a pisifera allele.

48. The method of claim 47, wherein the mutation is an AÆD mutation.

49. The method of claim 33 or 34, wherein detecting the presence of a non-functional nuclear localization signal of the SHELL polypeptide indicates the presence of a pisifera allele.

50. A kit for determining the shell phenotype of a palm plant, the kit comprising,

one or more oligonucleotide primer or probe that comprises:

a sequence of at least 18 (or 20, 22, 24, or more) consecutive nucleotides of SEQ ID NO:27; or;

a sequence 100% complementary to at least 18 (or 20, 22, 24, or more) consecutive nucleotides of SEQ ID NO:27,

wherein the one or more primers or probes independently hybridize to a sequence that is within, or within about, 5,000; 2,500; 1,000; 750; 500; 250; 200; 150; 100; 75; 50; 25, or 1 bp of a position in exon 1 of the SHELL gene selected from the group consisting of nucleotides 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 ,82, 83, 84, 85, 87, 88, 89, 90, 91, 92, 110, 114, or 122.

51. The kit of claim 50, wherein the primer or probe specifically hybridizes to palm plant DNA.

52. The kit of claim 50 or 51, wherein a detectable label is linked to the oligonucleotide.

53. The kit of claim 52, wherein the detectable label is fluorescent.

54. The kit of any of claims 50-53, further comprising a polynucleotide encoding a polypeptide comprising a sequence substantially (e.g., a least 80, 85, 90, 95, 97, 98, 99%) identical or identical to SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10, wherein the polynucleotide comprises a mutation relative to a wild-type, shAVROS, and shMPOB SHELL gene depicted in SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10.

55. An isolated nucleic acid comprising a polynucleotide encoding a polypeptide comprising a sequence substantially (e.g., a least 80, 85, 90, 95, 97, 98, 99%) identical or identical to SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10, wherein the polynucleotide comprises a mutation relative to a wild-type, shAVROS, and shMPOB SHELL gene depicted in SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10.

56. An expression cassette comprising a heterologous promoter operably linked to a polynucleotide encoding a polypeptide comprising a sequence substantially (e.g., a least 80, 85, 90, 95, 97, 98, 99%) identical or identical to SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10, wherein the polynucleotide comprises a mutation relative to a wild-type, shAVROS, and shMPOB SHELL gene depicted in SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10.

57. A plant comprising a heterologous expression cassette, the expression cassette comprising a heterologous promoter operably linked to a polynucleotide encoding a polypeptide comprising a sequence substantially (e.g., a least 80, 85, 90, 95, 97, 98, 99%)

identical or identical to SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10, wherein the polynucleotide comprises a mutation relative to a wild-type, shAVROS, and shMPOB SHELL gene depicted in SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10.

58. The plant of claim 57, wherein the plant is a palm plant.

59. The plant of claim 57 , wherein the polypeptide comprises SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10.

60. The plant of any of claims 57-59, wherein the plant comprises one pisifera allele of an endogenous SHELL gene.

61. The plant of any of claims 57-59, wherein the plant comprises two pisifera alleles of an endogenous SHELL gene.

62. The plant of claim any of claims 57-59, wherein the plant makes mature shells that are on average less than 2 mm thick.

63. A plant comprising a heterologous expression cassette, the expression cassette comprising a promoter operably linked to a polynucleotide, which polynucleotide, when expressed in the plant, reduces the amount of a SHELL polypeptide in a nucleus of the plant (compared to a control plant lacking the expression cassette), wherein reduced amount of nuclear SHELL polypeptide results reduced shell thickness in the plant.

64. The plant of claim 63, wherein the polynucleotide comprises at least 20 contiguous nucleotides, or the complement thereof, of an endogenous nucleic acid encoding a SHELL polypeptide substantially (e.g., a least 80, 85, 90, 95, 97, 98, 99%) identical or identical to SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10, wherein the polynucleotide comprises a mutation relative to a wild-type, shAVROS, and shMPOB SHELL gene depicted in SEQ ID NO: 3, 4, 5, 6, 7, 8, 9, or 10, and wherein expression of the polynucleotide reduces the amount of SHELL polypeptide in the nucleus of the plant.

65. The plant of claim 63, wherein, wherein the the polynucleotide encodes a SHELL polypeptide, or portion thereof, having a mutation in a nuclear localization signal of the SHELL polypeptide relative to a wild-type, shAVROS, and shMPOB SHELL gene.

66. The plant of claim 65, wherein the mutation is relative to a wild-type nuclear localization signal comprising or consisting of amino acids KRRNGLLKK (SEQ ID NO:30).

67. The plant of claim 65, wherein the mutation is relative to a wild-type nuclear localization signal comprising or consisting of amino acids R X K X X X X K R X X X X X X X X X X F C K R R X X X X K K (SEQ ID NO:33), where X is any amino acid.

68. The plant of claim any of claims 63-67, wherein the plant makes mature shells that are on average less than 2 mm thick.

69. A method of making the plant of any of claims 63-68, the method comprising introducing the expression cassette into a plant.

70. A method of cultivating the plant of any of claims 63-68.