Mads-box domain alleles for controlling shell phenotype in palm

Patent metadata

Field	Value
Publication number	US-12058968-B2
Application number	US-202017131384-A
Country	US
Kind code	B2
Filing date	Dec 22, 2020
Priority date	Jun 15, 2015
Publication date	Aug 13, 2024
Grant date	Aug 13, 2024

Abstract

Nucleic acid and polypeptide sequences for predicting and controlling shell phenotype in palm.

First claim

What is claimed is:

1. A method for reducing non- tenera contaminant seeds or plants from a plurality of Elaeis guineensis ( E. guineensis ) palm plants or seeds, the method comprising:
obtaining genomic sequence of the palm plants or seeds from alleles of a SHELL gene at a polymorphic marker, thereby determining the genotype of the plant or seed at the polymorphic marker, or
obtaining predicted shell phenotype of palm plants or seeds based on a genomic sequence of the alleles at the polymorphic marker,
wherein the polymorphic marker comprises:
(i) nucleotide 34 of exon 1 of the SHELL gene, wherein an G to C mutation of nucleotide 34 of exon 1 of the SHELL gene indicates the presence of a pisifera allele; or
(ii) nucleotide 67 of exon 1 of the SHELL gene, wherein an A to C mutation of nucleotide 67 of exon 1 of the SHELL gene indicates the presence of a pisifera allele; or
(iii) nucleotide 69 of exon 1 of the SHELL gene, wherein an A to T mutation of nucleotide 69 of exon 1 of the SHELL gene indicates the presence of a pisifera allele; or
(iv) nucleotide 70 of exon 1 of the SHELL gene, wherein a C to G mutation of nucleotide 70 of exon 1 of the SHELL gene indicates the presence of a pisifera allele; or
(v) nucleotide 71 of exon 1 of the SHELL gene, wherein a G to A mutation of nucleotide 71 of exon 1 of the SHELL gene indicates the presence of a pisifera allele; or
(vi) nucleotide 110 of exon 1 of the SHELL gene, wherein a T to A mutation of nucleotide 110 of exon 1 of the SHELL gene indicates the presence of a pisifera allele; or
(vii) nucleotide 122 of exon 1 of the SHELL gene, wherein a C to A mutation of nucleotide 122 of exon 1 of the SHELL gene indicates the presence of a pisifera allele; or
(viii) nucleotides 23-37 of exon 1 of the SHELL gene, wherein a 15 base pair deletion mutation corresponding to nucleotides 23-37 of exon 1 of the SHELL gene and causing an in frame deletion of five amino acids at positions 8 to 12 of the translated open reading frame of exon 1, indicates the presence of a pisifera allele;

wherein an allele encodes a SHELL protein comprising SEQ ID NO:24 and heterozygosity at the polymorphic marker indicates a tenera shell phenotype, and
segregating at least some of the plants or seeds into a group having reduced non- tenera contaminant seeds or plants compared to the plurality.

2. The method of claim 1 , comprising obtaining the predicted shell phenotype of palm plants or seeds based on the genomic sequence at the polymorphic marker.

3. The method of claim 1 , wherein the plants or seeds are 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) cross between two plants having the tenera shell phenotype, (iv) cross between dura and tenera palms, or (v) cross between tenera and pisifera palms.

4. The method of claim 1 , wherein the plants or seeds are 0-5 years old.

5. The method of claim 1 , wherein the plants or seeds are between zero and one year old.

6. The method of claim 1 , wherein the polymorphic marker comprises nucleotide 34 of exon 1 of the SHELL gene.

7. The method of claim 1 , wherein the polymorphic marker comprises nucleotide 67 of exon 1 of the SHELL gene.

8. The method of claim 1 , wherein the polymorphic marker comprises nucleotide 69 of exon 1 of the SHELL gene.

9. The method of claim 1 , wherein the polymorphic marker comprises nucleotide 70 of exon 1 of the SHELL gene.

10. The method of claim 1 , wherein the polymorphic marker comprises nucleotide 71 of exon 1 of the SHELL gene.

11. The method of claim 1 , wherein the polymorphic marker comprises nucleotide 110 of exon 1 of the SHELL gene.

12. The method of claim 1 , wherein the polymorphic marker comprises nucleotide 122 of exon 1 of the SHELL gene.

13. The method of claim 1 , wherein the polymorphic marker comprises nucleotides 23-37 of exon 1 of the SHELL gene.

14. The method of claim 1 , wherein the allele encoding the SHELL protein comprises SEQ ID NO:25.

Assignees

• Malaysian Palm Oil Board

Inventors

• Singh Rajinder
• Ti Leslie Low Eng
• Li Leslie Ooi Cheng
• Abdullah Meilina Ong
• Nookiah Rajanaidu
• Sambanthamurthi Ravigadevi
• Van Brunt Andrew
• Budiman Muhammad A
• Smith Steven W
• Lakey Nathan D
• Martienssen Rob
• Ordway Jared

Classifications

• Y02A40/146

  Genetically Modified [GMO] plants, e.g. transgenic plants · CPC title

• A01H5/10

  Seeds · CPC title

• C12N15/8261

  with agronomic (input) traits, e.g. crop yield · CPC title

• C07K14/415

  from plants · CPC title

• A01H5/08

  Fruits · CPC title