Gene controlling fruit color phenotype in palm

Patent metadata

Field	Value
Publication number	US-10669593-B2
Application number	US-201414226508-A
Country	US
Kind code	B2
Filing date	Mar 26, 2014
Priority date	Apr 8, 2013
Publication date	Jun 2, 2020
Grant date	Jun 2, 2020

Abstract

Methods, compositions, and kits for predicting and controlling fruit color in palm.

First claim

What is claimed is:

1. A method for determining a fruit color phenotype of an E. guineensis palm plant, the method comprising,
providing a sample from an E. guineensis palm plant or seed;
detecting in the sample presence or absence of a VIR gene alteration in a genomic region corresponding to SEQ ID NO:1 that comprises a VIR gene and confers a virescens phenotype to fruit, wherein the detecting comprises detecting the VIR gene alteration by amplification, hybridization, or nucleotide sequencing, wherein the gene alteration in causes the virescens phenotype, wherein the VIR gene alteration comprises a nucleotide change that results in a premature stop codon; and
segregating the E. guineensis palm plant or seed into groups based on the presence of the VIR gene alternation, wherein at least one group contains E. guineensis palm plants or seeds having the VIR gene alteration in the genomic region corresponding to SEQ ID NO: 1.

2. The method of claim 1 , wherein the VIR gene alteration generates a truncated protein compared to the protein encoded by SEQ ID NO:4.

3. The method of claim 1 wherein the VIR gene alteration results in the sequence of any one of SEQ ID NOS:7, 9, 11, 13, and 15, or the VIR gene alteration results in a sequence that encodes an amino acid sequence selected from the group consisting of SEQ ID NOS:5, 8, 10, 12, and 14.

4. The method of claim 1 , wherein the VIR gene encodes (i) a polypeptide at least 95% identical to SEQ ID NO:4.

5. The method of claim 1 , wherein the plant is less than 5 years old.

6. The method of claim 1 , wherein the plant is less than one year old.

7. The method of claim 1 , further comprising selecting the E. guineensis palm plant or seed for cultivation if the E. guineensis palm plant or seed has the VIR gene alteration.

8. The method of claim 7 , wherein the E. guineensis palm plant or seed is discarded if the E. guineensis palm plant or seed does not have the VIR gene alteration.

9. The method of claim 1 , wherein the segregating comprises segregating the E. guineensis palm plant or seed into a first group based on the presence of the VIR gene alteration and segregating the E. guineensis palm plant or seed into a second group based on the absence of the VIR gene alteration.

10. The method of claim 9 , wherein the absence of the VIR gene alteration results in a nigrescens phenotype.

11. The method of claim 1 , wherein the method further comprises amplifying genomic DNA from the sample prior to the detecting.

12. A method for determining a fruit color phenotype of an E. guineensis palm plant, the method comprising,
providing a sample from an E. guineensis palm plant or seed;
detecting in the sample presence or absence of a VIR gene alteration in a genomic region corresponding to SEQ ID NO:1 that comprises a VIR gene and confers a virescens phenotype to fruit, wherein the gene alteration causes the virescens phenotype, wherein the VIR gene alteration results the sequence of any one of SEQ ID NOS:7, 9, 11, 13, and 15, wherein the detecting comprises detecting the VIR gene alteration by amplification, hybridization or nucleotide sequencing, wherein the VIR gene alteration comprises a nucleotide change that results in a premature stop codon; and
segregating the E. guineensis palm plant or seed into groups based on the presence of the VIR gene alternation, wherein at least one group contains E. guineensis palm plants or seeds having the VIR gene alteration in the genomic region corresponding to SEQ ID NO: 1.

13. The method of claim 1 , wherein the detecting comprises obtaining the sequence of the VIR gene in the genomic region corresponding to SEQ ID NO:1.

14. The method of claim 1 , wherein the detecting comprises obtaining the sequence of the VIR gene in the genomic region corresponding to SEQ ID NO:1.

Assignees

• Malaysian Palm Oil Board
• Malaysian Pal Oil Board

Inventors

• Singh Rajinder
• Li Leslie Ooi Cheng
• Ti Leslie Low Eng
• Rahman Rahimah Abdul
• Abdullah Meilina Ong
• Nagappan Jayanthi
• Rosli Rozana
• Halim Mohd Amin Ab
• Nookiah Rajanaidu
• Kuang Lim Chan
• Azizi Norazah
• Sambanthamurthi Ravigadevi
• Martienssen Rob
• Smith Steven W
• Lakey Nathan D
• Van Brunt Andrew
• Ordway Jared
• Hogan Michael
• Wang Chunyan

Classifications

• C12Q1/6827

  for detection of mutation or polymorphism · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q1/6895 Primary

  for plants, fungi or algae · CPC title

• C12Q2600/13

  Plant traits · CPC title