Mantle phenotype detection in palm

Patent metadata

Field	Value
Publication number	US-9984200-B2
Application number	US-201514701425-A
Country	US
Kind code	B2
Filing date	Apr 30, 2015
Priority date	May 2, 2014
Publication date	May 29, 2018
Grant date	May 29, 2018

Abstract

Methods, compositions, kits, and computer program code are provided for predicting somaclonal abnormality (e.g., a Mantled phenotype) in a plant and or sorting plants based on the predicted presence or absence of somaclonal abnormality.

First claim

What is claimed is:

1. A method for detecting or predicting Mantle phenotype in an oil palm plant, the method comprising:
a) obtaining a biological sample from the plant;
b) detecting an increase or decrease in the methylation status of at least one cytosine within a differential methylation region (DMR) in the sample from the plant relative to a control locus, wherein the DMR is within a sequence of DNA at least 95% identical to SEQ ID NO:66; and
c) physically separating a plant predicted to have the Mantle phenotype from one or more plants predicted to lack the Mantle phenotype based on the detected methylation status.

2. The method of claim 1 , wherein the physically separating comprises selecting plants predicted to have Mantle phenotype for destruction.

3. The method of claim 1 , wherein the physically separating comprises selecting plants predicted to lack Mantle phenotype for cultivation.

4. The method of claim 3 , wherein the plants selected for cultivation are planted or transplanted.

5. The method of claim 3 , wherein the plants not selected for cultivation are discarded or destroyed.

6. The method of claim 3 , wherein the plants not selected for cultivation are treated to reduce the likelihood of Mantle phenotype.

7. The method of claim 1 , wherein the at least one cytosine is a first cytosine in a CHG sequence, wherein H is C, A, or T.

8. The method of claim 1 , wherein the DMR is within a DNA region in the sample from the plant, and wherein the DNA region is at least 95% identical to SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, or SEQ ID NO: 46.

9. The method of claim 1 , wherein the method comprises predicting the presence of Mantle phenotype when the methylation status of the at least one cytosine is reduced relative to a control locus.

10. The method of claim 9 , wherein the control locus is an endogenous control locus.

11. The method of claim 9 , wherein the control locus is an exogenous control locus.

12. The method of claim 1 , wherein the detecting an increase or decrease in the methylation status comprises bisulfite conversion.

13. The method of claim 1 , wherein the detecting an increase or decrease in the methylation status comprises digesting genomic DNA with a methylation-dependent endonuclease.

14. The method of claim 1 , wherein the detecting an increase or decrease in the methylation status comprises digesting genomic DNA with a methylation-sensitive endonuclease.

Assignees

• Malaysian Palm Oil Board

Inventors

• Abdullah Meilina Ong
• Eng Ooi Siew
• Ti Leslie Low Eng
• Singh Rajinder
• Nookiah Rajanaidu
• Sambanthamurthi Ravigadevi
• Jiang Nan
• Smith Steven W
• Lakey Nathan D
• Martienssen Rob
• Ordway Jared
• Hogan Michael

Classifications

• C12Q1/6895 Primary

  for plants, fungi or algae · CPC title

• C12Q2600/154

  Methylation markers · CPC title

• C12Q2600/158

  Expression markers · CPC title

• G06F19/18

  Physics · mapped topic

• C12N15/113

  Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; {Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing (when used in plants C12N15/8218)} · CPC title