Genome-wide analysis of allele specific expression imbalance and copy number variation in rice (Oryza sativa L.) under normal and drought conditions

Nelzo C Ereful, Kaye Malabanan, M Thomson, FE Merca, Antonio Laurena, David Lee, Ian Mackay, Hei Leung

Research output: Contribution to journalArticle

Abstract

To understand the possible roles of allele-specific expression (ASE) imbalance in genetic regulation of drought response in rice, IR64, a drought-sensitive indica and Apo, a drought-tolerant indica and their F1 hybrid were grown under normal and drought stress condition. SNPs were identified between the two parents and were used to identify parent-specific alleles in the F1 mRNA. The authors assayed 29 drought-responsive genes in the F1 hybrid for ASE imbalance by SNaPshot single-base extension assay. Surprisingly, results showed allele-specific copy number variation (CNV). This happens when, in a bi-allelic organism such as rice, one of the parent-specific alleles were replicated several times relative to the other allele. These asymmetric copies of alleles may contribute to ASE imbalance. To further investigate ASE imbalance in a genome-wide scale, the authors sequenced the total RNA transcripts of the same parents (Apo and IR64) and their F1 hybrid in both conditions. Analysis of reads revealed that more than 80% of the genes showed ASE imbalance. In a genome-wide scale, ASE imbalance occurs in both control and stress conditions indicating that such phenomenon is inherent to the organism regardless of the environmental conditions. The imbalance, however, is directed towards the maternal allele in both conditions. More than 25% of the whole transcript population exhibited 'dynamic' expression behavior between the two conditions, that is, a gene preferent
Original languageEnglish
JournalPhilippine Journal of Crop Science
Publication statusPrint publication - 2013

Fingerprint

Droughts
Oryza sativa
Alleles
drought
Genome
alleles
rice
genome
Oryza
Genes
genes
organisms
Population Dynamics
messenger RNA
Single Nucleotide Polymorphism
water stress
population dynamics
Mothers
RNA

Keywords

  • Rice
  • Allelic imbalance
  • Drought

Cite this

@article{e1af6c0b72c24726a28057292611a655,
title = "Genome-wide analysis of allele specific expression imbalance and copy number variation in rice (Oryza sativa L.) under normal and drought conditions",
abstract = "To understand the possible roles of allele-specific expression (ASE) imbalance in genetic regulation of drought response in rice, IR64, a drought-sensitive indica and Apo, a drought-tolerant indica and their F1 hybrid were grown under normal and drought stress condition. SNPs were identified between the two parents and were used to identify parent-specific alleles in the F1 mRNA. The authors assayed 29 drought-responsive genes in the F1 hybrid for ASE imbalance by SNaPshot single-base extension assay. Surprisingly, results showed allele-specific copy number variation (CNV). This happens when, in a bi-allelic organism such as rice, one of the parent-specific alleles were replicated several times relative to the other allele. These asymmetric copies of alleles may contribute to ASE imbalance. To further investigate ASE imbalance in a genome-wide scale, the authors sequenced the total RNA transcripts of the same parents (Apo and IR64) and their F1 hybrid in both conditions. Analysis of reads revealed that more than 80{\%} of the genes showed ASE imbalance. In a genome-wide scale, ASE imbalance occurs in both control and stress conditions indicating that such phenomenon is inherent to the organism regardless of the environmental conditions. The imbalance, however, is directed towards the maternal allele in both conditions. More than 25{\%} of the whole transcript population exhibited 'dynamic' expression behavior between the two conditions, that is, a gene preferent",
keywords = "Rice, Allelic imbalance, Drought",
author = "Ereful, {Nelzo C} and Kaye Malabanan and M Thomson and FE Merca and Antonio Laurena and David Lee and Ian Mackay and Hei Leung",
year = "2013",
language = "English",
journal = "Philippine Journal of Crop Science",

}

Genome-wide analysis of allele specific expression imbalance and copy number variation in rice (Oryza sativa L.) under normal and drought conditions. / Ereful, Nelzo C; Malabanan, Kaye; Thomson, M; Merca, FE; Laurena, Antonio; Lee, David; Mackay, Ian; Leung, Hei.

In: Philippine Journal of Crop Science, 2013.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome-wide analysis of allele specific expression imbalance and copy number variation in rice (Oryza sativa L.) under normal and drought conditions

AU - Ereful, Nelzo C

AU - Malabanan, Kaye

AU - Thomson, M

AU - Merca, FE

AU - Laurena, Antonio

AU - Lee, David

AU - Mackay, Ian

AU - Leung, Hei

PY - 2013

Y1 - 2013

N2 - To understand the possible roles of allele-specific expression (ASE) imbalance in genetic regulation of drought response in rice, IR64, a drought-sensitive indica and Apo, a drought-tolerant indica and their F1 hybrid were grown under normal and drought stress condition. SNPs were identified between the two parents and were used to identify parent-specific alleles in the F1 mRNA. The authors assayed 29 drought-responsive genes in the F1 hybrid for ASE imbalance by SNaPshot single-base extension assay. Surprisingly, results showed allele-specific copy number variation (CNV). This happens when, in a bi-allelic organism such as rice, one of the parent-specific alleles were replicated several times relative to the other allele. These asymmetric copies of alleles may contribute to ASE imbalance. To further investigate ASE imbalance in a genome-wide scale, the authors sequenced the total RNA transcripts of the same parents (Apo and IR64) and their F1 hybrid in both conditions. Analysis of reads revealed that more than 80% of the genes showed ASE imbalance. In a genome-wide scale, ASE imbalance occurs in both control and stress conditions indicating that such phenomenon is inherent to the organism regardless of the environmental conditions. The imbalance, however, is directed towards the maternal allele in both conditions. More than 25% of the whole transcript population exhibited 'dynamic' expression behavior between the two conditions, that is, a gene preferent

AB - To understand the possible roles of allele-specific expression (ASE) imbalance in genetic regulation of drought response in rice, IR64, a drought-sensitive indica and Apo, a drought-tolerant indica and their F1 hybrid were grown under normal and drought stress condition. SNPs were identified between the two parents and were used to identify parent-specific alleles in the F1 mRNA. The authors assayed 29 drought-responsive genes in the F1 hybrid for ASE imbalance by SNaPshot single-base extension assay. Surprisingly, results showed allele-specific copy number variation (CNV). This happens when, in a bi-allelic organism such as rice, one of the parent-specific alleles were replicated several times relative to the other allele. These asymmetric copies of alleles may contribute to ASE imbalance. To further investigate ASE imbalance in a genome-wide scale, the authors sequenced the total RNA transcripts of the same parents (Apo and IR64) and their F1 hybrid in both conditions. Analysis of reads revealed that more than 80% of the genes showed ASE imbalance. In a genome-wide scale, ASE imbalance occurs in both control and stress conditions indicating that such phenomenon is inherent to the organism regardless of the environmental conditions. The imbalance, however, is directed towards the maternal allele in both conditions. More than 25% of the whole transcript population exhibited 'dynamic' expression behavior between the two conditions, that is, a gene preferent

KW - Rice

KW - Allelic imbalance

KW - Drought

M3 - Article

JO - Philippine Journal of Crop Science

JF - Philippine Journal of Crop Science

ER -