Record Details

An integrated genomic strategy delineates candidate mediator genes regulating grain size and weight in rice

NIPGR Digital Knowledge Repository (NDKR)

View Archive Info
 
 
Field Value
 
Title An integrated genomic strategy delineates candidate mediator genes regulating grain size and weight in rice
 
Creator Malik, Naveen
Dwivedi, Nidhi
Singh, Ashok K.
Parida, Swarup K.
Agarwal, Pinky
Thakur, Jitendra K.
Tyagi, Akhilesh K.
 
Subject Natural variation in plants
Genetic association study
 
Description Accepted date: 02 March 2016
The present study deployed a Mediator (MED) genes-mediated integrated genomic strategy for understanding the complex genetic architecture of grain size/weight quantitative trait in rice. The targeted multiplex amplicon resequencing of 55 MED genes annotated from whole rice genome in 384 accessions discovered 3971 SNPs, which were structurally and functionally annotated in diverse coding and non-coding sequence-components of genes. Association analysis, using the genotyping information of 3971 SNPs in a structured population of 384 accessions (with 50–100 kb linkage disequilibrium decay), detected 10 MED gene-derived SNPs significantly associated (46% combined phenotypic variation explained) with grain length, width and weight in rice. Of these, one strong grain weight-associated non-synonymous SNP (G/A)-carrying OsMED4_2 gene was validated successfully in low- and high-grain weight parental accessions and homozygous individuals of a rice mapping population. The seed-specific expression, including differential up/down-regulation of three grain size/weight-associated MED genes (including OsMED4_2) in six low and high-grain weight rice accessions was evident. Altogether, combinatorial genomic approach involving haplotype-based association analysis delineated diverse functionally relevant natural SNP-allelic variants in 10 MED genes, including three potential novel SNP haplotypes in an OsMED4_2 gene governing grain size/weight differentiation in rice. These molecular tags have potential to accelerate genomics-assisted crop improvement in rice.
The authors gratefully acknowledge the financial support for this study provided by a research grant (102/IFD/SAN/2161/2013-14) from the Department of Biotechnology (DBT), Government of India. NM and ND acknowledge the CSIR (Council of Scientific and Industrial Research) for Senior Research Fellowship awards.
 
Date 2016-03-28T10:07:07Z
2016-03-28T10:07:07Z
2016
 
Type Article
 
Identifier Scientific Reports, 6: 23253
2045-2322
http://172.16.0.77:8080/jspui/handle/123456789/631
http://www.nature.com/articles/srep23253?trendmd-shared=0
10.1038/srep23253
 
Language en_US
 
Publisher Nature Publishing Group