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Genome-wide analysis of polymorphisms identified domestication-associated long low diversity region carrying important rice grain size/weight QTL

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Title Genome-wide analysis of polymorphisms identified domestication-associated long low diversity region carrying important rice grain size/weight QTL
 
Creator Kumar, Angad
Daware, Anurag
Kumar, Arvind
Kumar, Vinay
Krishnan S, Gopala
Mondal, Subhasish
Patra, Bhaskar Chandra
Singh, Ashok. K.
Tyagi, Akhilesh K.
Parida, Swarup K.
Thakur, Jitendra K.
 
Subject Association analysis
Domestication
Genome sequence
Grain size/weight
Low diversity region
Polymorphism
QTL
Rice
Selection sweep
 
Description Accepted date: 20 May 2020
Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication‐driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504,439 SNPs and 78,166 InDels. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and top four of them could be validated in mapping population, suggesting this study as a valuable resource for high‐throughput genotyping. A contiguous ~ 6 Mb long low diversity region (LDR) carrying a major grain weight QTL (harbouring OsTOR gene) was identified on chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication‐related traits including grain size/weight. The aus population retained more allelic variations in the LDR than japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from RiceSzWtBase database.
This work was financially supported by the grants BT/AB/NIPGR/SEED BIOLOGY/2012 and
BT/BI/04/069/2006 for establishing the Distributed Information Sub Centre (DISC) from
Department of Biotechnology (DBT), Government of India. AnK and VK acknowledge University
Grant Commission for the Senior Research Fellowship. AD acknowledges DBT for Senior Research
Fellowship and ArK acknowledges Short-term Research Fellowship from NIPGR. The authors are
thankful to DBT-eLibrary Consortium (DeLCON) for providing access to e-resources. We thank Dr.
Manoj Prasad, NIPGR for his valuable suggestions.
 
Date 2020-05-27T07:46:01Z
2020-05-27T07:46:01Z
2020
 
Type Article
 
Identifier Plant Journal, 103: 1525-1547
1365-313X
https://doi.org/10.1111/tpj.14845
https://onlinelibrary.wiley.com/doi/10.1111/tpj.14845
http://223.31.159.10:8080/jspui/handle/123456789/1065
 
Language en_US
 
Format application/pdf
 
Publisher John Wiley & Sons