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An efficient strategy combining SSR markers- and advanced QTL-seq-driven QTL mapping unravels candidate genes regulating grain weight in rice

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Title An efficient strategy combining SSR markers- and advanced QTL-seq-driven QTL mapping unravels candidate genes regulating grain weight in rice
 
Creator Daware, Anurag
Das, Sweta
Srivastava, Rishi
Badoni, Saurabh
Singh, Ashok K.
Agarwal, Pinky
Parida, Swarup K.
Tyagi, Akhilesh K.
 
Subject grain weight
QTL
QTL-seq
rice
SNP
SSR
 
Description Accepted date: 29 September 2016
Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16–74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7–8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice.
The authors gratefully acknowledge the financial support for this study provided by a research grant from the Department of Biotechnology (DBT), Government of India (102/IFD/SAN/2161/2013-14)
 
Date 2016-11-04T09:02:20Z
2016-11-04T09:02:20Z
2016
 
Type Article
 
Identifier Front. Plant Sc., 7: 1535
1664-462X
http://59.163.192.83:8080/jspui/handle/123456789/690
http://journal.frontiersin.org/article/10.3389/fpls.2016.01535/full
10.3389/fpls.2016.01535
 
Language en_US
 
Publisher Frontiers Media S.A.