title: Genome-wide association mapping of salinity tolerance in rice (Oryza sativa).
abstract: Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na(+)/K(+) ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5-18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na(+)/K(+) ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.
authors: National Research Centre on Plant Biotechnology, New Delhi 110012, India.
authors: Vinod
authors: V
authors: Kumar
authors: National Research Centre on Plant Biotechnology, New Delhi 110012, India.
authors: Anshuman
authors: A
authors: Singh
authors: National Research Centre on Plant Biotechnology, New Delhi 110012, India.
authors: S V Amitha
authors: SV
authors: Mithra
authors: Central Soil Salinity Research Institute, Karnal, Haryana 132001, India.
authors: S L
authors: SL
authors: Krishnamurthy
authors: National Research Centre on Plant Biotechnology, New Delhi 110012, India.
authors: Swarup K
authors: SK
authors: Parida
authors: National Research Centre on Plant Biotechnology, New Delhi 110012, India.
authors: Sourabh
authors: S
authors: Jain
authors: National Research Centre on Plant Biotechnology, New Delhi 110012, India.
authors: Kapil K
authors: KK
authors: Tiwari
authors: National Research Centre on Plant Biotechnology, New Delhi 110012, India.
authors: Pankaj
authors: P
authors: Kumar
authors: Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
authors: Atmakuri R
authors: AR
authors: Rao
authors: Central Soil Salinity Research Institute, Karnal, Haryana 132001, India.
authors: S K
authors: SK
authors: Sharma
authors: University of Delhi South Campus, New Delhi 110021, India.
authors: Jitendra P
authors: JP
authors: Khurana
authors: National Research Centre on Plant Biotechnology, New Delhi 110012, India.
authors: Nagendra K
authors: NK
authors: Singh
authors: National Research Centre on Plant Biotechnology, New Delhi 110012, India Central Rice Research Institute, Cuttack, Odisha 753006, India tmnrcpb@gmail.com.
authors: Trilochan
authors: T
authors: Mohapatra
mesh_terms: D032461:Chromosomes, Plant; D055106:Genome-Wide Association Study; D020412:Multifactorial Inheritance; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D055049:Salt Tolerance / Q000235:genetics*
keywords: genome-wide association study; infinium genotyping assay; rice; salt tolerance; single-nucleotide polymorphism
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