Abstract
Soil salinity is a major constraint to rice production in large inland and coastal areas around the world. Modern high yielding rice varieties are particularly sensitive to high salt stress. There are salt tolerant landraces and traditional varieties of rice but with limited information on genomic regions (QTLs) and genes responsible for their tolerance. Here we describe a method for rapid identification of QTLs for reproductive stage salt tolerance in rice using bulked segregant analysis (BSA) of bi-parental recombinant inbred lines (RIL). The number of RILs required for the creation of two bulks with extreme phenotypes was optimized to be thirty each. The parents and bulks were genotyped using a 50K SNP chip to identify genomic regions showing homogeneity for contrasting alleles of polymorphic SNPs in the two bulks. The method was applied to ‘CSR11/MI48’ RILs segregating for reproductive stage salt tolerance. Genotyping of the parents and RIL bulks, made on the basis of salt sensitivity index for grain yield, revealed 6,068 polymorphic SNPs and 21 QTL regions showing homogeneity of contrasting alleles in the two bulks. The method was validated further with ‘CSR27/MI48’ RILs used earlier for mapping salt tolerance QTLs using low-density SSR markers. BSA with 50K SNP chip revealed 5,021 polymorphic loci and 34 QTL regions. This not only confirmed the location of previously mapped QTLs but also identified several new QTLs, and provided a rapid way to scan the whole genome for mapping QTLs for complex agronomic traits in rice.
Highlights
Rice is the most important cereal crop with maximum contribution to the global food requirements
It is worthwhile to knowing the association between of stress susceptible index and various agro-morphological traits through simultaneous evaluation under normal and sodicity conditions to draw parallels and differences across important traits for selection in the target environments
The extreme tolerant and sensitive recombinant inbred lines (RIL) were selected based on their susceptibility index (SSI) for grain yield, which was a direct measure of salt tolerance and would provide independent line of evidence to those based on salt tolerance parameters
Summary
Rice is the most important cereal crop with maximum contribution to the global food requirements. High-throughput genotyping based on SNP arrays and generation sequencing (NGS) has evolved very fast during the last decade Using these technologies, BSA can identify large numbers of markers linked to the target genes or QTLs. One of the first studies to use bulked segregant analysis of RIL population was differential transcriptome analysis to identify candidate genes for salt tolerance using genome wide microarray [8]. The aim of present study was to rapidly identify additional STRS QTLs and candidate genes for salt sensitivity index (SSI) for grain yield in sodicity tolerant Indica rice variety CSR11 by bulked segregant analysis using high density SNP array
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