Mapping QTLs for Salt Tolerance in Rice (Oryza sativa L.) by Bulked Segregant Analysis of Recombinant Inbred Lines Using 50K SNP Chip

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.

Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize

“…As a result, the range of tolerance to abiotic stresses present in the grass family (Poaceae) far exceeds that present within any single grass species. However, to date, studies attempting to identify determinants of abiotic stress tolerance at a genetic or genomic level have predominantly focused on individual species (Chopra et al, 2017;Priest et al, 2014;Revilla et al, 2016;Tiwari et al, 2016;Waters et al, 2017). The majority of genetic changes with phenotypic effects can be broadly classified into two categories: those that alter protein-coding sequence and those that alter the regulation of gene expression.…”

Identifying QTLs Associated and Marker-Assisted Selection for Salinity Tolerance at the Seedling, Vegetative and Reproductive Stages in Rice (Oryza Sativa L.)

“…RM223 linked to salt tolerance gene at the distance of 6.3 cM on chromosome 8 at vegetative stage under EC = 10 dS.m -1 from F3 population of IR28/Doc Phung [12]. Tiwari et al, [13]. reported 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).…”

Genetic architecture of the maize kernel row number revealed by combining QTL mapping using a high-density genetic map and bulked segregant RNA sequencing

“…Based on two groups that show opposing phenotypes of interest traits, the distribution patterns of genome-wide alleles are examined by molecular markers, such as single nucleotide polymorphism (SNP) [16]. A non-random distribution of alleles between two groups likely indicates that this locus is linked with the trait of interest.…”