title: 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.
authors.affiliation: National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Sushma
authors.initials: S
authors.lastname: Tiwari
authors.affiliation: Central Soil Salinity Research Institute, Karnal, India.
authors.forename: Krishnamurthy
authors.initials: K
authors.lastname: Sl
authors.affiliation: Central Soil Salinity Research Institute, Karnal, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Kumar
authors.affiliation: National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Balwant
authors.initials: B
authors.lastname: Singh
authors.affiliation: Indian Agricultural Statistics Research Institute, New Delhi, India.
authors.forename: A R
authors.initials: AR
authors.lastname: Rao
authors.affiliation: National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Amitha
authors.initials: A
authors.lastname: Mithra Sv
authors.affiliation: National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Vandna
authors.identifier: http://orcid.org/0000-0002-6734-3169
authors.initials: V
authors.lastname: Rai
authors.affiliation: Division of Genetics, Indian Agricultural Research Institute, New Delhi, India.
authors.forename: Ashok K
authors.initials: AK
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India.
authors.forename: Nagendra K
authors.initials: NK
authors.lastname: Singh
mesh_terms: D002874:Chromosome Mapping; D004274:DNA, Recombinant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D007178:Inbreeding; D018895:Microsatellite Repeats / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012275:Oryza / Q000235:genetics* / Q000502:physiology*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D015203:Reproducibility of Results; D012098:Reproduction; D055049:Salt Tolerance / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics; D013997:Time Factors
chemical_list: D004274:DNA, Recombinant; D005819:Genetic Markers