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Assessment of genetic diversity in salt-tolerant rice and its wild relatives for ten SSR loci and one allele mining primer of salT gene located on 1st chromosome

Ganie, Showkat Ahmad, Karmakar, Joydip, Roychowdhury, Rajib, Mondal, Tapan Kumar, Dey, Narottam
Plant systematics and evolution 2014 v.300 no.7 pp. 1741-1747
DNA, Oryza rufipogon, genes, genetic variation, genome mining, genotype, loci, microsatellite repeats, molecular weight, phenotypic variation, quantitative trait loci, salt tolerance, wild relatives, wild rice
A heterogeneous collection of rice genotypes which included seven salt-tolerant rice lines, one salt-sensitive improved line, one wild rice (Oryza rufipogon) and one salt-tolerant wild rice relative (Porteresia coarctata) was screened with ten salt-tolerance-linked simple sequence repeat markers, of which nine were from the Saltol QTL mapped on rice 1st chromosome and the rest one from 8th chromosome, having high phenotypic variance for salt tolerance. Variation in molecular weight (in the form of base pairs) of the different amplified products using RM primers was used to find out the genetic relationship among the studied rice genotypes. Genomic DNA of the studied genotypes was also amplified with a reported allele mining primer for a salt-inducible gene (salT). The amplified products were sequenced and aligned to find out the closeness among the rice lines for the studied gene. Dendrogram derived from marker profiles showed partial similarity with salT gene-derived tree. Commonly, all the salt-tolerant lines were grouped into a single cluster, including IR36 (a salt-sensitive line) to which O. rufipogon (the wild rice) and P. coarctata (the wild rice relative) joined separately. The taxonomic identity and evolutionary relationship among the three groups (rice, wild rice and wild rice relative) were bioinformatically analysed using the nucleotide sequence of the studied salT gene.