Revealing Genetic Relationship and Prospecting of Novel Donors Among Upland Rice Genotypes Using qDTY-Linked SSR Markers

A total of 17 simple sequence repeat (SSR) markers linked to QTLs (qDTYs) governing grain yield under reproductive stage (RS) drought stress were used to assess the genetic relationship and prospecting new donors for qDTYs among 32 popular upland rice genotypes. These SSR markers generated a total of 36 alleles with an average allele count of 2.1 per locus. Polymorphic information content value of the markers ranged from 0.376 to 0.662 with an average value of 0.484. The expected heterozyogosity ranged from 0.381 to 0.632. STRUCTURE analysis divided the 32 genotypes into three sub-populations. Subsequent phenotyping revealed that all the tolerant genotypes were grouped into one sub-population, whereas the moderately tolerant and susceptible genotypes were grouped into separate sub-populations. Phylogenetic tree constructed by the unweighted neighbour-joining method also divided the genotypes into three clusters. The grouping pattern of genotypes into the clusters was similar to that into the STRUCTURE analysis, on the basis of drought tolerance level. The average value of genetic dissimilarity coefficient among the genotypes was observed to be 0.486. Furthermore, by combining genotyping data with phenotyping data, 16 new donors for 6 qDTYs were identified.