SSR Analysis of Genetic Diversity and Cold Tolerance in Temperate Rice Germplasm

A total of 23 elite rice cultivars from eight countries were evaluated for cold tolerance using two screening methods at Chuncheon Substation, National Institute of Crop Science (NICS), Republic of Korea. The rice cultivars Jinbu, Mustaqillik, and Avangard showed cold tolerance and high spikelet fertility (63–79%) in cold-water irrigation screening. Under greenhouse screening, five cultivars (Giza 177, Avangard, Mustaqillik, Jinbu, and Jungan) showed high cold tolerance and high spikelet fertility (71–81%). Simple sequence repeat (SSR) marker analysis of 21 genotypes revealed two major clusters, the japonica and indica groups, with a genetic similarity of 0.69. Out of 21 rice cultivars, only four (Giza 178 from Egypt, Attey and Zakha from Bhutan, and Millin from Australia) fell under the indica cluster. The cold-tolerant varieties Jinbu, Mustaqillik, and Avangard were clustered with the japonica group, which had genetic similarity of 0.83. These varieties are considered as potential germplasm that will help diversify the japonica gene pool for cold-tolerant rice breeding. A one-way linear analysis of variance identified a significant relationship between individual alleles and traits. Three SSR markers were significantly associated with spikelet fertility under cold-water irrigation on chromosomes 1, 2, and 7. Five SSR markers were associated with spikelet fertility under a cool-environment greenhouse on chromosomes 8, 9, 10, and 12. The SSR markers associated with cold tolerance may also be useful as selection markers in indica/japonica cross combinations to improve cold tolerance.