Association Analysis Of Rice Cold Tolerance At Early Growing Stage With SSR Markers Of Japonica Rice In Cold Region

Cold damage in the rice region around the world have different degrees of occurrence, which is an important factor affecting high and stable yield of rice. The frequency of chilling injury in the Northeast China and high altitude areas in Yunnan is higher, particularly in Heilongjiang province,especially rice is vulnerable to chilling injury at bud and seedling stage, which reduced the seed germination rate, seedling rot and weak seedling, affected the growth and development in the late growth stage, and then reduced the yield of rice. In this experiment, 220 japonica rice varieties in cold region were used to identification the rice cold tolerance at germination stage, budding stage and seedling stage. The 118 pairs of SSR markers which evenly distributed on 12 chromosomes of rice were used to association analysis, detecting the SSR markers associated with cold tolerance, discover superior alleles and carrier materials, providing theoretical basis and material basis for rice cold tolerance molecular assisted breeding. The main result of this study are as follows:1. Through the evaluation of 220 japonica rice materials in cold region about rice cold tolerance at germination stage, budding stage and seedling stage, relative germination rate was used as identification index of rice cold tolerance at germination stage, we get 33 cultivars that have better cold tolerance at germination stage, accounting for 15% of the total material, represented materials are Longjing 21, Mudanjiang 4 and Songjing 3; Seedling rate was used as identification index of rice cold tolerance at budding stage, we get 26 cultivars that have better cold tolerance at budding stage, accounting for 11.68% of the total material, represented materials are Longjing 21, Longjingxiang 1 and Hejiang 3; Leave discoloration indexes was used as identification index of rice cold tolerance at seedling stage, we get 15 cultivars that have better cold tolerance at seedling stage, accounting for 6.8% of the total material, represented materials are Kendao 12, Kenjing 4 and Mudanjiang 4.2. Correlation analysis on indexes of rice cold tolerance during the same period and the indexes of rice cold tolerance during the different periods, the result showed that: In the same period, relative germination rate, relative germination indexes and relative germination were extremely significant positive correlation; Leaf discoloration indexes with leaf rolling indexes were extremely significant positive correlation, with relative seedling height, relative root length,relative shoot dry weight and relative root dry weight were significantly or extremely significant negative correlation; Leaf rolling indexes with relative seedling height, relative root length and relative shoot dry weight were significantly or extremely significant negative correlation; Relative root length with relative seedling height, relative root dry weight and relative shoot dry weight were significantly or extremely significant positive correlation; relative shoot dry weigh and relative root dry weight were significantly positive correlation; In the different periods, seedling rate with relative germination rate, relative germination indexes, relative germination, leaf discoloration indexes, relative seedling height, relative root length and relative shoot dry weigh were significantly or extremely significant positive correlation; Relative germination rate with leaf discoloration indexes were significantly negative correlation, and with relative root length were significantly positive correlation; Relative germination with leaf discoloration indexes, leaf rolling indexes, relative root length and relative shoot dry weigh were significantly positive correlation; Relative germination indexes with leaf discoloration indexes, relative root length, relative seedling height and relative shoot dry weigh were significantly or extremely significant positive correlation.3.The analysis of population structure divides the 220 materials into two groups. 6903 combinations of two loci among 118 SSR primes were detected, and in these combinations,there exists some linkage disequilibrium in linear or nonlinear combination, 4505 of the LD loci in pairs were supported by R2 statistical probability(p<0.01), accounting for 65.26% of all loci combination, the average of r2 was 0.011.4. 220 varieties of japonica rice in cold region and 118 SSR markers were used to do association analysis on rice cold tolerance, the result is:five markers associated with rice cold tolerance were detected at germination stage, including four markers associated with relative germination rate, three markers associated with relative germination indexes, two markers associated with relative germination, add up 9 times association, the interpretation of the phenotypic variation rate was 4.23%-11.58%; four markers associated with the seedling rate of rice cold tolerance were detected at budding stage, the interpretation of the phenotypic variation rate was 3.79%-9.89%; sixteen markers associated with rice cold tolerance were detected at seedling stage, including four markers associated with leaf discoloration indexes, five markers respectively associated with leaf rolling indexes, relative root length and relative seedling height, one marker associated with relative shoot dry weight, three markers associated with relative root dry weight, add up 23 times association, the interpretation of the phenotypic variation rate was 2.73%-13.54%;5.By anglicizing these associated markers, a serial of elite alleles(a total of 71 elite alleles),loci and their carrier materials were screened out, some of the elite alleles is associated with multiple traits. For example: RM1220-161 bp simultaneously associated with relative germination rate, relative germination indexes, relative germination and relative seedling height, represented by the material Heijing 5, Songjing 8 and Songjing 11. At the same time, the study screen out a batch of materials which carried multiple elite alleles, such as Heijing 5 and Kendao 12(each with 10 elite allelic variation), Mudanjing 4 and Songjing 3(each with 9 elite allelic variation),Mudanjiang 1 and Longjing 29(each with 8 elite allelic variation), et al.