Study On Genetic Diversity Of Chinese Landrace And Improved Rice Varieties By SSR

Rice is the major food crops in our country. Making full use of the rich genetic diversity of rice germplasm resource and boarding the genetic background for breeding will be great importance for rice production in China. Up to now, a lot of studies about genetic diversity and population structure of Chinese cultivated rice have been reported. However, it is still not clear about the influence of the number and distribution of simple sequence repeat(SSR) makers used in analyzing the rice germplasm resource. Moreover, the study on genetic variation of Chinese landrace and improved varieties is less known. Thus, in our work, a total of 120 SSR markers were used to expose the minimum number of SSR markers and the effect of chromosome distribution according to the genetic diversity indexes, correlation coefficient, stand error, and cluster analysis. Among the 120 SSRs, 98 were used to analyze the genetic diversity and population structure of landrace and improved variety, and to explore the genetic differentiation between the two groups, so as to improve the effective use of genetic variation in the field of rice breeding. The main research results are as follows:A total of 120 SSR markers were used to analyze the genetic variation in 69 cultivated rice accessions with clear classifications. Assessing the genetic diversity and population structure, we exposed that the effect of the number of SSR markers on analyzing genetic variation in rice. The results showed that:(1) All 120 SSR markers revealed a total of 1 256 alleles.(2) The number of alleles per locus widely ranged from 2 to 27, with an average value of 10.5; Nei’s diversity index varied from 0.413 to 0.951, with a mean of 0.760.The chromosome distribution of the primer had no significant effect on genetic diversity and population relationship. The minimum number of SSR markers on analyzing genetic diversity in rice was 72. The number of SSR markers on analyzing population structure of rice was at least 64.Ninety~eight SSR markers were used to compare the genetic diversity in 202 Chinese cultivated rice varieties. The result showed that a high level genetic diversity in Chinese cultivated rice. All the 98 loci revealed a total of 1 350 alleles. The number of allele per locus(Na) ranged from 3 to 39, with an average of 14. The mean Nei’s genetic diversity of per locus(He) was 0.733, with a range from 0.125 to 0.955. The polymorphism information content(PIC) varied from 0.122 to 0.953, with a mean of 0.680. The number of rare alleles(the allele frequency < 5%)(Nr) was 913, and the genetic richness(Rs) was 8.33.There exited a significant difference in genetic diversity between landrace and improved rice varieties. Landrace(Na = 1 219, He = 0.747, PIC = 0.710, Nr = 756, Rs = 8.50) had more variation than improved rice(Na = 919, He = 0.704, PIC = 0.650, Nr = 529, Rs = 7.01).Diversity analysis in chromosome level demonstrated that only chromosome 1 of improved rice had higher genetic diversity than that of landrace. Further analysis showed interval specificity of genetic improvement in the level of whole genome for improved rice.