Population Structure of 93 Varieties of Rice ( Oryza Sativa L. subsp. Hsien Ting) in Qinba, China

Abstract BackgroundThe Qinba region is the transition region between indica and japonica varieties with a long history of indica varieties planting. 72,824 SNPs data based on GBS method, 48 pairs core primers of SSRs, and 15 agronomic traits were employed to explore the population structure of 93 rice varieties. The Mantel test was used to analyze the distance matrix generated using NlaIII-GBS only, MseI-GBS only, by combining NlaIII-GBS and MseI-GBS data and SSR.ResultIn this study, a total of 379 alleles were obtained using 48 pairs core primer of SSR, encompassing an average of 8.0 alleles per primer. The PPB and PIC was 88.65% and 0.77, respectively. Among these, RM278 possess the highest TNB and NPB, and the PPB in 29 pairs of SSR markers was 100%. RM176 showed the highest PIC. MAF was set to 0.05, and 39,872, 35,547 and 67,621 SNPs were obtained via NlaIII-GBS only, MseI-GBS only, and merged NlaIII-GBS and MseI-GBS data, respectively. The IBS genetic similarity coefficient average was 0.74. The results showed that the correlation between the genetic distance matrix based on NlaIII-GBS and MseI-GBS was the largest (R2=0.88), followed by NlaIII-GBS and SSR (R2=0.35), then by merged NlaIII-GBS and MseI-GBS data and SSR (R2=0.33), and the smallest by MseI-GBS and SSR (R2=0.27). The results showed that the 93 rice varieties could be clustered into two subgroups. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations. Tajima’s D value was 1.66, and the FST between the two populations was 0.61, and the Nm was 0.16.ConclusionThe population genetic variation explained by SNP was larger than that explained by SSR. Through cluster analysis, the 93 samples were divided into 2 subgroups, with more than 97% of the samples clustered into one subgroup. The gene flow of 93 samples used in this study is larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of indica varieties in the Qinba region. However, the genetic structure of the rice population is simple and lacked rare alleles.