Research on genetic diversity of Echinochloa based on RAD-seq
[Objective]The study was to analyze the genetic diversity level of Echinochloa spp. by SNP mark-ers,to discover the genetic relationship and structure between wild and cultivated material and to provide a basis for the protection of genetic diversity,and utilization of wild resources of Echinochloa spp.[Method]20 samples of wild Echinochloa and 24 samples of cultivated Echinochloa spp. were collected. The SNP markers of all samples were identified by RAD-seq.The phylogenetic analysis,principal component analysis,population genetic structure and ge-netic parameter were used to reveal the genetic structure and genetic diversity between wild and cultivated population.[Result]A total of 161.51 Gb sequence data was obtained,and 31,284 high-quality SNP loci were retained after filtering. The results of genetic structure indicated that 44samples of Echinochloa could be divided into 4 groups,among which group Ⅰ and Ⅱ were wild resources,and group Ⅲ and Ⅳ were cultivated resources. The nucleotide di-versity index (Pi) for 4 groups of Echinochloa was 0.000061～0.000154,the index of genetic differentiation (FST) was 0.2892～0.5078. The observed heterozygosity (HO) was 0.1151～0.2264 and the expected heterozygosity (HE) was 0.1007～0.2512.The nucleotide diversity index (Pi),observed heterozygosity (HO) and expected hetero-zygosity (HE) of wild group Ⅰ and Ⅱ were higher than those of cultivated group Ⅲ and Ⅳ.The genetic differentiation results indicated that genetic differentiation occurred between four groups,and wild group Ⅱ and cultivated group Ⅳ were the most significant difference.[Conclusion]SNP markers could distinguish wild Echinochloa and cultivated Echinochloa,which proved the feasibility of classifying Echinochloa. The highest genetic diversity level was found in wild Echinochloa group Ⅱ(E. crus-galli (L.),E. oryzoides and E. crus-galli var. zelayensis),however,in gen-eral,the level of genetic diversity of Echinochloa was lower;And it was speculated that genetic drift,human activities and pollination practices may be crucial reasons for the decline in genetic diversity and genetic differentiation of Echi-nochloa.
万方数据
维普
