基于简化基因组测序的稗草遗传多样性研究

Research on genetic diversity of Echinochloa based on RAD-seq

摘要:

【目的】利用 SNP 分子标记，分析稗草（Echinochloa spp.）种质资源（野生材料和栽培品种） 遗传多样性水平，揭示不同类型稗草种质资源之间的亲缘关系以及群体遗传结构差异，为稗草的遗传多样性保护、野生资源的开发利用奠定基础。【方法】以 20 份野生稗草和 24 份栽培稗草为材料，采用 RAD-seq 技术对各样本进行测序并开发 SNP 标记，通过构建系统进化树并进行主成分、群体遗传结构和遗传多样性参数分析，探讨遗传结构差异并评估不同群体间遗传多样性水平。【结果】测序产生的序列数据量为 161. 51 Gb，过滤后共获得 31 284 个高质量 SNP 位点。遗传结构分析结果将 44 份稗草资源划分为 4 个类群，类群Ⅰ和Ⅱ主要为野生资源，类群Ⅲ和Ⅳ主要为栽培资源。4 个类群间的遗传多样性指数（P_i） 为 0. 000 061~0. 000 154，遗传分化指数（FST）为 0. 289 2~0. 507 8，观测杂合度（H_O）为 0. 100 7~0. 226 4，期望杂合度（H_E）为 0. 140 4~0. 251 2，其中野生类群Ⅰ和Ⅱ的遗传多样性指数（P_i）、 观测杂合度（H_O）、期望杂合度（H_E）均高于栽培类群Ⅲ和Ⅳ；遗传分化结果表明 4 个类群两两之间均发生了显著的遗传分化，野生类群Ⅱ与栽培类群Ⅳ遗传分化最为显著。【结论】 SNP 标记能将野生稗草和栽培稗草区分开来，证实了在稗草分类方面的可行性；野生稗草群体的遗传多样性水平高于栽培稗草群体，其中野生类群Ⅱ（稗、水田稗、西来稗）遗传多样性水平最高，但总体上稗草遗传多样性水平偏低； 并推测遗传漂变、人类活动以及授粉方式可能是导致稗草植物遗传多样性水平下降和产生遗传分化的重要原因。

Abstract:

【Objective】 The study was to analyze the genetic diversity level of Echinochloa spp. by SNP markers，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 genetic 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 diversity index （P_i ） for 4 groups of Echinochloa was 0. 000 061~0. 000 154，the index of genetic differentiation （FST） was 0. 289 2~0. 507 8. The observed heterozygosity （H_O） was 0. 115 1~0. 226 4 and the expected heterozygosity （H_E） was 0. 100 7~0. 251 2. The nucleotide diversity index （P_i ），observed heterozygosity （H_O） and expected heterozygosity （H_E） 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 general，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 Echinochloa.