| 基于SLAF-seq的天竺桂群体遗传变异分析 |
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| 引用本文： | 杨颖,刘向东,段豪,芦治国. 基于SLAF-seq的天竺桂群体遗传变异分析[J]. 南京林业大学学报(自然科学版), 2022, 46(5): 33. DOI: 10.12302/j.issn.1000-2006.202009001 |
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| 作者姓名： | 杨颖 刘向东 段豪 芦治国 |
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| 作者单位： | 江苏省中国科学院植物研究所,江苏省落羽杉属树木种质创新与繁育工程研究中心,江苏 南京 210014 |
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| 基金项目： | 江苏省科技计划重点及面上项目(BE2017372);江苏省林业科技创新与推广项目(LYKJ[2020]24) |
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| 摘 要： | 【目的】探讨我国天竺桂资源的遗传多样性及群体的空间分布格局。【方法】分别对来自7个天然群体的30份天竺桂资源进行特异位点扩增片段测序(specific-locus amplified fragment sequencing, SLAF-seq)。基于检测到的SNP位点信息进行遗传变异分析。【结果】各样品的平均测序深度为15.11倍,开发获得 1 296 000个SLAF标签,其中377 250个SLAF标签在不同样品间具有多态性,共包含3 409 402个群体SNP,经过滤,最终获得268 821个高度一致性的群体SNP。基于这些SNP的系统进化分析发现,天竺桂是由中国东部向中国西部逐渐进化的。系统进化、主成分分析和群体结构分析均表明,来自5省(直辖市)7个天然群体的群体内变异小于群体间变异。30份天竺桂资源可分为2个大的亚群,其中,第1亚群位于中国第2阶梯上,第2亚群位于中国第3阶梯上,2个亚群间被大兴安岭—太行山脉—巫山—雪峰山山脉阻隔。第2亚群又可进一步分为3个小亚群,其中,来自浙江省和安徽桃岭的为第1个小亚群,来自安徽霍山的为第2个小亚群,而来自河南伏牛山的为第3个小亚群,第1个和第2个小亚群间被长江阻隔。【结论】山脉和湖泊的阻隔可能是造成天竺桂遗传分化的重要因素。本研究首次揭示天竺桂遗传结构及地理变化规律,为我国天竺桂资源的有效利用与科学保护提供理论依据。
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| 关 键 词： | 天竺桂 SLAF-seq SNP 遗传分析 |
| 收稿时间： | 2020-09-01 |
Genetic variation analysis of Cinnamomum japonicum populations based on SLAF-Seq technique |
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| Abstract: | 【Objective】Cinnamomum japonicum is a kind of protected tree species with important economic value, wild C. japonicum is a valuable genetic resource for breeding and improvement, and also is an important plant genetic resource in China. This study explored the genetic diversity and population spatial distribution pattern of C. japonicum resources in China, and laid a theoretical foundation for the protection and utilization of the resources.【Method】Specific focus amplified fragment sequencing (SLAF-seq) was performed on 30 individuals from seven populations of five provinces or municipality including Zhejiang, Anhui, Henan, Chongqing and Yunnan to develop SLAF and SNP(single nucleotide polymorphism) markers. 【Result】A total of 100.78 Mb reads data were obtained from 30 samples. After clustering the reads of different samples, a total of 1 296 000 SLAF tags were obtained. The average sequencing depth of each sample was 15.11. 377 250 SLAFs were polymorphic among different samples, and 3 409 402 SNPs were obtained from the polymorphic SLAF tags. After filtering, 268 821 population SNPs with high consistency were finally obtained. Phylogenetic analysis of these SNPs showed that C. japonicum was evolved from eastern to western China. Phylogenetic, principal component and population structure analysis all showed that the intra-population variation of the seven natural populations was smaller than the inter-population variation. The 30 individuals can be divided into two large groups, among which, the first group contained the resources collected from the second ladder of China, and the second contained resources from the third ladder of China. The two groups were separated by the Great Khingan-Taihang Mountains-Wushan Mountains-Xuefeng Mountain range. The second group can be further divided into three small subgroups, among which, those from Anhui Taoling and Zhejiang Province were included in the first subgroup, those from Anhui Huoshan were included in the second subgroup, and those from Henan Province were included in the third subgroup. The first and the second subgroup were separated by the Yangtze River. 【Conclusion】The barriers caused by mountains and lakes are important factors of the genetic differentiation of C. japonicum resources. This study reveals for the first time the genetic structure and geographical variation of C. japonicum, providing a theoretical basis for the effective utilization and scientific protection of the resources of C. japonicum. |
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| Keywords: | Cinnamomum japonicum specific-locus amplified fragment sequencing(SLAF-seq) single nucleotide polymor phism (SNP) genetic analysis |
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