基于SLAF-seq技术的甘蔗遗传多样性和选择信号分析

Analysis on genetic diversity and selection signal of sugarcane based on SLAF-seq technology

[目的]通过对不同甘蔗群体进行遗传多样性和选择性清除分析,了解甘蔗基因组中受人工选择的区域及优良基因,以期为甘蔗分子育种提供参考。[方法]对83份甘蔗栽培种和24份细茎野生种共107份材料进行简化基因组测序,以甘蔗割手密基因组为参考,获得基因组SNP基因型数据,分析群体遗传多样性、不同群组的分化系数(Fst),并以此为基础进行选择信号扫描分析。[结果](1)栽培种与细茎野生种群体之间的Fst=0.216,栽培种群体的核苷酸多样性(π=8.93×10^(-6))高于细茎野生种群体(π=6.11×10^(-6))。(2)选择性清除分析得到72个基因组区域,对前5%的基因组区域进一步分析,共检测到439个基因。对候选基因进行基因功能注释,发现受选择基因主要富集在泛素蛋白转移酶活性过程、核苷酸结合过程和热反应过程等,包括抗病蛋白RGA2、谷胱甘肽S-转移酶、钾转运蛋白等抗性基因。[结论]107份甘蔗材料可分为两个亚群,且抗性基因在甘蔗育种过程中得到了强烈的选择。

[Purpose]The mining of elite gene based on genetic diversity and selection signal of different sugarcane populations will provide new sights into the molecular breeding of sugarcane.[Method]Single nucleotide polymorphism(SNP)markers for the whole genome of 107 sugarcane materials(83 modern cultivated Saccharum spp.and 24 wild S.spontaneum L.populations)were generated through specific-locus amplified fragment sequencing.Using the genome of S.spontaneum as the reference,genetic diversity and coefficient of differentiation(Fst)of the samples were measured based on the SNP markers,and then were scanned for the selection signals.[Result]The coefficient of differentiation between the cultivated and wild populations was 0.216,and the nucleotide diversity of the cultivated group(π=8.93×10^(-6))was higher than that of the wild group(π=6.11×10^(-6)).Referring to the S.spontaneum genome,72 selective regions were obtained in the genomic regions,and 439 genes were further filtrated from the top 5%of the selective regions.Gene ontology enrichment analysis showed that the selected genes were enriched in the regions which regulated ubiquitin protein transferase activity,nucleotide binding and heat reaction,including many known resistance genes,such as resistance protein RGA2,glutathione S-transferase and potassium transporter,etc.[Conclusion]The 107 sugarcane materials can be divided into 2 subgroups,and the resistance genes were highly selected in the process of sugarcane breeding.