基于GBS测序的全基因组SNP揭示大凉山玉米地方品种资源的亲缘关系与遗传分化  

Phylogenetic relationship and genetic differentiation of maize landraces revealed by genome-wide SNP developed by genotyping-by-sequencing in Daliangshan Mountain area,China

作　　者：冷益丰 罗樊 陈从顺[1] 丁鑫 蔡光泽[1,2] LENG Yifeng;LUO Fan;CHEN Congshun;DING Xin;CAI Guangze(College of Agricultural Science,Xichang University,Xichang 615013,Sichuan,China;Panxi Crops Research and Utilization Key Laboratory of Sichuan Province,Xichang 615013,Sichuan,China)

机构地区：[1]西昌学院农业科学学院,四川西昌615013 [2]攀西特色作物研究与利用四川省重点实验室,四川西昌615013

出　　处：《浙江农业学报》2024年第1期32-47,共16页Acta Agriculturae Zhejiangensis

基　　金：国家自然科学基金(32060485);攀西特色作物研究与利用四川省重点实验室基金(XNFZ2114);西昌学院科研项目(YBZ201901)。

摘　　要：玉米地方品种是玉米育种种质的重要来源,其类型丰富、部分性状田间表现突出,常含有可利用的优良抗性基因。大凉山因其独特的地理位置和光热资源,生产中积累了各具特色的玉米地方品种,但缺乏系统的遗传研究,导致本区域的玉米育种利用进展缓慢。本研究利用基因分型测序(genotyping-by-sequencing,GBS)技术,对收集自大凉山不同地方的360份玉米地方品种资源进行亲缘关系与遗传分化分析。通过高通量测序,产生有效数据250.99 GB,所有样本获得1 659 033 712个clean reads,平均reads数量为4 608 427,平均raw base为0.70 GB,clean base为0.67 GB。各样本的Q20平均值大于等于94.57%,Q30平均值大于等于87.14%,平均GC含量48.20%。经过SNP calling并过滤,获得124 342个单核苷酸多态性(SNP)位点、32 063个插入缺失(InDel)位点(其中插入位点15 738个、缺失位点16 325个)。邻接法构建的系统进化树将360份玉米地方品种群体分成A和B两大类群,支持玉米杂优两群学说;结合主成分分析表明,两群亲缘关系较远,呈现遗传分化;群体结构分析进一步把其分成9个亚群。类群A与B之间的群体分化指数(F_(st))为0.462 2,类群A的核苷酸多样性(πA)高于类群B;选择性清除分析得到96个基因组区域,对前5%的基因组区域进一步分析,共检测到418个基因。对候选基因进行基因功能注释,发现富集的基因组区域中包含寒冷响应基因、缺水响应基因、病菌响应基因等与逆境应答相关的基因。研究结果为大凉山玉米地方品种资源的保护和遗传改良提供了参考依据。Maize landraces are important source of maize breeding germplasm,with diverse types and outstanding field performance for some traits,often containing excellent resistance genes that can be utilized in breeding.Due to the unique geographical location and light-thermal resources of Daliangshan Mountain area,many maize landraces with distinctive characteristics had been accumulated here in maize production.However,the lack of systematic genetic research on these varieties had resulted in slow progress in maize breeding and utilization in this region.In this study,the genotyping-by-sequencing(GBS) technique was used to conduct phylogenetic and genetic differentiation analyses on 360 maize landraces collected from different regions of Daliangshan Mountain area.Through high-throughput sequencing analysis,250.99 GB of effective data was generated,with a total of 1 659 033 712 clean reads from all samples,with an average read count of 4 608 427 and an average raw base of 0.70 GB and clean base of 0.67 GB.The average Q20 value of all samples was greater than or equal to 94.57%,the average Q30 value was greater than or equal to 87.14%,and the average GC content was 48.20%.After SNP calling and filtering,124 342 single nucleotide polymorphism(SNP) loci and 32 063 insertion-deletion(InDel) loci(including 15 738 insertion loci and 16 325 deletion loci) were obtained.The neighbor-joining method was used to construct a phylogenetic tree,which clearly divided the 360 maize landraces into 2 major groups,A and B,supporting the two-group theory of maize heterosis.Principal component analysis also showed that the 2 groups were distantly related and presented genetic differentiation.Further population structure analysis divided the 2 major groups into 9 subgroups.The F-statistics(F_(st)) value between group A and group B was 0.462 2,and the nucleotide diversity(π) of group A was higher than that of group B.In the selective sweep analysis,96 genomic regions were identified,and 418 genes were further filtrated from the top 5% of the

关 键 词：玉米 大凉山 地方品种 基因分型测序 亲缘关系 

分 类 号：S513[农业科学—作物学]