基于SNP芯片的甘蓝型油菜遗传多样性和群体遗传结构分析

Genetic Diversity and Genetic Structure Analysis of Brassica napus by SNP Chips

为揭示四川油菜核心种质的遗传多样性和群体遗传结构,提高甘蓝型油菜种质利用效率,本研究利用油菜50K基因芯片对201个育种亲本品系进行全基因组SNP位点分析,利用Powermarker软件计算SNP位点的Nei’s基因多样性指数(H)、主要等位基因频率(MAF)和多态性信息含量(PIC)和供试材料的遗传距离,进行聚类和群体结构分析。结果表明,共筛选到17243个SNP位点,平均每条染色体分布907个多态性位点,位点的Nei’s基因多样性指数(H)、主要等位基因频率(MAF)和多态性信息含量(PIC)平均值分别为0.351、0.738、0.282;201份供试材料遗传距离在0.0001~0.5298之间,平均为0.3505,Kinship值为0的占59.90%;供试材料可分成6个大类,分别为:保持系(1个品系:SC223)、远缘杂交种质(2个品系:SC001和SC273)、复合杂交油菜种质(2个品系:SC119和SC175)、征集种质(1个品系:SC017)、混合来源Ⅰ(16个品系:征集的优良品系SC034等,复合杂交保持系种质SC103等和恢复系SC249)和混合来源Ⅱ(179份:征集的优良品系,远缘杂交后代,复合杂交保持系种质和恢复系),群体结构分成13个亚群,可进行杂种优势预测。研究结果表明供试育种亲本种质遗传多样性丰富,为甘蓝型油菜杂种优势利用和育种种质创新提供理论依据。

In order to reveal the genetic diversity and population genetic structure of Sichuan rapeseed core collection and improve the utilization efficiency of Brassica napus germplasm.The whole genomic SNP analysis was applied to 201 accessions of rapeseed using 50K gene chip.The primary data were screened using Visual Basic software,then applied Powermarker for Nei’s gene diversity index(H),major allele frequency(MAF)and polymorphism information content(PIC)of each SNP loci,genetic distances among accessions,clustering analysis and population structure analysis.The results indicated that 17243 SNP loci were screened according to the deletion rate of SNP markers and the evenness of chromosome distribution,with an average of 907 polymorphic loci distributed on each chromosome.The Nei’s gene diversity index(H),major allele frequency(MAF)and polymorphism information content(PIC)of the loci were 0.351,0.738 and 0.282 respectively.The genetic distance between tested materials ranged from 0.0001 to 0.5298,with an average of 0.3505.The Kinship value of 59.90%of the samples was 0.All accessions could be divided into 6 categories,named:maintainer lines group(SC223),wild hybridization offsprings group(SC001 and SC273),multicross offsprings group(SC119 and SC175),collected germplasm group(SC017),mixed sourceⅠ(16 lines:collected germplasm SC034,multicross offsprings SC103,restorer line SC249)and mixed sourceⅡ(179 lines:collected germplasm,wild hybridization offsprings,multicross offsprings,restorer lines),and the population structure can be divided into 13 subgroups,can be used to well predict heterosis.The results showed that the tested materials had rich genetic diversity,which could reflect the genetic relationship of the tested materials objectively,providing theoretic evidences for heterosis utilization and breeding innovation.