169份不同遗传背景玉米自交系的遗传多样性分析

Genetic diversity of 169 maize inbred lines with different genetic backgrounds

  • 摘要: 【目的】 解析玉米自交系遗传多样性和群体遗传结构,为广西玉米育种实践提供理论参考。【方法】 以169份不同遗传背景的玉米自交系为材料,以7份广西骨干自交系和3份我国其他地方的骨干自交系为对照,用10K SNP玉米芯片对其进行全基因组扫描,通过遗传相似度、系统进化、主成分和血缘同源确认(IBD)等分析其遗传多样性及群体遗传结构。【结果】 筛选获得7565个高质量可用SNP分子标记,分布在10条染色体上,平均每条染色体上有756个,标记检出率均在97.12%以上,平均检出率达99.57%。174个玉米自交系的杂合率为0.21%~7.28%,平均为0.86%,有144个玉米自交系杂合率不高于1.00%,但有5个玉米自交系的杂合率偏高(31.29%~36.36%)。174份材料间的遗传相似度为0.486~0.999,平均为0.609,其中2个广西选育的西南骨干自交系B24(ZNC442)和CK_D2(桂A10341)与其他材料间的遗传相似度平均值分别为0.642和0.629。由系统发育进化树可知,包含10个参考自交系在内的179个玉米自交系划分为Reid群和热带亚热带群两大类,其中Reid群含13个自交系,占比为7.26%,热带亚热带群含166个自交系,占比为92.74%。热带亚热带群又可细分为7个亚群,其中以Suwan群和CM群为主,分别含56和51个自交系,占比分别为31.28%和28.49%。主成分分析结果显示,PCA1v3中玉米自交系聚类情况与系统发育进化树聚类结果基本一致,能明显区分Reid群和热带亚热带群,且热带亚热带群中大多自交系分布在CM群和Suwan群参考自交系附近。IBD分群结果显示,Reid群、Suwan群、CM群和A群的自交系数量分别有21、47、64和47个。系统进化分析、主成分分析和IBD分群韦恩图显示,三者共属Reid群、Suwan群、CM群和A群的自交系数量分别为12、35、18和11个。【结论】 广西玉米自交系来源复杂,遗传背景相似,不同分析方法的划分结果并不完全一致,需结合育种实践进行类群划分。广西选育的西南骨干玉米自交系ZNC442和桂A10341均属于A群,最理想组配模式为A群×Reid群,其次是A群×Suwan群和A群×CM群。

     

    Abstract: 【Objective】 To analyze the genetic diversity and population genetic structure of different maize inbred lines,which could provide theoretical reference for maize breeding practice in Guangxi. 【Method】 A total of 169 maize inbred lines with different genetic backgrounds were used as materials, with 7 Guangxi backbone inbred lines and 3 backbone inbred lines from other places in China were as control. The whole genome of maize inbred lines was scanned by10K SNP maize chip. The genetic diversity and population genetic structure were analyzed by genetic similarity, phylogeny, principal components and homology identification(IBD).【Result】 A total of 7565 high-quality and available SNP molecular markers were identified, which were distributed across 10 chromosomes, with an average of 756 markers per chromosome. The detection rate of these markers was all above 97.12%, with an average detection rate of 99.57%. The heterozygosity rate of the 174 maize inbred lines ranged from 0.21% to 7.28%, with an average of 0.86%.Among them, 144 maize inbred lines had a heterozygosity rate not exceeding 1.00%, while the heterozygosity rate of 5 maize inbred lines was relatively high(31.29% to 36.36%). The genetic similarity among the 174 samples ranged from 0.486 to 0.999, with an average of 0.609. Among these, the 2 southwestern core inbred lines bred in Guangxi, B24(ZNC442) and CK_D2(Guangxi A10341), had average genetic similarity values of 0.642 and 0.629 with other materials respectively. The phylogenetic tree showed that the 179 maize inbred lines, including 10 reference inbred lines, were divided into 2 major groups: Reid group and the tropical/subtropical group. The Reid group contained 13 inbred lines, accounting for 7.26%,while the tropical/subtropical group contained 166 inbred lines, accounting for 92.74%. The tropical/subtropical group could be further divided into 7 subgroups, with the Suwan group and the CM group being the main ones, containing 56 and 51 inbred lines respectively, accounting for 31.28% and 28.49%. The principal component analysis(PCA) results showed that the clustering of maize inbred lines in PCA1v3 was basically consistent with the clustering results of the phylogenetic tree, clearly distinguishing the Reid group from the tropical/subtropical group. Most inbred lines in the tropical/subtropical group were distributed near the reference inbred lines of the CM group and the Suwan group. The IBD clustering results showed that the Reid group, Suwan group, CM group and A group had 21, 47, 64 and 47 inbred lines respectively. The Venn diagram of phylogenetic analysis, principal component analysis and IBD grouping Venn diagram showed that the number of inbred lines shared by the Reid group, Suwan group,CM group and A group were 12, 35, 18 and 11 respectively. 【Conclusion】 The maize inbred lines in Guangxi have complex origin and similar genetic backgrounds. The classification results obtained from different analytical methods are not entirely consistent. Therefore, it is necessary to integrate breeding practice to conduct group classification. The southwest backbone maize inbred lines ZNC442 and Gui A10341 bred in Guangxi belong to A group. The best mating pattern is A group × Reid group,followed by A group × Suwan group and A group × CM group.

     

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