基于SNP分子标记的128份糯玉米种质遗传多样性和类群结构分析

Genetic diversity and population structure of 128 waxy maize germplasms based on SNP molecular markers

  • 摘要: 【目的】分析不同基因型糯玉米种质的遗传多样性和类群结构,为广西糯玉米种质创新利用提供参考依据。【方法】利用10K芯片对128份糯玉米种质进行全基因组扫描,分析其遗传多样性和类群结构,并调查植株、花期和果穗的13个性状,分析不同类群种质的性状差异。【结果】7561个SNP分子标记基本均匀覆盖整个玉米基因组,主要等位基因频率(MAF)为0.500~0.969,平均为0.702;基因多样性(GD)为0.061~0.500,平均为0.388;多态信息含量(PIC)为0.059~0.375,平均为0.307。聚类分析和PCoA分析均可将128份糯玉米种质划分为3个类群,分别为地方种类群、京科—中糯类群、本地糯类群;地方种类群和本地糯类类群的GD分别为0.354和0.343,PIC分别为0.282和0.280,低于京科—中糯类群的GD(0.377)和PIC(0.298),表明地方种类群和本地糯类类群的遗传多样性较低,且类群划分结果具有一定的地理和生态区域特征;甜糯玉米与糯玉米划分在同一类群,其原因是甜糯玉米是从糯玉米中选育的一种新型鲜食玉米。分子方差分析(AMOVA)结果显示,不同类群间存在明显的遗传变异,占总遗传变异的10.8%,自交系间的遗传变异为73.1%,自交系内的遗传变异为16.1%。相关分析结果显示,花期对京科-中糯类种质具有较突出的负向调控作用,而株高、穗位高等植株性状对本地糯类种质的正向调控作用较大。对于京科-中糯类温带种质,花期延迟对雄花性状及穗行数和穗粗等果穗性状有负调控作用,这可能是亚热带生态气候环境对温带血缘种质影响的结果。而对于本地糯类热带种质,株高、穗位高对果穗穗行数和行粒数正向调控作用更大,但过高的穗位高也易导致产量性状穗粗下降。【结论】不同类型的糯玉米种质遗传多样性存在一定差异,具有一定的地理和生态区域特点,在植株、花期和果穗等性状的相关性和互作机制也存在明显差异。

     

    Abstract: 【Objective】To explore the genetic diversity and population structure of waxy maize germplasm of different genotypes, which could provide references for the innovative utilization of waxy maize germplasm in Guangxi. 【Method】In this study, 128 waxy maize germplasms were scanned by 10K microarray to analyze their genetic diversity and population structure. And the 13 traits of plant, flowering and ears were investigated, the differences among the different germplasm populations were analyzed. 【Result】A total of 7561 SNP molecular markers basically evenly covered the entire maize genome. The main allele frequencies(MAF) ranged from 0.500 to 0.969, with an average of 0.702. The genetic diversity(GD) ranged from 0.061 to 0.500, with an average of 0.388. The content of polymorphic information(PIC) ranged from 0.059 to 0.375, with an average of 0.307. Cluster analysis and PCoA analysis divided the 128 waxy maize germplasms into 3 populations, namely local germplasm population, Jingke-Zhongnuo population and local waxy population. The GD of the local germplasm population and the local waxy population were 0.354 and 0.343 respectively, and the PIC were 0.282 and 0.280 respectively, which were lower than the GD(0.377) and PIC(0.298) of the Jingke-Zhongnuo population, indicating that the genetic diversity of the local germplasm population and local waxy population was relatively low. Moreover, the results of population classification had certain geographical and ecological regional characteristics; sweet waxy maize and waxy maize were classified in the same population because sweet waxy maize was a new type of fresh maize selected from waxy maize. The results of molecular analysis of variance(AMOVA) showed that there were obvious genetic variations among different populations, accounting for 10.8% of the total genetic variations. The genetic variations among inbred lines were 73.1%, and those within inbred lines were 16.1%. The results of the correlation analysis showed that the flowering period had a relatively prominent negative regulatory effect on Jingke-Zhongnuo population germplasms, while the plant traits such as plant height and ear height had a greater positive regulatory effect on the local waxy population germplasm. For the temperate germplasms of Jingke-Zhongnuo population, the delay of flowering period had negative regulation effect the traits of male flowers and the traits of panicles such as ear row number and ear diameter. This might be the result of the influence of the subtropical ecological climate environment on the temperate bloodline germplasm. For local waxy tropical germplasms, plant height and ear height had greater positive regulatory effect on ear row number and grains numbers per row. However, an excessively high ear height couold also easily lead to a decrease in the yield trait of ear diameter. 【Conclusion】There are certain differences in the genetic diversity among different types of waxy maize germplasms, which have certain geographical and ecological regional characteristics, and there are also obvious differences in the correlation and interaction mechanism of plant, flowering and ear traits.

     

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