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

【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.