关键词: 玉米, 选择信号, 群体分化指数, 群体间扩展单倍型纯合度, 开花基因

Abstract:

【Objective】 Maize was first domesticated in tropical areas, but it has been cultivated widely in the temperate regions after natural and artificial selection. Flowering time is not only the key component of the entire growth period, but also a major adaptive trait during the dispersal process from tropical to temperate conditions. Thus, identifying the selected gene regions responsible for the adaptation to temperate zones, and discovering the genes that are involved in flowering time could provide a molecular basis for improving maize and for dissecting its flowering mechanism. 【Method】 We analyzed the haplotype data of 30 temperate and 21 tropical maize inbred lines. High quality SNP (single nucleotide polymorphism) markers were obtained after filtering out SNPs with high missing rates and low allele frequencies. These high quality SNPs were annotated by SNPeff. Principle component analysis (PCA) of the genotypic data of temperate and tropical maize was performed to further validate the population structure of these samples. Using high quality SNP markers that were present in tropical and temperate populations, we calculated the selection signal using the fixation index (F_ST) and cross population extended haplotype homozygosity (XP-EHH) methods. The top 1% of values was used as a significant threshold to identify the candidate selected signals. The candidate selected genes that we selected from temperate and tropical maize were identified based on their SNP annotation. The function of these selected genes was characterized furtherly by the GO enrichment analysis using agriGO. To identify the genes for flowering time that were under selection, bioinformatics databases were examined that contained relevant data on maize. 【Result】 By analyzing the high depth resequencing data, we found 14123408 and 8791673 SNPs in tropical and temperate populations, respectively. The identified SNPs were mainly distributed in the intergenic regions. There were 204752 high quality SNPs that coexisted in temperate and tropical populations. PCA indicated that temperate and tropical maize can be divided into two groups. The top 1% of F_ST value and XP-EHH were 0.3059, 3.2681, and a total of 557 and 1 913 candidate genes were identified by F_ST and XP-EHH methods, respectively. Many candidate genes were highly related to regulation of flowering time, which included ZmCCT9, COL1 and GRMZM2G387528. ZmCCT9 is a vital gene for regulating flowering time, and it negatively regulated the floral activator gene ZCN8, which cause the late flowering time phenotype under long-day conditions. COL1 positively interacts with the FT protein to promote the transition of flowering time to adapt to the long-day environment. Functional annotations of GRMZM2G387528 revealed that it was a phytochrome interacting factor, and interacts with photoperiod gene ZmphyB1. 【Conclusion】 Our study revealed that tropical maize had higher genetic diversity than temperate maize. A series of genes that were under selection during the adaptation to tropical to temperate conditions were predicted, and we further explored the genes that were involved in flowering during this process.

Key words: maize, selection signal, fixation index, cross population extended haplotype homozygosity, flowering time genes