Favorable haplotypes and associated genes for flowering time and photoperiod sensitivity identified by comparative selective signature analysis and GWAS in temperate and tropical maize

Publication date: Available online 11 December 2019Source: The Crop JournalAuthor(s): Zhiwei Li, Xiaogang Liu, Xiaojie Xu, Jiacheng Liu, Zhiqin Sang, Kanchao Yu, Yuxin Yang, Wenshuang Dai, Xin Jin, Yunbi XuAbstractOn the basis of growing environment, maize can largely be classified into temperate and tropical groups, leaving extensive genetic variation and evolutionary signatures in the maize genome. To identify candidate genes governing flowering time and photoperiod sensitivity, selective signature analysis and SNP- and haplotype-based GWAS were performed using 39,350 high-quality SNP markers in temperate and tropical maize groups consisting of 410 inbred lines phenotyped in three representative experiments in different latitudes. Selective signature analysis revealed 106 selective-sweep regions containing 423 candidate genes involved mainly in biological regulation and biosynthesis pathways. Among these genes, 25 overlapped with known genes governing flowering time and photoperiod sensitivity and 37 were also detected by GWAS for days to tassel, anthesis-silk interval, and photoperiod sensitivity measured by days to silking. Only two of the candidate genes governing flowering time overlapped selective signals. Most haplotype alleles within significant haplotype loci showed the same direction of effect on flowering time and photoperiod sensitivity. The inbred lines carrying GATT at HapL499 (haplotype locus 499) on chromosome 1 had relatively short flowering times. Lines car...
Source: The Crop Journal - Category: Food Science Source Type: research