Favorable Haplotypes And Associated Genes Identified By Comparative Selective Signature Analysis And Gwas Using Temperate And Tropical Maize

Maize(Zea mays L.),originated in Balsas River Basin of southwestern Mexico,can be largely classified into temperate and tropical groups based on growing environments.Understanding genetic variation in different maize groups will facilitate identifying candidate genes and favorable haplotypes related to flowering time and photoperiod sensitivity under selection during maize domestication and improvement,which is critical for introduction,improvement and application of exotic germplasm.In this study,candidate genes and favorable haplotypes were identified by selective signatures analysis,genome-wide association analysis,haplotype analysis and GO enrichment analysis of temperate and tropical maize groups.The conclusions are provided as follows:The association panel consisting of temperate and tropical maize groups was evaluated in Shunyi(Beijing),Xinxiang(Henan)and Sanya(Hainan).With the decrease of latitude,the number of days to flowering was shortened for both temperate and tropical maize groups,but the latter had relatively longer flowering time.Compared with temperate maize group,tropical maize group was more sensitive to photoperiod as revealed by the relative phenotypic differences between the two near-iso environments(Shunyi-Sanya;Xinxiang-Sanya).To identified favorable haplotype associated with flowering time and photoperiod sensitivity,haplotype loci containing at least two SNPs were extracted using all consecutive SNPs with LD coefficients greater than 0.8.From 39,350 quality SNPs(minor allele frequency > 0.05,missing rate < 20%),14,359 SNPs were used to construct 4,166 haplotype loci with 11,707 haplotype alleles,each locus containing 3.5 SNPs(ranging from 2 to 75)and 2.8 haplotype alleles within an average length of 26.2 kb.A total of 106 significant selective signature signals were identified in the temperate maize by selective signature analysis of temperate and tropical maize groups.GO enrichment analysis of protein-coding genes from selective regions in temperate maize indicated that genes were significantly enriched in pathways related to biological regulation,biological biosynthesis and response to stimuli.A total of 78 signals significantly associated with flowering time traits were identified with the association panel consisting of temperate and tropical maize inbred lines(63 by SNP-based GWAS and 15 by haplotype-based GWAS),while 35 significantly associated signals were identified for photoperiod sensitivity(24 by SNP-based GWAS and 11 by haplotype GWAS).Additionally,haplotype loci associated with flowering time explained 18.6%,17.5%,and 17.7% of phenotypic variation for days to tassel,days to silk and days to anthesis,respectively,while haplotype loci associated with photoperiod sensitivity explained 14.8%,11.2% and 15.5% of phenotypic variation as measured by the relative differences under two contrasting environments for these three traits,respectively.Haplotype-based GWAS indicated that haplotype alleles within significant haplotype loci had the same direct of effects on flowering time and photoperiod sensitivity as identified across multi-locations and multi-traits.The inbred lines carrying GATT at HapL499(on chromosome 1)had relatively shorter flowering time,while the inbred lines carrying CA at HapL4054(on chromosome 10),TA at HapL4055(on chromosome 10)and GTTGT at HapL978(on chromosome 2)were less sensitive to photoperiod compared to other haplotype alleles at the same loci.Notably,CA and CG at HapL4054 and TA and TG at HapL4055 had opposite effects on photoperiod sensitivity.Also,haplotype-based GWAS improved the proportion of phenotypic variation explained compared with SNP-based GWAS.