Genome-wide association study of heading and flowering dates and construction of its prediction equation in Chinese common wheat

Abstract

Heading date is one of the most important traits in wheat breeding as it affects adaptation and yield potential. A genome-wide association study (GWAS) using the 90 K iSelect SNP genotyping assay indicated that a total of 306 loci were significantly associated with heading and flowering dates in 13 environments in Chinese common wheat from the Yellow and Huai wheat region. Of these, 105 loci were significantly correlated with both heading and flowering dates and were found in clusters on chromosomes 2, 5, 6, and 7. Based on differences in distribution of the vernalization and photoperiod genes among chromosomes, arms, or block regions, 13 novel, environmentally stable genetic loci were associated with heading and flowering dates, including RAC875_c41145_189 on 1DS, RAC875_c50422_299 on 2BL, and RAC875_c48703_148 on 2DS, that accounted for more than 20% phenotypic variance explained (PVE) of the heading/flowering date in at least four environments. GWAS and t test of a combination of SNPs and vernalization and photoperiod alleles indicated that the Vrn-B1, Vrn-D1, and Ppd-D1 genes significantly affect heading and flowering dates in Chinese common wheat. Based on the association of heading and flowering dates with the vernalization and photoperiod alleles at seven loci and three significant SNPs, optimal linear regression equations were established, which show that of the seven loci, the Ppd-D1 gene plays the most important role in modulating heading and flowering dates in Chinese wheat, followed by Vrn-B1 and Vrn-D1. Additionally, three novel genetic loci (RAC875_c41145_189, Excalibur_c60164_137, and RAC875_c50422_299) also show important effect on heading and flowering dates. Therefore, Ppd-D1, Vrn-B1, Vrn-D1, and the novel genetic loci should be further investigated in terms of improving heading and flowering dates in Chinese wheat. Further quantitative analysis of an F recombinant inbred lines population identified a major QTL that controls heading and flowering dates within the Ppd-D1 locus with PVEs of 28.4% and 34.0%, respectively; this QTL was also significantly associated with spike length, peduncle length, fertile spikelets number, cold resistance, and tiller number.

Molecular and Transcriptional Regulation of Seed Development in Cereals: Present Status and Future Prospects

“…Wheat 1000-grain weight qTgw.nwipb-4DS; qTgw.nwipb-6AL [72] wsnp_Ex_c32624_41252144, BS00021705_51 [73] Grain yield, TKW, spike weight, spike length rs36032, rs4772, rs736, rs50187, rs59282 [74] Heading and flowering dates RAC875_c41145_189, Excalibur_c60164_137, RAC875_c50422_299, Ppd-D1, Vrn-B1, Vrn-D1 [75] Grain weight and grain number TaGW2-6A, Rht-B1, Vrn-D1a [56] Rice Yield associated loci qSN8 and qSPB1 [76] Heading date Ghd8/OsHAP3H [77,78] Panicle trait DENSE AND ERECT PANICLE 1 (DEP1) [79,80] Grain length and yield OsLG3 [81] Heading date and yield potential Hd1, Ghd7, and DTH7 [82] Grain yield and quality traits qPH1/OsGA20ox2, qDF3/OsMADS50, PL, QDg1, qGW-5b, grb7-2, qGL3/GS3, Amy6/Wx gene and OsNAS3…”

Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.)

“…In light of their importance, extensive studies have been performed to identify the genes and loci underlying spike architecture and spike-related traits. Based on the 90 K iSelect SNP genotyping assay, 306 loci were found to be significantly associated with heading and flowering dates in 375 Chinese common wheat and these loci were also associated with spike length, peduncle length, fertile spikelet number, cold resistance, and tiller number [ 14 ]. The Q locus, encoding an AP2-like transcription factor, is one of widely studied domestication genes regulating spike compactness, brittle rachises and grain morphology [ 15 ].…”

Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.)

“…The Q locus, encoding an AP2-like transcription factor, is one of the well-known and widely studied domestication genes regulating spike compactness, brittle rachises and grain morphology [14]. Based on the 90 K iSelect SNP genotyping assay, 306 loci were found to be signi cantly associated with heading and owering dates in 375 Chinese common wheat and these loci were also associated with spike length, peduncle length, fertile spikelet number, cold resistance, and tiller number [15]. FLOWERING LOCUS C (FLC) is reported act as a major regulator gene of owering time in Arabidopsis [16].…”