Allelic Variation in Developmental Genes and Effects on Winter Wheat Heading Date in the U.S. Great Plains

Heading date in wheat (Triticum aestivum L.) and other small grain cereals is affected by the vernalization and photoperiod pathways. The reduced-height loci also have an effect on growth and development. Heading date, which occurs just prior to anthesis, was evaluated in a population of 299 hard winter wheat entries representative of the U.S. Great Plains region, grown in nine environments during 2011–2012 and 2012–2013. The germplasm was evaluated for candidate genes at vernalization (Vrn-A1, Vrn-B1, and Vrn-D1), photoperiod (Ppd-A1, Ppd-B1 and Ppd-D1), and reduced-height (Rht-B1 and Rht-D1) loci using polymerase chain reaction (PCR) and Kompetitive Allele Specific PCR (KASP) assays. Our objectives were to determine allelic variants known to affect flowering time, assess the effect of allelic variants on heading date, and investigate changes in the geographic and temporal distribution of alleles and haplotypes. Our analyses enhanced understanding of the roles developmental genes have on the timing of heading date in wheat under varying environmental conditions, which could be used by breeding programs to improve breeding strategies under current and future climate scenarios. The significant main effects and two-way interactions between the candidate genes explained an average of 44% of variability in heading date at each environment. Among the loci we evaluated, most of the variation in heading date was explained by Ppd-D1, Ppd-B1, and their interaction. The prevalence of the photoperiod sensitive alleles Ppd-A1b, Ppd-B1b, and Ppd-D1b has gradually decreased in U.S. Great Plains germplasm over the past century. There is also geographic variation for photoperiod sensitive and reduced-height alleles, with germplasm from breeding programs in the northern Great Plains having greater incidences of the photoperiod sensitive alleles and lower incidence of the semi-dwarf alleles than germplasm from breeding programs in the central or southern plains.普通小麦（*Triticum aestivum* L.）及其他小粒谷类作物的抽穗期受春化途径与光周期途径调控，矮秆基因位点同样会对作物生长发育产生影响。抽穗期指扬花期前的生育时期，本研究以299份具有美国大平原区域代表性的硬冬小麦种质系为研究群体，于2011-2012年和2012-2013年共9个环境下开展抽穗期表型鉴定。本研究采用聚合酶链式反应（PCR）与竞争性等位基因特异性PCR（KASP）技术，对该种质资源的春化通路候选基因（Vrn-A1、Vrn-B1、Vrn-D1）、光周期通路候选基因（Ppd-A1、Ppd-B1、Ppd-D1）以及矮秆通路候选基因位点（Rht-B1、Rht-D1）进行基因分型。本研究的目标包括：明确已知影响开花时间的等位变异类型，评估等位变异对抽穗期的调控效应，以及解析等位基因与单倍型的地理及时空分布变化。本研究通过分析加深了对不同环境条件下发育基因调控小麦抽穗期分子机制的理解，可为当前及未来气候情景下小麦育种策略优化提供理论支撑。候选基因的显著主效应及其两两互作效应，在各环境下平均可解释44%的抽穗期表型变异。在所检测的基因位点中，Ppd-D1、Ppd-B1及其互作效应可解释大部分抽穗期表型变异。近一个世纪以来，美国大平原地区种质资源中光周期敏感等位基因Ppd-A1b、Ppd-B1b与Ppd-D1b的频率呈逐渐下降趋势。此外，光周期敏感等位基因与矮秆等位基因的分布存在显著地理差异：相较于美国大平原中部与南部地区育种项目的种质资源，北部大平原育种项目的种质资源中光周期敏感等位基因频率更高，而半矮秆等位基因频率更低。