National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome, Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Plant Commun. 2024 May 13;5(5):100879. doi: 10.1016/j.xplc.2024.100879. Epub 2024 Mar 14.
Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.
Spike 结构影响粒重和每穗粒数，这是小麦（Triticum aestivum L.）粒产量的两个主要组成部分。然而，复杂的小麦基因组和各种环境因素的影响给鉴定影响穗部特征的因果基因带来了挑战。在这里，我们通过整合控制小麦幼穗发育的基因组变异和基因调控网络信息，系统地鉴定了参与穗部特征形成的基因。我们通过全基因组关联研究和元 QTL 分析鉴定了 170 个与穗长、每穗小穗数和每穗粒数变异相关的基因座。我们通过整合转录组、组蛋白修饰、染色质可及性、eQTL 和蛋白质-蛋白质互作组数据，构建了双脊期和小花原基期幼穗的基因调控网络，分别以小穗分生组织和小花分生组织为主。从这些网络中，我们鉴定了 169 个位于 76 个 QTL 区域的枢纽基因，其多态性与穗部特征的变异显著相关。验证了 TaZF-B1、VRT-B2 和 TaSPL15-A/D 在建立小麦穗结构中的作用。本研究为理解穗部特征提供了有价值的分子资源，并证明了将遗传分析和发育调控网络相结合是解析复杂特征的一种稳健方法。
