Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
Kika de la Garza Plant Materials Center, National Resources Conservation Service, US Department of Agriculture, Kingsville, TX, 78363, USA.
Theor Appl Genet. 2022 Aug;135(8):2577-2592. doi: 10.1007/s00122-022-04096-x. Epub 2022 Jul 2.
We investigate the genetic basis of panicle architecture in switchgrass in two mapping populations across a latitudinal gradient, and find many stable, repeatable genetic effects and limited genetic interactions with the environment. Grass species exhibit large diversity in panicle architecture influenced by genes, the environment, and their interaction. The genetic study of panicle architecture in perennial grasses is limited. In this study, we evaluate the genetic basis of panicle architecture including panicle length, primary branching number, and secondary branching number in an outcrossed switchgrass QTL population grown across ten field sites in the central USA through multi-environment mixed QTL analysis. We also evaluate genetic effects in a diversity panel of switchgrass grown at three of the ten field sites using genome-wide association (GWAS) and multivariate adaptive shrinkage. Furthermore, we search for candidate genes underlying panicle traits in both of these independent mapping populations. Overall, 18 QTL were detected in the QTL mapping population for the three panicle traits, and 146 unlinked genomic regions in the diversity panel affected one or more panicle trait. Twelve of the QTL exhibited consistent effects (i.e., no QTL by environment interactions or no QTL × E), and most (four of six) of the effects with QTL × E exhibited site-specific effects. Most (59.3%) significant partially linked diversity panel SNPs had significant effects in all panicle traits and all field sites and showed pervasive pleiotropy and limited environment interactions. Panicle QTL co-localized with significant SNPs found using GWAS, providing additional power to distinguish between true and false associations in the diversity panel.
我们在跨越纬度梯度的两个作图群体中研究柳枝稷穗型结构的遗传基础，发现许多稳定、可重复的遗传效应，以及与环境的有限遗传相互作用。草类植物的穗型结构受基因、环境及其相互作用的影响，表现出很大的多样性。多年生禾本科植物穗型结构的遗传研究有限。在这项研究中，我们通过多环境混合 QTL 分析，评估了穗型结构的遗传基础，包括在十个美国中部田间试验点种植的杂交柳枝稷 QTL 群体中的穗长、一级分枝数和二级分枝数。我们还使用全基因组关联（GWAS）和多元自适应收缩分析，在三个田间试验点生长的柳枝稷多样性群体中评估遗传效应。此外，我们在这两个独立的作图群体中搜索穗型性状的候选基因。总体而言，在三个穗型性状的 QTL 作图群体中检测到 18 个 QTL，在多样性群体中检测到 146 个不连锁的基因组区域影响一个或多个穗型性状。12 个 QTL 表现出一致的效应（即无 QTL 与环境互作或无 QTL×E），且大多数（6 个中的 4 个）具有 QTL×E 的效应表现出特定地点的效应。大多数（59.3%）显著的部分连锁多样性群体 SNP 在所有穗型性状和所有田间试验点均有显著效应，表现出普遍的多效性和有限的环境互作。穗型 QTL 与 GWAS 发现的显著 SNP 共定位，为区分多样性群体中的真实和虚假关联提供了额外的能力。
