Table_1_Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study.XLSX

Sugarcane (Saccharum spp.) is an efficient crop mainly used for sugar and bioethanol production. High yield and high sucrose of sugarcane are always the fundamental demands in sugarcane growth worldwide. Leaf angle and size of sugarcane can be attributed to planting density, which was associated with yield. In this study, we performed genome-wide association studies (GWAS) with a panel of 216 sugarcane core parents and their derived lines (natural population) to determine the genetic basis of leaf angle and key candidate genes with +2, +3, and +4 leaf at the seedling, elongation, and mature stages. A total of 288 significantly associated loci of sugarcane leaf angle at different developmental stages (eight phenotypes) were identified by GWAS with 4,027,298 high-quality SNP markers. Among them, one key locus and 11 loci were identified in all three stages and two stages, respectively. An InDel marker (SNP Ss6A_102766953) linked to narrow leaf angle was obtained. Overall, 4,089 genes were located in the confidence interval of significant loci, among which 3,892 genes were functionally annotated. Finally, 13 core parents and their derivatives tagged with SNPs were selected for marker-assisted selection (MAS). These candidate genes are mainly related to MYB transcription factors, auxin response factors, serine/threonine protein kinases, etc. They are directly or indirectly associated with leaf angle in sugarcane. This research provided a large number of novel genetic resources for the improvement of leaf angles and simultaneously to high yield and high bioethanol production.

甘蔗（Saccharum spp.）是一种高效的作物，主要用于糖和生物乙醇的生产。在全球范围内，高产量和高蔗糖含量始终是甘蔗生长的基本需求。甘蔗的叶角和叶片大小可归因于种植密度，这与产量相关。在本研究中，我们使用216个甘蔗核心亲本及其衍生系（自然群体）进行了全基因组关联分析（GWAS），以确定叶角及其在幼苗、伸长和成熟阶段的+2、+3和+4关键候选基因的遗传基础。通过GWAS和4,027,298个高质量的单核苷酸多态性（SNP）标记，共识别出在不同发育阶段（八个表型）的甘蔗叶角288个显著关联位点。其中，一个关键位点在三个阶段以及两个阶段中被识别。获得了一个与狭叶角相关的插入/缺失（InDel）标记（SNP Ss6A_102766953）。总体而言，在显著位点的置信区间内定位了4,089个基因，其中3,892个基因具有功能注释。最终，选出了13个标记的甘蔗核心亲本及其衍生系，用于标记辅助选择（MAS）。这些候选基因主要与MYB转录因子、生长素响应因子、丝氨酸/苏氨酸蛋白激酶等相关，它们直接或间接地与甘蔗的叶角相关。本研究为提高叶角、高产以及高生物乙醇产量提供了大量的新颖遗传资源。