Data_Sheet_3_Genome-Wide Association Study in Pseudo-F2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates.zip

Switchgrass (Panicum virgatum) is a native prairie grass and valuable bio-energy crop. The physiological change from juvenile to reproductive adult can draw important resources away from growth into producing reproductive structures, thereby limiting the growth potential of early flowering plants. Delaying the flowering of switchgrass is one approach by which to increase total biomass. The objective of this research was to identify genetic variants and candidate genes for controlling heading and anthesis in segregating switchgrass populations. Four pseudo-F2 populations (two pairs of reciprocal crosses) were developed from lowland (late flowering) and upland (early flowering) ecotypes, and heading and anthesis dates of these populations were collected in Lafayette, IN and DeKalb, IL in 2015 and 2016. Across 2 years, there was a 34- and 73-day difference in heading and a 52- and 75-day difference in anthesis at the Lafayette and DeKalb locations, respectively. A total of 37,901 single nucleotide polymorphisms obtained by exome capture sequencing of the populations were used in a genome-wide association study (GWAS) that identified five significant signals at three loci for heading and two loci for anthesis. Among them, a homolog of FLOWERING LOCUS T on chromosome 5b associated with heading date was identified at the Lafayette location across 2 years. A homolog of ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5, a light modulator in the circadian clock associated with heading date was detected on chromosome 8a across locations and years. These results demonstrate that genetic variants related to floral development could lend themselves to a long-term goal of developing late flowering varieties of switchgrass with high biomass yield.

柳枝稷（Switchgrass，学名Panicum virgatum）是一种本土草原草本植物，亦是极具价值的生物能源作物。从幼龄营养生长阶段向生殖成熟阶段的生理转变，会将重要资源从营养生长转向生殖结构的构建，进而限制早开花植株的生长潜力。延迟柳枝稷的开花时间，是提升其总生物量的有效途径之一。本研究旨在从分离柳枝稷种群中，鉴定调控抽穗期与开花盛期的遗传变异与候选基因。研究以低地（晚开花型）和高地（早开花型）生态型为亲本，构建了4个伪F2种群（包含2对互交组合），并于2015年与2016年分别在印第安纳州拉斐特（Lafayette, IN）与伊利诺伊州迪卡尔布（DeKalb, IL）两地采集了这些种群的抽穗期与开花盛期数据。两年试验数据显示，拉斐特与迪卡尔布两地的抽穗期差异分别达34天与73天，开花盛期差异分别达52天与75天。通过对种群进行外显子组捕获测序（exome capture sequencing），共获得37901个单核苷酸多态性（single nucleotide polymorphisms, SNP）位点，将这些位点用于全基因组关联分析（genome-wide association study, GWAS）后，在3个与抽穗期相关的位点上鉴定出5个显著关联信号，在2个与开花盛期相关的位点上鉴定出2个显著关联信号。其中，在跨两年的拉斐特试验点中，于5b染色体上检测到一个与抽穗期相关的开花位点T（FLOWERING LOCUS T, FT）同源基因；在8a染色体上检测到一个与抽穗期相关的拟南芥伪反应调控因子5（ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5, APRR5）同源基因，该基因作为生物钟中的光调控因子，可在多试验点与年份中稳定被检测到。本研究结果表明，与花发育相关的遗传变异，可为培育高生物量产量的晚开花柳枝稷品种这一长期目标提供理论支撑与实践方向。