State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji, 831100, Xinjiang, China.
Theor Appl Genet. 2024 Aug 22;137(9):207. doi: 10.1007/s00122-024-04703-z.
Two genomic regions associated with FFBN and HFFBN and a potential regulatory gene (GhE6) of HFFBN were identified through the integration of RTM-GWAS and meta‑QTL analyses. Abstract The first fruit branch node (FFBN) and the height of the first fruit branch node (HFFBN) are two important traits that are related to plant architecture and early maturation in upland cotton. Several studies have been conducted to elucidate the genetic basis of these traits in cotton using biparental and natural populations. In this study, by using 9,244 SNP linkage disequilibrium block (SNPLDB) loci from 315 upland cotton accessions, we carried out restricted two-stage multilocus and multiallele genome-wide association studies (RTM-GWASs) and identified promising haplotypes/alleles of the four stable and true major SNPLDB loci that were significantly associated with FFBN and HFFBN. Additionally, a meta-quantitative trait locus (MQTL) analysis was conducted on 274 original QTLs that were reported in 27 studies, and 40 MQTLs associated with FFBN and HFFBN were identified. Through the integration of the RTM-GWAS and meta‑QTL analyses, two stable and true major SNPLDBs (LDB_5_15144433 and LDB_16_37952328) that were distributed in the two MQTLs were identified. Ultimately, 142 genes in the two genomic regions were annotated, and three candidate genes associated with FFBN and HFFBN were identified in the genomic region (A05:14.64-15.64 Mb) via RNA-Seq and qRT‒PCR. The results of virus-induced gene silencing (VIGS) experiments indicated that GhE6 was a key gene related to HFFBN and that GhDRM1 and GhGES were important genes associated with early flowering in upland cotton. These findings will aid in the future identification of molecular markers and genetic resources for developing elite early-maturing cultivars with ideal plant characteristics.
两个与 FFBN 和 HFFBN 相关的基因组区域以及 HFFBN 的一个潜在调控基因 (GhE6) 是通过 RTM-GWAS 和荟萃 QTL 分析的整合来鉴定的。
第一个果实分枝节点 (FFBN) 和第一个果实分枝节点高度 (HFFBN) 是两个与陆地棉株型和早期成熟相关的重要性状。已经有几项研究使用双亲和自然群体来阐明这些性状的遗传基础。在这项研究中，通过使用来自 315 个陆地棉品系的 9244 个 SNP 连锁不平衡块 (SNPLDB) 位点，我们进行了受限两阶段多基因多等位基因全基因组关联研究 (RTM-GWAS)，并鉴定了与 FFBN 和 HFFBN 显著相关的四个稳定和真实的主要 SNPLDB 位点的有希望的单倍型/等位基因。此外，对 27 项研究中报道的 274 个原始 QTL 进行了荟萃数量性状基因座 (MQTL) 分析，鉴定出与 FFBN 和 HFFBN 相关的 40 个 MQTL。通过 RTM-GWAS 和荟萃-QTL 分析的整合，鉴定出分布在两个 MQTL 中的两个稳定和真实的主要 SNPLDB (LDB_5_15144433 和 LDB_16_37952328)。最终，在两个基因组区域注释了 142 个基因，并通过 RNA-Seq 和 qRT-PCR 在基因组区域 (A05:14.64-15.64 Mb) 中鉴定出与 FFBN 和 HFFBN 相关的三个候选基因。病毒诱导基因沉默 (VIGS) 实验的结果表明，GhE6 是与 HFFBN 相关的关键基因，而 GhDRM1 和 GhGES 是与陆地棉早期开花相关的重要基因。这些发现将有助于未来鉴定分子标记和遗传资源，以开发具有理想株型特征的优质早熟品种。
