Integrating RTM-GWAS and meta‑QTLs uncovers the genomic regions and candidate genes for the first fruit branch node and its height in upland cotton

Abstract The first fruit branch node (FFBN) and height of the first fruit branch node (HFFBN) are two important traits related to plant architecture and early maturation in upland cotton. Several studies have been performed to elucidate the genetic basis of FFBN and HFFBN 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-QTL analysis was conducted on 274 original QTLs reported in 27 studies, and 40 MQTLs for FFBN and HFFBN were detected. Through the integration of 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 were annotated in the two genomic regions, and three candidate genes for FFBN and HFFBN were identified in the genomic region (A05:14.64–15.64 Mb) by RNA-Seq and qRT‒PCR. The results of virus-induced gene silencing (VIGS) experiments indicated that GhE6was 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.