Identification of candidate genes for key fibre‐related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions

Abstract

Summary Fine mapping QTLs and identifying candidate genes for cotton fibre‐quality and yield traits would be beneficial to cotton breeding. Here, we constructed a high‐density genetic map by specific‐locus amplified fragment sequencing (SLAF‐seq) to identify QTLs associated with fibre‐quality and yield traits using 239 recombinant inbred lines (RILs), which was developed from LMY22 (a high‐yield Gossypium hirsutumL. cultivar) × LY343 (a superior fibre‐quality germplasm with G. barbadenseL. introgressions). The genetic map spanned 3426.57 cM, including 3556 SLAF‐based SNPs and 199 SSR marker loci. A total of 104 QTLs, including 67 QTLs for fibre quality and 37 QTLs for yield traits, were identified with phenotypic data collected from 7 environments. Among these, 66 QTLs were co‐located in 19 QTL clusters on 12 chromosomes, and 24 QTLs were detected in three or more environments and determined to be stable. We also investigated the genomic components of LY343 and their contributions to fibre‐related traits by deep sequencing the whole genome of LY343, and we found that genomic components from G. hirsutum races (which entered LY343 via its G. barbadense parent) contributed more favourable alleles than those from G. barbadense. We further identified six putative candidate genes for stable QTLs, including Gh_A03G1147 (GhPEL6), Gh_D07G1598 (GhCSLC6) and Gh_D13G1921 (GhTBL5) for fibre‐length QTLs and Gh_D03G0919 (GhCOBL4), Gh_D09G1659 (GhMYB4) and Gh_D09G1690 (GhMYB85) for lint‐percentage QTLs. Our results provide comprehensive insight into the genetic basis of the formation of fibre‐related traits and would be helpful for cloning fibre‐development‐related genes as well as for marker‐assisted genetic improvement in cotton.

Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.)

“…The genes from LP QTLs were enriched in several pathways, including hormone and ROS regulation pathways, such as "regulation of gibberellic acid mediated signaling pathway", "positive regulation of reactive oxygen species metabolic process" and "brassinosteroid biosynthetic process". They were also enriched in carbohydrate metabolism processes, such as "glucose metabolic process" and "hexose biosynthetic process", which was consistent with the previous reports that these GO items play crucial roles in fiber development [11,21]. In addition, we identified 14, 21 and 10 genes related to "Golgi vesicle transport", "plant-type secondary cell wall biogenesis" and "glucose metabolic process", respectively, however, none of these process-related genes were found in the QTL regions of BNPP or SBW (Additional file 12: Fig.…”

Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.)

“…The genes from LP QTLs were enriched in several pathways, including hormone and ROS regulation pathways, such as "regulation of gibberellic acid mediated signaling pathway", "positive regulation of reactive oxygen species metabolic process" and "brassinosteroid biosynthetic process". They were also enriched in carbohydrate metabolism processes, such as "glucose metabolic process" and "hexose biosynthetic process", which was consistent with the previous reports that these GO items play crucial roles in fiber development [11,21]. In addition, we identified 14, 21 and 10 genes related to "Golgi vesicle transport", "plant-type secondary cell wall biogenesis" and "glucose metabolic process", respectively, however, none of these processrelated genes were found in the QTL regions of BNPP or SBW (Additional file 12: Figure S5 and Additional file 11: Table S7).…”

Genome-wide association study reveals genetic variation and candidate genes of lint yield components under salt field conditions in cotton (Gossypium hirsutum L.)

“…S4 and Additional file 11: Table S7). The genes from LP QTLs mainly enriched in several pathways, including "regulation of organ growth", hormone and ROS regulation such as "regulation of gibberellic acid mediated signaling pathway", "positive regulation of reactive oxygen species metabolic process", "brassinosteroid biosynthetic process" and "defense response by cell wall thickening", and carbohydrate metabolism such as "glycosylation", "glucose metabolic process", "monosaccharide biosynthetic process" and "hexose biosynthetic process", which was consistent with the previous reports that these Go items played the crucial roles in fiber development [11,21]. In addition, we identified 14, 21 and 10 genes related to "Golgi vesicle transport", "plant-type secondary cell wall biogenesis" and "glucose metabolic process", respectively, however, none of these processrelated genes were found in the QTL regions of BNPP and SBW (Additional file 12: Fig.…”