QTL analysis of agronomic, fiber quality, and abiotic stress tolerance traits in a recombinant inbred population of pima cotton

Abstract

Pima cotton (Gossypium barbadense L.) is grown for its superior fiber quality in four U.S. states and in several other countries. However, there is a lack of information on major and stable quantitative trait loci (QTL) for fiber quality and agronomic traits and abiotic stress tolerance across different environments. In this study, a genetic linkage map based on 403 simple sequence repeat (SSR) markers was developed for the Pima S‐6/89590 intraspecific mapping population consisting of 161 recombinant inbred lines (RILs). Through the evaluation of the RIL population in seven field tests for agronomic traits and fiber quality in the four pima cotton‐growing U.S. states and four greenhouse tests for drought and salinity tolerance, a total of 156 QTL were detected. Eight QTL clusters and four hotspots were further identified, and many of the QTL and their clusters and hotspots were consistent with previous studies that will be useful for marker‐assisted selection. Using a basic local alignment search tool (BLAST) search against the sequenced Pima 3‐79 genome, 26, 16, 32, 14, 127, and 14 candidate genes were predicted for 15 stable QTL on six chromosomes (chromosomes 3, 10, 12, 19, 21, and 24, respectively), for fiber quality traits and abiotic stress tolerance. These genomic regions were rich in genes related to fiber developments and abiotic stress responses. This study provides important information on new and stable QTL across environments for developing superior American pima cotton.

Quantitative Trait Locus Mapping for Fusarium Wilt Race 4 Resistance in a Recombinant Inbred Line Population of Pima Cotton (Gossypium Barbadense)

“…The RIL population was developed from a cross of FOV4-resistant Pima S-6 [ 21 ] with a susceptible Pima germplasm line 89590 [ 22 ], through a single-seed descent method [ 23 ]. F1 plants were self-pollinated to produce individual F2 plants which were subsequently advanced to RILs through several generations of repeated self-pollination on an individual F2 plant basis.…”

“…The RILs were genotyped with a total of 403 SSR polymorphic loci which were produced from 200 SSR primer pairs, because each primer pair produced one to multiple polymorphic markers [ 23 ]. The primer sequences for the SSR markers are available from the CottonGen database ( , accessed on 1 September 2022).…”

“…The primer sequences for the SSR markers are available from the CottonGen database ( , accessed on 1 September 2022). DNA was extracted using a cTAB-based quick extraction method [ 25 ], followed by PCR and gel electrophoresis, as detailed by Abdelraheem et al [ 23 ]. The linkage map was constructed using JoinMap version 4.0 software [ 26 ].…”

Quantitative Trait Locus Mapping and Identification of Candidate Genes for Resistance to Fusarium Wilt Race 7 Using a Resequencing-Based High Density Genetic Bin Map in a Recombinant Inbred Line Population of Gossypium barbadense

“…However, QTL mapping for FOV resistance using linkage analysis and GWAS has been almost exclusively focused on Upland cotton. There have been a few reports using SSRs in genomic studies of G. barbadense (Abdelraheem et al, 2013(Abdelraheem et al, , 2015(Abdelraheem et al, , 2020Wang et al, 2013), and no high density linkage map has been published for G. barbadense because a low level of polymorphisms in SSR markers within the species.…”

A GWAS Identified a Major QTL for Resistance to Fusarium Wilt (Fusarium Oxysporum f. sp. Vasinfectum) Race 4 in a MAGIC Population of Upland Cotton and a Meta-Analysis of QTLs for Fusarium Wilt Resistance

“…Most recently, 13 FOV4 resistance QTLs were identi ed on six chromosomes, i.e., A08 (c8), D02 (c14), D03 (c17), D05 (c19), D07 (c16), and D13 in the US Upland cotton with 25,677 SNP markers through a genome-wide association study (GWAS) of 367 US Upland accessions(Abdelraheem et al 2020a). Seven QTLs for FOV4 resistance were mapped on six chromosomes (D02/c14, D03/c17, D05/c19, D06/c25, D08/c24, and D11/c21) using 163 RILs of a G. barbadense cross from FOV4-resistant Pima S-6 × susceptible 89590 with 403 SSR markers(Abdelraheem et al 2020b). Although many QTLs conferring FW resistance have been mapped on all chromosomes except for a few chromosomes including A04 (c4) and D10 (c20), major effect resistance QTLs are located on only a few chromosomes(Zhang et al 2015a,b; Abdelraheem et al 2017).…”