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In cotton, most agronomic traits are controlled by polygenes. In this study, 110 F6 recombinant inbred lines (RILs), derived from Upland cotton cross NC05AZ06 x NC11‐2100, were used to develop a linkage map and to identify quantitative trait loci (QTL) for six fiber quality traits, three yield traits, and plant height. These RILs were genotyped using the CottonSNP63K array and phenotyped for fiber quality, yield traits, and plant height in 2‐year field trials. Analysis of variance revealed significant (p < 0.05) differences among RILs for all traits studied, and the heritability estimates were moderate (30%–60%) to high (> 60%). Both positive and negative correlations were observed for fiber quality and yield traits. A total of 3,774 polymorphic SNP markers were used to develop a genetic map with an average marker density of 1.54 SNP/cM. Thirty QTL for fiber quality traits, yield traits, and plant height were detected on 15 different chromosomes, explaining 6.80%–20.02% of the phenotypic variance (PVE). Of these, 14 were major QTL (PVE > 10%), and three major QTL were detected in both years. Candidate gene analysis in the major QTL detected in both years and plant height QTL with PVE of 20.02% revealed five putative genes for fiber quality traits and one putative gene for plant height. The linkage map and identified QTL along with the candidate genes in the study could serve as additional breeding resources for Upland cotton genetic improvement. Core Ideas: A RIL population derived from accessions with maximum allele diversity was used for QTL mapping of fiber quality and yield traits, and plant height in cotton.Broad sense heritability of the 10 agronomic traits studied ranged from moderate (30%–60%) to high (>60%) values.Thirty QTL, including 14 major QTL, of which 3 major stable QTL, were detected for fiber quality and yield traits, and plant height. [ABSTRACT FROM AUTHOR]

Key message: Identification and genomic characterization of major resistance locus against cotton bacterial blight (CBB) using GWAS and linkage mapping to enable genomics-based development of durable CBB resistance and gene discovery in cotton. Cotton bacterial leaf blight (CBB), caused by Xanthomonas citri subsp. malvacearum (Xcm), has periodically been a damaging disease in the USA. Identification and deployment of genetic resistance in cotton cultivars is the most economical and efficient means of reducing crop losses due to CBB. In the current study, genome-wide association study (GWAS) of CBB resistance using an elite diversity panel of 380 accessions, genotyped with the cotton single nucleotide polymorphism (SNP) 63 K array, and phenotyped with race-18 of CBB, localized the CBB resistance to a 2.01-Mb region in the long arm of chromosome D02. Molecular genetic mapping using an F6 recombinant inbred line (RIL) population showed the CBB resistance in cultivar Arkot 8102 was controlled by a single locus (BB-13). The BB-13 locus was mapped within the 0.95-cM interval near the telomeric region in the long arm of chromosome D02. Flanking SNP markers, i04890Gh and i04907Gh of the BB-13 locus, identified from the combined linkage analysis and GWAS, targeted it to a 371-Kb genomic region. Candidate gene analysis identified thirty putative gene sequences in the targeted genomic region. Nine of these putative genes and two NBS-LRR genes adjacent to the targeted region were putatively involved in plant disease resistance and are possible candidate genes for BB-13 locus. Genetic mapping and genomic targeting of the BB13 locus in the current study will help in cloning the CBB-resistant gene and establishing the molecular genetic architecture of the BB-13 locus towards developing durable resistance to CBB in cotton. [ABSTRACT FROM AUTHOR]

Improving fiber quality and yield are major research objectives for cotton breeders in the United States. Identifying broadly existing and stable quantitative trait loci (QTLs) related to fiber quality is critical to properly utilizing genomic resources in cotton improvement programs. An F6 recombinant inbred line (RIL) population derived from the cross of NC05AZ21 × TX‐2324 was used to develop linkage maps and for QTL analysis of six fiber quality traits and lint percentage. The Illumina 63K single nucleotide polymorphism (SNP) array was used to genotype the RIL population. Analysis of variance of phenotypic trait data showed significant differences among lines and years for all traits tested. The heritability for tested traits ranged from 0.56 to 0.91. Genetic mapping was performed using 3,009 polymorphic SNP markers on the RILs. We constructed a genetic map with a total length of 4,983.73 cM and an average distance of 1.66 cM between markers. The linkage map corresponded well with the Upland cotton (Gossypium hirsutum L.) sequence‐based physical map. Thirty‐two QTLs with additive effects for lint percentage and fiber quality traits were identified on 15 chromosomes, explaining 7.9–22.2% of the phenotypic variance. The majority of these QTLs were mapped in the D subgenome, indicating that functional mutations in the D subgenome are responsible for the major fiber quality improvements in Upland cotton. Furthermore, five QTL clusters were located on four chromosomes (Chr.05, Chr.18, Chr.19, and Chr.26), which may explain the strong correlation between fiber quality traits measured. The QTLs identified in the current study could be targeted for marker‐assisted selection and map‐based cloning of fiber quality traits in Upland cotton. Core Ideas: QTL mapping using a SNP array on a recombinant inbred line population was performed.The genetic map of SNPs corresponded well with the sequence‐based physical map.Thirty‐two QTLs for six fiber quality traits and lint percentage were identified.The D subgenome harbored the majority of QTLs for fiber quality in Upland cotton.QTLs for fiber quality traits clustered on a handful of chromosomal regions. [ABSTRACT FROM AUTHOR]

Threshability is an important crop domestication trait. The wild wheat progenitors have tough glumes enveloping the floret that make spikes difficult to thresh, whereas cultivated wheats have soft glumes and are free-threshing. In hexaploid wheat, the glume tenacity gene Tg along with the major domestication locus Q control threshability. The Q gene was isolated recently and found to be a member of the AP2 class of transcription factors. However, only a few studies have reported on the tough glume trait. Here, we report comparative mapping of the soft glume ( sog) gene of diploid Triticum monococcum L. and tenacious glume ( Tg) gene of hexaploid T. aestivum L. using chromosome-specific SSR and RFLP markers. The sog gene was flanked by Xgwm71 and Xbcd120 in a 6.8 cM interval on chromosome 2AmS of T. monococcum whereas Tg was targeted to a 8.1 cM interval flanked by Xwmc503 and Xfba88 on chromosome 2DS of T. aestivum. Deletion bin mapping of the flanking markers assigned sog close to the centromere on 2AS, whereas Tg was mapped to the most distal region on 2DS. Both 2AS and 2DS maps were colinear ruling out the role of chromosome rearrangements for their non-syntenic positions. Therefore, sog and Tg are not true orthologues suggesting the possibility of a diverse origin. [ABSTRACT FROM AUTHOR]