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To incorporate root traits that improve water use efficiency (WUE) in cotton (Gossypium hirsutum L.) variety development, harnessing the genetic variability for root traits is essential. The objectives of this study were to characterize the US upland cotton core set for root traits and WUE and determine the traits associated with WUE. The core set includes 23 of the 381 accessions of the cotton diversity panel and represents 74% of the allelic diversity in US upland cotton. Plants were grown in polyvinyl chloride columns (125‐cm height, 15‐cm diameter) in a greenhouse in 2021–2022 and 2022–2023. Half of the columns contained a synthetic hardpan (1 cm thickness, 300 PSI penetration resistance) at a depth of 25 cm. Plants were harvested when >50% of the population opened bolls. Based on 16 root‐ and shoot‐traits, water use, and WUE, Deltapine 14, Station Miller, and Southland M1 were the best performers, and Toole, Paymaster HS200, Western Stormproof, CD3HCABCUH‐1‐89, and PD 2164 were the poor performers irrespective of the presence or absence of hardpan stress to root growth. The WUE of the core set genotypes was positively correlated with very fine root (diameter <0.25 mm) length, surface area, and volume and total root weight (correlation coefficient ≥0.45). These traits serve as beneficial root traits for developing new varieties with enhanced WUE. The identified genotypes and traits will be valuable for developing the next generation of water‐use‐efficient cotton varieties with a broad genetic base through advanced breeding techniques involving genomic tools and genetic diversity. Core Ideas: The US upland cotton core set includes significant genetic variability for water use efficiency and root traits.Root weight and very fine root (diameter <0.25 mm) length, surface area, and volume improve water use efficiency.Deltapine 14, Station Miller, and Southland M1 possessed beneficial root traits and high water use efficiency.The identified root traits and genotypes would be useful resources for cotton variety development. [ABSTRACT FROM AUTHOR]

Thrips are major early season insect pests that cause significant economic damage in Upland cotton in the U.S. Development and deployment of resistant cultivars is the most effective and ecologically sustainable means of reducing thrips damage in cotton. Interspecific hybridization and backcrossing were performed to introgress thrips resistance from Pima cotton (Gossypium barbadense L.) accession Coastland 320 into Upland cotton (Gossypium hirsutum L.) cultivars Acala Maxxa (AM) and Fiber Max 966 (FM966). Backcross populations were screened for thrips resistance in thrips screening summer field nurseries in North Carolina. Thirty-two BC2F2 plants with thrips resistance were identified and backcrossed further to develop BC3F2 plants. Eleven AM derived BC2F2 resistant plants and 21 FM966 derived BC2F2 resistant plants were genotyped using CottonSNP63K array to identify the Pima chromatin in the introgression lines (ILs). In the ILs, introgressed Pima chromatin was detected on chromosomes A01, A08, A09, A10, A11, D10, D11, D12, and D13. Of these, four ILs, two each in AM and FM966 background, showed overlapped introgressed Pima chromatin on chromosomes A10 and D11. Further, four introgression lines, two each in AM and FM966 background, shared a common Pima introgression on chromosome D13. Characterization of thrips species in the screening nursery showed that predominant thrips species were tobacco thrips (Frankliniella fusca (Hinds)) followed by western flower thrips (Frankliniella occidentalis (Pergande)). The identified ILs with thrips resistance should be a useful source of genetic variability for developing Upland cotton cultivars with pest resistance. [ABSTRACT FROM AUTHOR]

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]

Bacterial blight (BB), caused by Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease to cotton production in many countries. In the U.S., Xcm race 18 is the most virulent and widespread race and can cause serious yield losses. Planting BB-resistant cotton cultivars is the most effective method of controlling this disease. In this study, 335 U.S. Upland cotton accessions were evaluated for resistance to race 18 using artificial inoculations by scratching cotyledons on an individual plant basis in a greenhouse. The analysis of variance detected significant genotypic variation in disease incidence, and 50 accessions were resistant including 38 lines with no symptoms on either cotyledons or true leaves. Many of the resistant lines were developed in the MAR (multi-adversity resistance) breeding program at Texas A&M University, whereas others were developed before race 18 was first reported in the U.S. in 1973, suggesting a broad base of resistance to race 18. A genome-wide association study (GWAS) based on 26,301 single nucleotide polymorphic (SNP) markers detected 11 quantitative trait loci (QTL) anchored by 79 SNPs, including three QTL on each of the three chromosomes A01, A05 and D02, and one QTL on each of D08 and D10. This study has identified a set of obsolete Upland germplasm with resistance to race 18 and specific chromosomal regions delineated by SNPs for resistance. The results will assist in breeding cotton for BB resistance and facilitate further genomic studies in fine mapping resistance genes to enhance the understanding of the genetic basis of BB resistance in cotton. [ABSTRACT FROM AUTHOR]

Key message: A high-resolution GWAS detected consistent QTL for resistance to Verticillium wilt and Fusarium wilt race 4 in 376 U.S. Upland cotton accessions based on six independent replicated greenhouse tests. Verticillium wilt (VW, caused by Verticillium dahliae Kleb.) and Fusarium wilt (FOV, caused by Fusarium oxysporum f.sp. vasinfectum Atk. Sny & Hans) are the most important soil-borne fungal diseases in cotton. To augment and refine resistance quantitative trait loci (QTL), we conducted a genome-wide association study (GWAS) using high-density genotyping with the CottonSNP63K array. Resistance of 376 US Upland cotton accessions to a defoliating VW and virulent FOV4 was evaluated in four and two independent replicated greenhouse tests, respectively. A total of 15 and 13 QTL for VW and FOV4 resistances were anchored by 30 (on five chromosomes) and 56 (on six chromosomes) significant single nucleotide polymorphic (SNPs) markers, respectively. QTL on c8, c10, c16, and c21 were consistent in two or more tests for VW resistance, while two QTL on c8 and c14 were consistent for FOV4 resistance in two tests. Two QTL clusters on c16 and c19 were observed for both VW and FOV4 resistance, suggesting that these genomic regions may harbor genes in response to both diseases. Using BLAST search against the sequenced TM-1 genome, 30 and 35 candidate genes were identified on four QTL for VW resistance and on three QTL for FOV4 resistance, respectively. These genomic regions were rich in NBS-LRR genes presented in clusters. The results create opportunities for further studies to determine the correlations of field resistance with these QTL, molecular examinations of VW and FOV4 resistances, marker-assisted selection (MAS) and eventual cloning of QTL for disease resistance in cotton. [ABSTRACT FROM AUTHOR]

Assessing genetic diversity and population structure is prerequisite to the systematic utilization and conservation of germplasm resources of crop plants. The genetic diversity and population structure in a combined panel of 557 Gossypium hirsutum L. accessions including 375 cultivars and 182 race stocks using 114 pairs of simple sequence repeat primers were evaluated in the current study. Six G. barbadense L. accessions were included as an out-group. Genotyping the diversity panel of 563 accessions with the markers identified a total of 819 alleles and 662 alleles within G. hirsutum. Population structure analysis identified one G. barbadense group and five G. hirsutum groups corresponding to southwestern cultivars, Mexican collections, western cultivars, southeastern and mid-south cultivars, and Guatemalan collections. Average genetic distance of 0.253 indicated a moderate level of genetic diversity in this panel. Analysis of molecular variance revealed a low level of differentiation among cultivated cotton groups compared to landrace accessions. Genetic diversity and population structure analyses suggest landraces of Guatemala could be a potential source of novel genetic variability for U.S. cotton. Further, multiple core sets with different levels of allele richness were identified. The diversity panel and the core sets identified could be a good resource for broadening the genetic base of U.S. cotton and for genetic analysis of agronomic traits. [ABSTRACT FROM AUTHOR]

Three hundred and ninety-one Gossypium hirsutum and 34 Gossypium barbadense accessions were screened for thrips resistance under field conditions at the Upper Coastal Plain Research Station in Rocky Mount, North Carolina in years 2014 and 2015. Visual damage ratings, thrips counts, and seedling dry weights were recorded at 2.5, 3.5, and 4.5 wk after planting, respectively. Population density and thrips arrival times varied between years. Data from the three separate damage scoring dates provided a better estimate of resistance or susceptibility to thrips than ratings from the individual dates over the season. Tobacco thrips [ Frankliniella fusca (Hinds) (Thysanoptera: Thripidae)], followed by western flower thrips [ Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae)], were the dominant thrips species observed in the study. Five resistant G. barbadense accessions and five moderately resistant upland cotton accessions were identified from field evaluations. Greenhouse experiments were conducted in Fall 2015 and Spring 2016 to determine if plant height, growth rate, leaf pubescence, and leaf area were significantly different in resistant and susceptible groups of G. hirsutum and G. barbadense accessions identified from the field screenings. Leaf pubescence and relative growth rate were significantly higher in resistant accessions compared with susceptible accessions in absence of thrips. There was no difference for plant height and leaf area between resistant and susceptible groups. Results suggest thrips-resistant plants have a possible competitive advantage through faster growth and higher trichome density, which limits thrips movement. [ABSTRACT FROM AUTHOR]

Measuring maturity in Upland cotton (Gossypium hirsutum L.) cultivar trials is a simple calculation of percentage of first harvest to total harvest when most trials are harvested twice. This provides a rough estimate of maturity. Today, cotton trials are rarely harvested twice because of the use of synthetic boll-opening agents. Breeding programs in states such as Arkansas and North Carolina have estimated maturity by either visually estimating percentage bolls open or actually counting open and closed (green) bolls. This study was conducted to determine the optimum combination of replicates, years, and locations of data needed to show 1 d difference in maturity between cultivars. Data were used from the Arkansas testing program for years 2005 through 2012 and from North Carolina for years 2007 through 2012. Arkansas program estimates percentage bolls open visually in all replicates and North Carolina program counts number of open and closed bolls in a short section of each plot in two replicates. For the Arkansas method, we would need to collect data from four replicates, 2 yr, and five locations or four replicates, 3 yr, and three locations. For North Carolina we would need 3 yr, four replicates, and three locations; or 3 yr, three replicates, and five locations; or 3 yr, five replicates, and two locations to provide the same level of precision. Single-year data could detect a 2 d difference in maturity using the Arkansas method and a 4 d difference in maturity using the North Carolina method. The Arkansas method is quicker and provides fairly accurate data on maturity and would be the recommended method to follow. [ABSTRACT FROM AUTHOR]

Upland cotton ( Gossypium hirsutum L.) hybrids display commercially useful levels of heterosis for lint yield. Cotton lint yield is primarily a multiplicative product of boll number and lint per boll, both of which can be further dissected into sub-components. Relationships among the yield components are complex where they further interact with the environment. To identify different yield components of hybrid cotton lint yield and their relationship with environment, three cotton varieties, DP51, STV474 and LA887 and, their respective hybrids were evaluated for lint yield components across five environments. Heterosis was observed for lint yield as well as yield components. The relationship between heterosis and mean environmental yield was negative for two hybrid combinations, whereas one hybrid showed increased heterosis from low to high yielding environments. Boll number was the major yield component contributing to lint yield. However, yield components contributing to the change in heterosis from low to high yielding environments were different for the three hybrids. The change in lint yield heterosis across environments was correlated with lint per boll and lint per seed for DP51 × STV474 and LA887 × DP51. Whereas, bolls number and boll retention were the main yield components contributing to higher lint yield heterosis of STV474 × LA887 in low yielding environments. Results also reveal effects of parental entries on lint yield as well as relationship of heterosis and environment. [ABSTRACT FROM AUTHOR]

Molecular cytogenetic techniques, especially Fluorescence In situ Hybridization (FISH) and Genomic In situ Hybridization (GISH), are excellent tools to study the structure and function of chromosomes, polyploidy, aneuploidy, alien gene introgression and genome evolution and physical mapping of genes. For many applications, in situ hybridizations require reliable and efficient methods of chromosome preparation with well preserved and dispersed chromosomes and little or no cell wall debris. However, such protocols have not yet been published for cotton mitotic chromosome preparations. In the current study, an improved method for preparing mitotic metaphase chromosomes of tetraploid cotton was developed. Root tips were collected from lab-grown three-day-old cotton seedlings and pre-treated with high-pressure nitrous oxide (N2O). Following fixation with acetic acid, root tip meristems were removed, enzymatically digested, gently macerated, and then processed to create suspensions of protoplasts in acetic acid and methanol. Suspended protoplasts were then dropped onto a glass slide in order to distribute the protoplasts and spread the chromosomes. Using this approach, acceptable mitotic indexes and high-quality chromosomal spreads with no cell wall debris were obtained. This drop method of preparing chromosome spreads was tested for its compatibility for in situ hybridization using rDNA as probe in FISH. Additionally, varying pre-treatment times with N2O were investigated. Our results show that the combination of a 95-minute N2O pre-treatment, a 55-minute enzymatic degradation, and the "drop method" efficiently produce cotton mitotic metaphase preparations. This new method will expectedly improve the efficiency and efficacy of GISH, FISH, and single-copy multicolor FISH, which will have a multitude of ramifications in cotton genetics and breeding. [ABSTRACT FROM AUTHOR]

• Significant variation in tolerance to drought and salt and resistance to thrips were observed within a diversity panel of 376 US Upland cotton • GWAS identified 11 and 15 common QTL between tests for drought and salt tolerance, respectively. • Eight QTL were identified for thrips resistance on five chromosomes. • Thirteen QTL clusters were detected on 11 chromosomes. Among the 13 QTL clusters, the one on D03 contained a QTL for thrips resistance and four QTL for abiotic resistance. Upland cotton (Gossypium hirsutum L.) is the most important fiber-producing crop, and its seedlings are sensitive to abiotic and biotic stresses including drought, salt and thrips [ Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae)]. In this study, an association mapping panel of 376 Upland cotton accessions was evaluated to identify quantitative trait loci (QTL) for thrips resistance in two replicated tests and drought (DT) and salt tolerance (ST) each in three replicated tests. Significant genotypic differences were detected for severity rating-based thrips resistance and morphological traits (including plant height, fresh shoot weight, fresh root weight, dry shoot weight and dry root weight (except for ST), and physiological traits (including chlorophyll content reading, stomatal conductance, photosynthesis rate, transpiration, and leaf temperature) under DT and ST conditions. Heritability estimates were low for physiological traits, moderate for morphological traits measured for both DT and ST and moderate to high for thrips resistance. Based on a genome-wide association study (GWAS) using 26,301 polymorphic SNPs, 53 and 78 QTL were detected for DT and ST, respectively, on all 26 chromosomes except for A02, A04, A06, A12 and D07. Eleven and 15 QTL were common between tests for DT and ST, respectively. Twenty-three of 131 QTL were common between DT and ST. Eight QTL were identified for thrips resistance on five chromosomes (A09, D01, D02, D03 and D11). Thirteen QTL clusters were detected on 11 chromosomes (i.e., A01, A08, D01, D02, D03, D05, D06, D10, D11, D12, and D13). Among the 13 QTL clusters, the one on D03 contained a QTL for thrips resistance and four QTL for abiotic resistance. This study represented the first attempt to map thrips resistance QTL in cotton, providing important information for biotic and abiotic stress resistance to select QTL that will be useful for marker-assisted selection (MAS) in cotton. [ABSTRACT FROM AUTHOR]