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Researchers have used quantitative genetics to map cotton fiber quality and agronomic performance loci, but many alleles may be population or environment-specific, limiting their usefulness in a pedigree selection, inbreeding-based system. Here, we utilized genotypic and phenotypic data on a panel of 80 important historical Upland cotton (Gossypium hirsutum L.) lines to investigate the potential for genomics-based selection within a cotton breeding program's relatively closed gene pool. We performed a genome-wide association study (GWAS) to identify alleles correlated to 20 fiber quality, seed composition, and yield traits and looked for a consistent detection of GWAS hits across 14 individual field trials. We also explored the potential for genomic prediction to capture genotypic variation for these quantitative traits and tested the incorporation of GWAS hits into the prediction model. Overall, we found that genomic selection programs for fiber quality can begin immediately, and the prediction ability for most other traits is lower but commensurate with heritability. Stably detected GWAS hits can improve prediction accuracy, although a significance threshold must be carefully chosen to include a marker as a fixed effect. We place these results in the context of modern public cotton line-breeding and highlight the need for a community-based approach to amass the data and expertise necessary to launch US public-sector cotton breeders into the genomics-based selection era. [ABSTRACT FROM AUTHOR]

Commercial production of Pima cotton (Gossypium barbadense L.) in the United States is currently limited to the western United States and West Texas. Before the 1930s, Pima cotton was produced in coastal regions of the southeast United States. However, in an effort to escape yield and economic losses caused by the boll weevil, which invaded the United States in the 1920s, production of long‐season Pima cotton was eliminated and shifted to shorter‐season upland cotton (Gossypium hirsutum L.). Today, the value of Pima cotton fiber is nearly double that of upland cotton. We hypothesized that Pima cotton could be successfully cultivated in the southeast United States because of the eradication of the boll weevil, alongside improvements in genetics and production practices. We evaluated the agronomic performance, fiber quality, and net economic return of 48 Pima genotypes in field trials conducted during 2018 and 2019 in Florence, SC, compared with two popular commercial upland cultivars. We also evaluated the impact of the ginning method (saw vs. roller) on fiber quality. On average, in comparison with upland cotton, the lint yield of Pima genotypes was reduced by half. However, most of the Pima genotypes produced higher‐quality fibers compared with the upland checks. Surprisingly, the ginning method appeared to have little impact on fiber quality. Net return analysis revealed no significant differences among several of the higher‐yielding, higher‐quality Pima genotypes and the upland genotypes in this study, indicating that the reintroduction of a Pima production system in the southeast United States may be feasible. Core Ideas: Compared with upland genotypes, Pima genotypes had premium fiber quality but yielded 50% less.The ginning method had little impact on fiber quality parameters.The net return of the highest‐yielding Pima genotypes was not different from the upland checks. [ABSTRACT FROM AUTHOR]

Future cotton production systems need improved fiber quality to meet global market demands and provide the textile industry with high‐quality fiber. To achieve this, cotton (Gossypium hirsutum L.) breeding programs must develop cultivars that overcome the negative relationship between agronomic performance and fiber quality. Since 1935, the USDA‐ARS Pee Dee germplasm enhancement program has prioritized improving fiber quality while also maintaining or enhancing agronomic performance. Along with a number of other breeding programs, the Pee Dee program documented that the negative relationship between agronomic performance and fiber quality is most often caused by genetic linkage. Several of these breeding programs have demonstrated that the negative genetic linkage can be overcome. In this study, we test the hypothesis that three Pee Dee germplasm lines previously identified as rare recombinants can generate populations with a decreased negative relationship between agronomic performance and fiber quality. The results suggest that two of the three Pee Dee germplasm lines generate populations with a decreased negative relationship and presumably transmit beneficial allelic combinations for lint percent and fiber quality traits in coupling phase linkage with one another or fixed in offspring. [ABSTRACT FROM AUTHOR]

Determination of an efficient number of testing locations in multiple-location tests for cotton (Gossypium hirsutum L.) fiber quality can allow removal of unnecessary locations while maintaining the statistical power in detection of genotype (g) by environment (e) interactions. Fiber quality data from Regional High-Quality (RHQ) tests from 2011 to 2016 were used to determine an ef- ficient number of locations in the tests for fiber quality and relationships among locations for their representativeness and ability to discriminate among genotypes. Covariance parameters of g, location (l), and gl in the original RHQ tests were estimated in a random model. The simulating data with varying number of locations omitted from the original tests were created by performing 100 unique simulations. When locations were reduced to five, the standard deviations (std) of gl increased from 18 to 37% compared to the original tests. Further reduction of locations to four or less increased std of gl from 30 to 217% compared to the original tests. Therefore, five locations were determined to be an efficient number of locations in tests for fiber quality. The discriminating ability and representativeness of the eight locations for fiber properties were calculated as their distances to an "ideal environment", which was designed as a center in GGE biplot graphs for representativeness and discriminating ability. The relationships among locations were different across years. However, by averaging the distances across testing years, the locations of Stoneville, MS; Keiser, AR; Lubbock, TX; and College Station, TX were identified as the most representative testing sites for fiber properties. [ABSTRACT FROM AUTHOR]

Competition with manmade fibers has increased focus on upland cotton (Gossypium hirsutum L.) fiber quality, especially upper half mean length (FL), for industry stakeholders and breeders. The purpose of this study was to characterize the effect of qFL‐Chr.25, a quantitative trait locus (QTL) introgressed from G. barbadense L. originally identified in 'Sealand 883'. The QTL was deployed within four genetic backgrounds: Acala SJ4, Paymaster HS26, Deltapine 50 (DP 50), and Georgia 2004089 (GA089), each representing the gene pools of the major US cotton‐growing regions: the US Southwest, Texas High Plains, Mississippi Delta, and US Southeast, respectively. In highly related bulked sister lines (BSLs), the effect of qFL‐Chr.25 was significant in the DP 50 (1.4 mm) and GA089 (1 mm) backgrounds in trials grown in Tifton, GA, in 2014 and 2015. In multilocation trials planted across the Cotton Belt in 2011 of 25 lines from each of the four backgrounds carrying the G. barbadense allele and 25 without the introgressed allele, FL of the QTL(+) lines were numerically higher than the QTL(−) lines by 0.9 mm, though not statistically significant. Recombinant genotypes recovered from the Paymaster HS26 and GA089 backgrounds, and development of additional simple sequence repeat (SSR) markers within the QTL region, allowed further refinement of the qFL‐Chr.25 region's boundaries from ∼2.2 to 0.8 Mb. Although variable effects were seen from this QTL, observation in a more isogenic state such as the BSLs and recombinant lines made the effect of the QTL more apparent. Incorporation of this QTL into breeding programs aided by these newly developed SSR markers should help in the utilization of this introgression to improve cotton fiber quality. [ABSTRACT FROM AUTHOR]

Interspecific introgression lines are important resources for plant breeders to access novel alleles from exotic germplasm. The Pee Dee breeding program developed several extra‐long staple "Sealand" germplasm lines that presumably contain sea island cotton (Gossypium barbadense L.) chromatin introgressed into upland cotton (Gossypium hirsutum L.). The objectives of this study were to identify the G. barbadense chromatins in the Sealand lines, 542 and 883, and evaluate their effects on fiber quality. A total of 31 putative G. barbadense chromatins were detected, including 12 segments on seven chromosomes that were unique to Sealand 542 and 10 segments on five chromosomes that were unique to Sealand 883, and the remaining nine segments were common to both the Sealand lines. Sealand 542 and 883 mapping populations were created to identified 28 quantitative trait locus (QTL) regions associated with fiber quality traits, including six for elongation, four for fineness, five for short fiber content, five for strength, three for length, and five for fiber uniformity. At least 13 QTLs were detected on the G. barbadense introgressed chromosomal segments. Favorable alleles for 17 QTLs were contributed by the Sealand lines, and the genetic effects of five loci were stably expressed across environment and generation. Stable expression of G. barbadense fiber quality alleles in the Sealand lines and the absence of these alleles in upland germplasm make these introgression lines a valuable resource for fiber quality improvement. In particular, marker‐assisted introgression of the qFL‐Chr25 locus from Sealand 883 should result in improved fiber length, whereas that of qMIC‐Chr24 from Sealand 542 should result in finer fiber. [ABSTRACT FROM AUTHOR]

Key message: Significant associations between candidate genes and six major cotton fiber quality traits were identified in a MAGIC population using GWAS and whole genome sequencing. Upland cotton (Gossypium hirsutum L.) is the world's major renewable source of fibers for textiles. To identify causative genetic variants that influence the major agronomic measures of cotton fiber quality, which are used to set discount or premium prices on each bale of cotton in the USA, we measured six fiber phenotypes from twelve environments, across three locations and 7 years. Our 550 recombinant inbred lines were derived from a multi-parent advanced generation intercross population and were whole-genome-sequenced at 3× coverage, along with the eleven parental cultivars at 20× coverage. The segregation of 473,517 single nucleotide polymorphisms (SNPs) in this population, including 7506 non-synonymous mutations, was combined with phenotypic data to identify seven highly significant fiber quality loci. At these loci, we found fourteen genes with non-synonymous SNPs. Among these loci, some had simple additive effects, while others were only important in a subset of the population. We observed additive effects for elongation and micronaire, when the three most significant loci for each trait were examined. In an informative subset where the major multi-trait locus on chromosome A07:72-Mb was fixed, we unmasked the identity of another significant fiber strength locus in gene Gh_D13G1792 on chromosome D13. The micronaire phenotype only revealed one highly significant genetic locus at one environmental location, demonstrating a significant genetic by environment component. These loci and candidate causative variant alleles will be useful to cotton breeders for marker-assisted selection with minimal linkage drag and potential biotechnological applications. [ABSTRACT FROM AUTHOR]