Cotton Breeding Programs Research Articles

Factors responsible for yield improvement in new Gossypium hirsutum L. cotton cultivars

The factors responsible for yield progress can be analysed through yield determinant frameworks. These conceptual models consider factors such as crop growth dynamics, partitioning of vegetative and reproductive biomass and yield components to provide insights into the factors responsible for observed genetic gains and opportunities for future gains. The aim of this study was to use direct cultivar comparison to assess the rate of genetic gain in the CSIRO (Australia) cotton breeding program, and to understand how factors within a conceptual yield determinant framework relate to yield performance. Using field experimentation, yield progress of 16.1 kg lint ha−1 y−1 was observed in ten cultivars released between 1968 and 2012. This study identified that selection pressure has resulted in improvements in total dry matter (TDM), harvest index (HI), lint percentage and carbon assimilation. While gains have been made in these four parameters, improvements in lint yield have largely been driven by altering HI through increasing lint percentage. Although improvements have been made in TDM, the reproductive allocation of total biomass and the amount and efficiency of light capture has not been altered in modern cultivars. Future gains in lint yield will require the concurrent maintenance of harvest index while producing larger plants with more fruiting branches that capture more incident radiation with increased efficiency. As the collection of phenotype data such as biomass, boll number, boll size and radiation use efficiency at the scale required in a commercial breeding program is largely aspirational, we conclude in the short term improvements may be achieved through direct selection for yield. Future efforts should be placed in increasing early season growth rates, and in the longer term enhancing carbon assimilation rates. Importantly, due to trait associations and the effects of trade-offs between functional components, factors within a conceptual framework must not be considered in isolation.

ESTIMATES OF GENETIC PARAMETERS FOR SELECTION OF COLORED COTTON FIBER1

ABSTRACT Naturally-colored cotton fiber has received attention from breeding programs in the semiarid region of northeastern Brazil due to an increased interest in its fibers. Therefore, this study aimed to select genotypes of colored cotton fiber for agronomic and technological fiber characteristics for the Brazilian semi-arid conditions. The experiment was carried out in two environments (Patos-PB and Apodi-RN) in Brazil during the 2016 growing season. The experimental design was in randomized blocks with four replications. Treatments consisted of eleven colored fiber genotypes and three controls (BRS Topázio, BRS Rubi, and BRS Verde). The following traits were assessed: seed cotton yield (SCY, kg ha-1), lint percentage (LP, %), lint length (LEN, mm), lint strength (STR, gf tex-1), and lint micronaire (MIC, µg in-1). The data were submitted to individual and joint variance analyses, and means were grouped by the Scott and Knott (1974) test at 0.05 probability. Genotypes showed variability in all traits, which allows genetic gains in subsequent cycles of selection. The genotypes BRS Topázio, CNPA 2002 10245, and CNPA 2002 10327 presented the best estimates for the assessed traits, thus they can be selected for future studies in cotton breeding programs in the semiarid region.

Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement.

Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs.

Registration of CA 4007 cotton germplasm line for water‐limited production

AbstractIncreasing demands for irrigation and declining water availability are becoming critical issues in the Texas High Plains, the primary cotton (Gossypium hirsutum L.) growing area of the United States. Developing breeding lines suitable for water‐limited production is an important objective of the Texas A&M AgriLife Research cotton breeding program in Lubbock. CA 4007 cotton germplasm (Reg. no. GP‐1062, PI 691459) was derived from a 1993 cross of Verhalen V83‐116 with CA 2159, informal historical releases developed by cotton breeding programs at Oklahoma State University and Texas A&M AgriLife Research in Lubbock, respectively. Performance testing for yield, fiber quality, and other related agronomic properties was conducted in rainfed and irrigated conditions during the 2007, 2008, and 2009 growing seasons. Based on yield performance and other agronomic properties, CA 4007 was included in experiments to evaluate cotton genotypes’ response to moisture stress and its impact on yield, fiber quality, and other agronomic traits. Results indicate that CA 4007 germplasm developed from lines released in two southwestern United States public breeding programs produced good yield and fiber quality under water‐limited production across several growing seasons when compared to commercial production check cultivars in the Texas High Plains.

EVALUATION OF COTTON (GOSSYPIUM SPP.) GERMPLASM FOR HEAT TOLERANCE UNDER NORMAL AND LATE PLANTING TIME

The objective of this study was to determine cotton (Gossypium ssp.) germplasm for heat tolerance under normal and late planting time. For this aiming 200 cotton genotypes and five check varieties (Gloria, SG 125, Flash, Ozbek 105 and Candia) were evaluated under two different temperature regimes and experiments were conducted according to the augmented design with four blocks. Field studies were carried out at the GAP International Agricultural Research and Training Center’s experimental area in Diyarbakır, Turkey, in 2016 cotton growing season. In the study heat susceptibility index was used for discriminate to the genotypes for heat tolerance. Genotypes were classified into four groups based on the heat susceptibility index. The results of this study indicated that five cotton genotypes (TAM 139-17 ELS, CIM-240, Haridost, MNH-990 and AzGR-11835) were in highly heat tolerant, 28 genotypes were found heat tolerant, 56 genotypes were in the moderately heat tolerant and other 120 genotypes were observed susceptible for heat tolerance. Based on the heat susceptibility index, five cotton genotypes can be used as parent for heat tolerance improvement in the cotton breeding program where high temperature is a limiting factor for seed cotton yield.

Merging of Plant Breeding and Pathology: A History of Cotton Breeding at Auburn

Understanding the focus and history of a breeding program allows fellow researchers to build upon prior knowledge and helps determine the best expertise for specific objectives. To date, the cotton-breeding program at Auburn University has had a series of breeders that have worked directly with a plant pathologist. Homer Tisdale, the program’s first breeder, was hired in 1913 with the goal of Fusarium wilt (FOV) resistance, a focus that was destined to become fundamental to the program. With the discovery of a "hot" field in Tallassee, Alabama, the program soon combined cotton variety testing and FOV screening tests. This led to the release of the most iconic variety of the program – Auburn 56 and characterizing of the relationship between root knot nematode and FOV. In 1965, the program shifted to a USDA cotton genetics project, led by R.L. Shepherd, who refined screening techniques and identified multiple sources of root knot nematode resistance. He released 40 cotton breeding lines, the most in the program’s history, which ended in 1984 when the USDA lab was moved to Mississippi. In the late 1990’s, breeder David Weaver joined a region-wide effort to investigate reniform nematode resistance. The current program, led by Jenny Koebernick, has a large emphasis on disease resistance. In 2019, attention shifted to identifying sources of resistance for the cotton leaf roll dwarf virus, collaborating directly with plant pathologists and entomologists. Overall, the greatest contribution of the program has been the synergy created between breeding and pathology that has helped advance cotton resistance to nematodes, fusarium wilt and bacterial blight.

Genetic parameters and path analysis of traits of upland cotton for the brazilian semi-arid region

Upland cotton fiber is one of the most used natural fibers in the production of textile materials worldwide. For this reason, the selection of genotypes that meet the industry’s requirements is one of the main goals of cotton breeding programs. This study aimed to estimate the phenotypic and genotypic correlations among fiber traits and identify the direct and indirect effects of these traits on seed cotton yield of upland cotton genotypes in the semi-arid Brazilian Northeast. This study assessed 21 upland cotton genotypes from a complete diallel cross without reciprocals. The design was randomized blocks, with three replications and 21 treatments. The experiment was conducted in the municipality of Patos - PB, in 2015. The statistical analysis consisted of analysis of variance by the F test, phenotypic and genotypic correlation analysis, and path analysis. The studied materials revealed genetic variability for all traits. Path analysis has shown that the traits fiber elongation, fiber strength, and fiber fineness have a direct positive effect on seed cotton yield.

Estimation of Protein and Fatty Acid Composition in Shell‐Intact Cottonseed by Near Infrared Reflectance Spectroscopy

AbstractRapid and accurate analysis of cottonseed protein content and the composition of fatty acids (especially, saturated fatty acids) is often required in cotton production and breeding programs. This study aimed to establish a set of effective estimation models for these parameters. Near infrared reflectance spectroscopy (NIRS) calibration equations using partial least‐squares regression for protein concentration, oil concentration, and five fatty acids of shell‐intact cottonseeds were established based on 90 varieties, and the prediction abilities of the calibration models were verified using 45 other varieties. The prediction abilities of the NIRS calibration equations were basically consistent with external validation results. Each equation was assessed based on the ratio of performance to deviation (RPDp). Protein content and seed total fatty acid (STA) content had high RPDp values (3.687 and 3.530, respectively), whereas cottonseed kernel total fatty acid (KTA) content, linoleic acid (18:2), stearic acid (18:0), myristic acid (14:0), and palmitic acid (16:0) exhibited relatively high RPDp (2.866, 2.836, 2.697, 2.676, and 2.506, respectively). The calibration model for oleic acid (18:1) had a low RPDp (1.945). The results indicated that NIRS can be used to rapidly determine contents of STA, KTA, protein, stearic acid (18:0), myristic acid (14:0), and palmitic acid (16:0) in shell‐intact cottonseed.

Evaluation of the genetic diversity of fibre quality traits in upland cotton (Gossypium hirsutum L.) inferred from phenotypic variations

BackgroundEvaluating phenotypic traits is very important for the selection of elite lines in Gossypium hirsutum L. Cotton breeders are interested in using diverse genotypes in hybridization that can segregate for traits of interested with the possibility of selection and genetic gain. Information on phenotypic and molecular diversity helps the breeders for parental selection.MethodsIn this study, 719 global collections of G. hirsutum L. were evaluated for five fibre-related traits during two consecutive years in eight different environments. A series of phenotypic data for fibre quality traits were obtained and the elite accessions were further screened using principal component analysis and phylogenetic tree construction based on single nucleotide polymorphism markers.ResultsWe found that fibre quality traits showed a wide range of variation among the G. hirsutum accessions over 2 years. In general, accessions from outside China tended to have higher fibre length (FL) and fibre strength (FS) than did Chinese accessions. Among different regional accessions in China, North/Northwest accessions tended to have the highest FL, FS and best fibre macronaire. By assessing five fibre quality traits over 2 years with genotypic data, 31 elite germplasms reaching double-thirty quality values (FL ≥ 30 mm and FS ≥ 30 cN·tex− 1) were selected.ConclusionsThis study provided a detailed phenotypic diversity description of a population representing a wide range of upland cotton germplasm. Our findings provide useful information about possible elite fibre quality parents for cotton breeding programs.

Registration of Four Germplasm Lines of Upland Cotton with High Fiber Quality

Four upland cotton (Gossypium hirsutum L.) germplasm lines, NC18‐11 (Reg. no. GP‐1056, PI 690771), NC18‐12 (Reg. no. GP‐1057, PI 690772), NC18‐13 (Reg. no. GP‐1058, PI 690773), and NC18‐14 (Reg. no. GP‐1059, PI 690774), were developed by the Department of Crop and Soil Sciences at North Carolina State University. These four cotton lines had improved fiber quality traits and exhibited 915.5 to 1180.9 kg ha−1 lint yield. All four lines were derived from a random mated population using multiple parental lines. The four lines were compared with commercial cultivars ‘DP393’, ‘Sure‐Grow 747’, and ‘UA48’ over 2 yr using a replicated randomized complete block design in Clayton, NC. Lines NC18‐11, NC18‐12, and NC18‐13 had significantly (p = 0.05) better micronaire values than the checks and significantly higher strength values (8.3–25.3%) than DP393, Sure‐Grow 747, and the parental lines. These three lines also had significantly (p = 0.05) greater upper half mean length values (4.9–11.6%) than DP393 and Sure‐Grow 747. Germplasm line NC18‐14 had a 15.4 to 62.5% significantly (p = 0.05) higher fiber elongation value than all checks and parental lines and showed 5.0 to 12.8% more lint fraction than the checks. These lines could be additional sources of genetic variability for cotton breeding programs focusing on improving fiber quality traits while still producing more than 900 kg ha−1 of lint.

Flavonoid accumulation in spontaneous cotton mutant results in red coloration and enhanced disease resistance

Cotton, the leading natural fiber, is cultivated worldwide, but its production is seriously threatened by pathogens. Accordingly, the selection of resistant cultivars has become a key priority of cotton breeding programs. In this study, a spontaneous mutant with red coloration (S156) and a control cultivar (S78) were used as experimental materials for a comparative analysis. Metabolomic analysis revealed the enrichment of flavonoids in S156 leaves compared with S78 leaves, and transcriptomic analysis revealed the upregulated expression of flavonoid biosynthesis genes in S156 leaves relative to S78 leaves. In addition, the red mutant showed a significantly increase in resistance to Verticillium dahliae, a fungal pathogen that poses a major threat to cotton production. The pathogen invasion process was suppressed in the red cotton cultivar. This study reveals the mechanism underlying the red coloration of S156 cotton and indicates the great potential of red cotton in pathogen- and insect-resistant breeding of cotton.

Rapid Isolation of Loss‐of‐Function Mutations for Dominant Traits: A Case Study Using Photoperiod Sensitivity Trait in Pima Cotton

In its natural state, cotton (Gossypium spp.) is a perennial that flowers only under short‐day conditions. Early selection efforts eliminated this photoperiod requirement, allowing cotton cultivation to shift predominantly to annual growth under long summer daylengths throughout the world. Photoperiod sensitivity persists in many wild cottons and remains a major barrier to the introgression of beneficial alleles into elite breeding material. Identification of the variation and genetic factors underlying photoperiod response in cotton is needed to fully harness the genetic diversity of wild cotton and broaden the cultivated germplasm pool. Genetic variants, especially loss‐of‐function mutations in dominant genes conferring photoperiod sensitivity, would be highly valuable in this regard. After mutagenizing pima cotton (G. barbadense L.) seeds heterozygous for the major photoperiod response gene Gb_Ppd1 with γ rays, we identified plants no longer sensitive to photoperiod. Genetic analysis of BC1F1 plants derived from backcrossing the mutants with their photoperiod‐insensitive parent confirmed the loss‐of‐function mutations were allelic with Gb_Ppd1. Characterization of the mutants with molecular markers confirmed that all but one were deletions of Gb_Ppd1. Further, genotyping localized Gb_Ppd1 to a 12‐Mb region on chromosome D10. The newly identified genomic region and loss‐of‐function mutants may help assist with the identification and functional validation of candidate genes for photoperiod response in cotton, facilitating the valuable introgression of genetic diversity into cotton breeding programs.

A high density SLAF-seq SNP genetic map and QTL for seed size, oil and protein content in upland cotton

BackgroundCotton is a leading natural fiber crop. Beyond its fiber, cottonseed is a valuable source of plant protein and oil. Due to the much higher value of cotton fiber, there is less consideration of cottonseed quality despite its potential value. Though some QTL controlling cottonseed quality have been identified, few of them that warrant further study are known. Identifying stable QTL controlling seed size, oil and protein content is necessary for improvement of cottonseed quality.ResultsIn this study, a recombinant inbred line (RIL) population was developed from a cross between upland cotton cultivars/lines Yumian 1 and M11. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to construct a genetic map that covered 3353.15 cM with an average distance between consecutive markers of 0.48 cM. The seed index, together with kernel size, oil and protein content were further used to identify QTL. In total, 58 QTL associated with six traits were detected, including 13 stable QTL detected in all three environments and 11 in two environments.ConclusionA high resolution genetic map including 7033 SNP loci was constructed through specific locus amplified fragment sequencing technology. A total of 13 stable QTL associated with six cottonseed quality traits were detected. These stable QTL have the potential for fine mapping, identifying candidate genes, elaborating molecular mechanisms of cottonseed development, and application in cotton breeding programs.

Assessing the Breeding Potential of Thirteen Day‐Neutral Landrace Accessions in an Upland Cotton Breeding Program

ABSTRACTAn untapped genetic resource available to cotton (Gossypium hirsutum L.) breeding programs is represented by the primitive, upland cotton landrace collection. Primarily due to their photoperiodic nature, efforts to utilize these resources have been slow. To complement efforts to develop day‐neutral converted germplasm lines, we identified a number of naturally occurring day neutral landrace genotypes and evaluated their breeding potential when crossed to elite upland germplasm lines and cultivars. The mean performance of parental lines and F2 hybrids along with genetic effect estimates indicate that naturally occurring day‐neutral landrace genotypes provided average agronomic performance while increasing fiber quality performance. Results suggest that crosses derived from naturally occurring day‐neutral genotypes and elite upland lines result in new allelic combinations that interact in both an additive and nonadditive way. However, it appears that several naturally occurring day‐neutral genotypes transmit negatively correlated alleles for agronomic performance and fiber quality that often display opposite additive and nonadditive effects. These negatively correlated allele combinations present a major challenge for cotton breeding programs. Future efforts that determine the percentage of “new” alleles present in the landrace germplasm, along with innovative breeding methods focused on efficiently capturing beneficial alleles, are needed to expand the cotton genetic base.

Genomic analysis of marker-associated fiber development genes in upland cotton (Gossypium hirsutum L)

Understanding genetic control of fiber development is essential for cotton improvement. This study analyzed several thousand fiber Unigenes in Upland cotton (Gossypium hirsutum). They included 2423 Unigenes for fiber initiation (IN), 1841 for fiber elongation (EL) and 86 for secondary cell wall deposition (SCWD). These Unigenes were located on recombination hotspots between At and Dt subgenomes with nearly equal frequency (51% vs. 49%). Sequence analysis with Upland cotton TM-1 genome assembly showed that 477 IN, 464 EL, 20 SCWD and 367 non-fiber Unigenes intersect with predicted coding sequences. There were 140 IN, 118 EL and one SCWD Unigenes that do not overlap between individual stages of fiber development. Annotation of top scoring Unigenes with Kyoto encyclopedia of genes and genomes indicated mitochondrial biogenesis for IN Unigene #18205, conversion of PRPP to histidine for IN #25329, and spliceosome pathways for IN #24380. EL Unigene #11669 appeared to be responsible for septum site-determining protein, EL #11916 for vacuolar protein, and EL #17251 for protein trichome birefringence-like 33. One SCWD Unigene #190099 was responsible for legumin A-like protein. In addition, Unigene #03070 overlapped three fiber development stages and involved in fatty acid biosynthesis. Unigenes that shared same genomic positions for all fiber stages are of particular interest as they may have possible pleiotropic function. On the other hand, Unigenes from one fiber development stage that did not share with any other stage may have stage-specific function. This information would be useful for plant breeders to exploit fiber genes in cotton breeding programs.

Development of the correction procedure for High Volume Instrument elongation measurement

Cotton spinning mills need high-quality fibers to maintain their manufacturing efficiency. Machinery throughput is increasing and it could translate into more processes with higher breaking stress. Consequently, more fibers are susceptible to breaking or damage. To face this problem, breeders must develop new varieties whose fibers can better withstand this mechanical stress. The main tool utilized in cotton breeding programs is the High Volume Instrument (HVI), which reports in a short time measurements such as micronaire, length, color, and strength. This instrument can also determine fiber elongation, but there is no current correction method for it. Both elongation and strength factor into the work-to-break of fibers, which plays a direct role in fiber breakage and spinning performance. The objective of this work was to develop cotton elongation standards, devise a correction procedure for HVI lines, evaluate measurement stability, and validate these results with a set of independent samples. Two commercial bales, one with low and one with high HVI elongation, were identified as potential elongation standards. The potential standards were produced and evaluated. After validation, they were used to correct HVI lines against Stelometer (STrength-ELOngation-METER) measurements. An independent set of samples was tested on corrected HVIs to confirm the effectiveness of the elongation corrected measurements. The HVI data were at least as good as the Stelometer data, with increased data acquisition speed and precision. This research can help cotton breeders to improve fiber elongation and strength at the same time, resulting in better fibers for yarn spinning.

A novel variant of Gh_D02G0276 is required for root-knot nematode resistance on chromosome 14 (D02) in Upland cotton.

MAGIC population sequencing and virus-induced gene silencing identify Gh_D02G0276 as a novel root-knot nematode resistance gene on chromosome 14 in Upland cotton. The southern root-knot nematode [RKN; Meloidogyne incognita (Kofoid & White)] remains the primary yield-limiting biotic stress to Upland cotton (Gossypium hirsutum L.) throughout the southeastern USA. While useful genetic markers have been developed for two major RKN resistance loci on chromosomes 11 (A11) and 14 (D02), these markers are not completely effective because the causative genes have not been identified. Here, we sequenced 550 recombinant inbred lines (RILs) from a multi-parent advanced generation intercross (MAGIC) population to identify five RILs that had informative recombinations near the D02-RKN resistance locus. The RKN resistance phenotypes of these five RILs narrowed the D02-RKN locus to a 30-kb region with four candidate genes. We conducted virus-induced gene silencing (VIGS) on each of these genes and found that Gh_D02G0276 was required for suppression of RKN egg production conferred by the Chr. D02 resistance gene. The resistant lines all possessed an allele of Gh_D02G0276 that showed non-synonymous mutations and was prematurely truncated. Furthermore, a Gh_D02G0276-specific marker for the resistance allele variant was able to identify RKN-resistant germplasm from a collection of 367 cotton accessions. The Gh_D02G0276 peptide shares similarity with domesticated hAT-like transposases with additional novel N- and C-terminal domains that resemble the target of known RKN effector molecules and a prokaryotic motif, respectively. The truncation in the resistance allele results in a loss of a plant nuclear gene-specific C-terminal motif, potentially rendering this domain antigenic due to its high homology with bacterial proteins. The conclusive identification of this RKN resistance gene opens new avenues for understanding plant resistance mechanisms to RKN as well as opportunities to develop more efficient marker-assisted selection in cotton breeding programs.

Accuracy, Precision, and Harvesting Efficiency of a Cotton Plot Picker Installed with an Automatic Weighing System in a Cotton Breeding Program

Many cotton breeding programs in the U.S. have installed an automatic weighing system in a cotton plot picker to increase operating efficiency in recent years. However, no experimental data are available to document the reliability of such a system. The objective of this study was to evaluate the accuracy, precision, and harvesting efficiency of a two-row cotton plot picker installed with an automatic weighing system with two scales based on results from replicated field tests from 2013 to 2016. Three tests each year, each containing 32 genotypes were arranged in a randomized complete block design in two-row plots by 10 m in length. The 2013 to 2015 results showed a highly significant positive correlation in seedcotton weights between the two rows of the same plot for each genotype harvested and weighed by the two scales in the picker, indicating that the two scales are consistent and reliable. In three tests in 2016, one row of each two-row plot was harvested by the picker, and seedcotton weight was compared with another row harvested by hand. A highly significant positive correlation was detected between the two harvesting methods that had similar coefficients of variation (16.14% for hand harvest vs. 16.90% for mechanical harvest). The two-row plot picker harvested a total of 368 single-row plots (10-m long) in six hours daily, whereas hand harvest by one person averaged two plots in four hours. An average of 417 kg ha-1 was lost due to the mechanical harvest.

Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints.

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

Genomic divergence in cotton germplasm related to maturity and heterosis.

Commercial varieties of upland cotton (Gossypium hirsutum) have undergone extensive breeding for agronomic traits, such as fiber quality, disease resistance, and yield. Cotton breeding programs have widely used Chinese upland cotton source germplasm (CUCSG) with excellent agronomic traits. A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles. Here, we analyzed 10,522 high-quality single-nucleotide polymorphisms (SNP) with the CottonSNP63K microarray in 137 cotton accessions (including 12 hybrids of upland cotton). These data were used to investigate the genetic diversity, population structure, and genomic characteristics of each population and the contribution of these loci to heterosis. Three subgroups were identified, in agreement with their known pedigrees, geographical distributions, and times since introduction. For each group, we identified lineage-specific genomic divergence regions, which potentially harbor key alleles that determine the characteristics of each group, such as early maturity-related loci. Investigation of the distribution of heterozygous loci, among 12 commercial cotton hybrids, revealed a potential role for these regions in heterosis. Our study provides insight into the population structure of upland cotton germplasm. Furthermore, the overlap between lineage-specific regions and heterozygous loci, in the high-yield hybrids, suggests a role for these regions in cotton heterosis.