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Summary of rare alleles found in Upland cotton accessions grouped in clusters based on STrUCTUre analysis
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Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton. Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag t...
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Context 1
... sequences for all SSr markers are publically available and were obtained from Cotton Marker Database now housed in CottonGen (http:// www.cottongen.org). Supplemental Table S2 includes the list of 135 SSr primers with their repeat motif and chro- mosomal locations as reported in literature. All forward primers were modified by adding a M13 sequence of 19 bases to their 5′end. ...
Context 2
... of the acces- sions included in group 2 were adapted to southeast zone of cotton growing area in the United States and included Sealand accessions and lines from Coker breeding program. Group 2 had highest number of rare alleles (alleles with frequency less than 5 %) detected within a group (Table 2). Group 3 (indicated blue in Fig. 3) mostly included acces- sions from the southwest region of cotton belt representing cotton breeding program for plains cotton. ...
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Citations
... Cultivated cotton shows a fair amount of diversity in growth, morphological, and agronomic traits (Campbell et al., 2010). However, genetic base in cultivated cotton, especially in tetraploid species, is much lower than in wild and landrace accessions of cotton (Campbell et al., 2010;Gowda et al., 2023;Gutierrez et al., 2002;Kaur et al., 2017;McCarty et al., 2018;Tyagi et al., 2014;. This narrow genetic diversity of cotton was due to the initial bottleneck encountered during polyploidization and domestication process and the continuous re-selection of superior germplasms during breeding and broad adoption of transgenic cultivars (Rungis et al., 2005;Van Esbroeck et al., 1999;Wendel et al., 1992). ...
Cotton grown in the United States are day‐length insensitive annuals and are grown under long‐day summers. Photoperiod sensitivity, present in tropical wild and landraces endemic to the center of origin and diversity, is a major barrier for the introgression of tropical gene pool into the US cotton. Previously, we mapped the major photoperiod response locus Gb_Ppd1 on chromosome D06 of Pima cotton (Gossypium barbadense L.). In the current study, an F2 population of 2112 gametes was used to fine map the Gb_Ppd1 locus. Two sequence‐tagged‐site and nine kompetitive allele‐specific polymerase chain reaction (KASP) markers were developed and the Gb_Ppd1 locus was fine mapped to 1.1 cM region flanked by novel markers 17‐KASP‐8, 17‐KASP‐10, and 15‐PR‐10A. The closely linked markers identified 2.10 Mb region in the G. barbadense genome that contained 18 putative gene sequences. A candidate gene Gbar_D06G014560 showed high homology to VASCULAR PLANT ONE ZINC FINGER PROTEIN 1 involved in photoperiodism in Arabidopsis. We evaluated the diagnostic polymorphisms for the flanking markers on a diversity panel of 91 Pima accessions. These markers would be useful in marker‐assisted selection of photoperiod response in cotton breeding. Further, quantitative gene expression analysis indicated that the CONSTANS (CO)/FLOWERING LOCUS T (FT) system is conserved in the photoperiod response pathway in Pima cotton, while CO and FT are likely not the causal genes underlying flowering time at the Gb_Ppd1 locus. The Gb_Ppd1 gene may be an upstream regulatory sequence in the FT gene pathway that controls photoperiodism in photoperiod‐sensitive cotton by affecting the CO/FT interaction under long‐day‐length conditions.
... Considering the genetic vulnerability of modern cotton cultivars to climate change and associated stresses, enhancing the genetic base of breeding populations would benefit cotton breeding programs in developing climate-resilient varieties. As recognized by cotton breeders, variety development programs can be greatly improved through better parental selection for generating segregating populations (Tyagi et al., 2014). For this effort to be successful, the assessment of allelic diversity and population structure and sampling of genetic diversity are the first steps. ...
... Kuraparthy et al. (unpublished data) assembled a cotton diversity panel of 381 accessions of modern and obsolete cotton cultivars released between 1850 and 2005 (Tyagi et al., 2014). These accessions represent more than 100 years of upland cotton breeding and capture the broad genetic diversity available in US cotton. ...
... These accessions represent more than 100 years of upland cotton breeding and capture the broad genetic diversity available in US cotton. The diversity panel was genotyped with 120 genome-wide simple sequence repeats markers to establish the genetic diversity and population structure in tetraploid cotton (Tyagi et al., 2014). Recently, the same research group genotyped the diversity panel with single nucleotide polymorphisms (SNP) markers using 63K Cotton SNP array (Hulse-Kemp et al., 2015) and used it successfully in the genome-wide association studies to genetically map and identify novel genes for leaf shape, fiber quality, yield, abiotic stress tolerance, and bacterial leaf blight resistance (Abdelraheem et al., 2020(Abdelraheem et al., , 2021Andres et al., 2017;Gowda et al., 2022Gowda et al., , 2023. ...
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.
... Intensive selection and repeated use of few germplasm lines as the parental lines in hybridization programs led to the reduced genetic diversity in cotton germplasm pool. As a result, opportunities for improving fiber quality traits in cotton are limited [34]. Therefore, it is necessary to broaden the genetic diversity of cotton by exploring the novel source of genetic variations present in the: primary (viz., landraces and wild tetraploids), secondary (viz., wild diploids), and tertiary gene pools [35]. ...
Natural fibers have garnered considerable attention owing to their desirable textile properties and advantageous effects on human health. Nevertheless, natural fibers lag behind synthetic fibers in terms of both quality and yield, as these attributes are largely genetically determined. In this article, a comprehensive overview of the natural and synthetic fiber production landscape over the last 10 years is presented, with a particular focus on the role of scientific breeding techniques in improving fiber quality traits in key crops like cotton, hemp, ramie, and flax. Additionally, the article delves into cutting-edge genomics-assisted breeding techniques, including QTL mapping, genome-wide association studies, transgenesis, and genome editing, and their potential role in enhancing fiber quality traits in these crops. A user-friendly compendium of 11226 available QTLs and significant marker-trait associations derived from 136 studies, associated with diverse fiber quality traits in these crops is furnished. Furthermore, the potential applications of transcriptomics in these pivotal crops, elucidating the distinct genes implicated in augmenting fiber quality attributes are investigated. Additionally, information on 11257 candidate/characterized or cloned genes sourced from various studies, emphasizing their key role in the development of high-quality fiber crops is collated. Additionally, the review sheds light on the current progress of marker-assisted selection for fiber quality traits in each crop, providing detailed insights into improved cultivars released for different fiber crops. In conclusion, it is asserted that the application of modern breeding tools holds tremendous potential in catalyzing a transformative shift in the textile industry. KEY POINTS Natural fibers possess desirable properties, but they often lag behind synthetic fibers in terms of both quality and quantity. Genomic-assisted breeding has the potential to improve fiber quality traits in cotton, hemp, ramie, and flax. Utilizing available QTLs, marker-trait associations, and candidate genes can contribute to the development of superior fiber crops, underscoring the significance of advanced breeding tools.
... This has allowed for the incorporation of potential candidate genes for various beneficial traits that could not be achieved through traditional methods of crop improvement. The application of genetic engineering in cotton began in 1987 with the development of the first genetically engineered cotton plant for resistance against bollworm [44,112]. Since then, genetic engineering tools have been further utilized to address challenges posed by both biotic and abiotic constraints in cotton. ...
The cotton plant, Gossypium hirsutum L., is one of the four cultivated cotton varieties grown in tropical environments primarily for its natural fiber. Cotton is cultivated by many farmers in Ethiopia as a source of income in both rainfed and irrigated areas. It can also create job opportunities for thousands of individuals. In addition to its fiber, the by-products are utilized for various purposes. Despite these advantages, the production of cotton faces challenges from both biotic and abiotic constraints. Among these, insect pests such as Helicoverpa armigera and Pectinophora gossypiella are significant threats to cotton in Ethiopia, and managing these pests through insecticide spraying is difficult due to their concealed feeding habits. The extensive use of different types of insecticides poses numerous challenges to humans, animals, and the environment. Moreover, these pests have developed resistance to multiple insecticides. Therefore, finding environmentally friendly alternatives for pest control is crucial. However, the limited genetic diversity among cotton germplasms presents a breeding challenge for developing cultivars that can overcome various production constraints. In plant breeding, molecular markers are valuable tools for measuring and identifying economically important traits that are otherwise difficult to assess visually. Molecular markers are essential for plant breeders in the development of cotton cultivars that meet market demands. Additionally, advancements in recombinant DNA technology offer the potential to improve crops with limited genetic diversity, such as cotton. Through genetic engineering, desirable traits such as insect resistance, herbicide tolerance, increased lint strength, length, and fineness can be introduced to cotton, adding value to the crop. This technology can help farmers achieve lower production costs, protect them from hazardous chemical exposure, ensure environmental safety, and maximize potential profits by reducing pest infestation at the early boll formation stage and providing high-quality cotton lint.
... pedigree information [5] and different molecular markers [6][7][8][9][10]. Next-generation sequencing technology makes it possible to generate thousands to millions of SNPs for hundreds of cotton germplasm accessions [2,3]. ...
Upland cotton (Gossypium hirsutum) is the most important plant producing natural fibers for the textile industry. In this study, we first investigated the phenotypic variation of seven agronomic traits of 273 diverse cotton accessions in the years 2017 and 2018, which were from 18 geographical regions. We found large variations among the traits in different geographical regions and only half of the traits in either years 2017 or 2018 followed a normal distribution. We then genotyped the collection with 81,612 high quality SNPs. Phylogenetic tree and population structure revealed a diverse genetic structure of the core collection, and geographical diversification was an important factor, but account for part of the variances of genetic diversification. We then performed genome-wide association study for the seven traits in the years 2017 and 2018, and the average values of each trait in the two years, respectively. We identified a total of 19 significant marker-trait associations and found that Pollen Ole e 1 allergen/extension could be the candidate gene associated with the fall-off cotton bolls from the last three branches. In addition, large variations were observed for the heritability of traits in the years 2017 and 2018. These results provide new potential candidate genes for further functional validation, which could be useful for genetic improvement and breeding of new cotton cultivars with better agronomic performances.
... At the Pee Dee Research and Education Center (PDREC), we had access to 44 of the 53 upland cotton mini-core collection genotypes [46]. For the remaining nine genotypes, insufficient seed was available for propagation. ...
Cotton is an economically important crop. However, the yield gain in cotton has stagnated over the years, probably due to its narrow genetic base. The introgression of beneficial variations through conventional and molecular approaches has helped broaden its genetic base to some extent. The growth habit of cotton is one of the crucial factors that determine crop maturation time, yield, and management. This study used 44 diverse upland cotton genotypes to develop high-yielding cotton germplasm with reduced regrowth after defoliation and early maturity by altering its growth habit from perennial to somewhat annual. We selected eight top-scoring genotypes based on the gene expression analysis of five floral induction and meristem identity genes (FT, SOC1, LFY, FUL, and AP1) and used them to make a total of 587 genetic crosses in 30 different combinations of these genotypes. High-performance progeny lines were selected based on the phenotypic data on plant height, flower and boll numbers per plant, boll opening date, floral clustering, and regrowth after defoliation as surrogates of annual growth habit, collected over four years (2019 to 2022). Of the selected lines, 8×5-B3, 8×5-B4, 9×5-C1, 8×9-E2, 8×9-E3, and 39×5-H1 showed early maturity, and 20×37-K1, 20×37-K2, and 20×37-D1 showed clustered flowering, reduced regrowth, high quality of fiber, and high lint yield. In 2022, 15 advanced lines (F8/F7) from seven cross combinations were selected and sent for an increase to a Costa Rica winter nursery to be used in advanced testing and for release as germplasm lines. In addition to these breeding lines, we developed molecular resources to breed for reduced regrowth after defoliation and improved yield by converting eight expression-trait-associated SNP markers we identified earlier into a user-friendly allele-specific PCR-based assay and tested them on eight parental genotypes and an F2 population.
... Some of the studies included specific breeding programs such as the Pee Dee program (Billings et al. 2021) or Acala program (Zhang et al. 2005). The majority of the studies were focused on the cultivated types (Tyagi et al. 2014) or the landraces (Kaur et al. 2017). Further, many of these early studies used less polymorphic PCR-based markers (Ditta et al. 2018;Zhu et al. 2019b). ...
... A total of 663 accessions of G. hirsutum were used for the genetic diversity analysis and genome-wide association studies (GWAS) of the photoperiod response trait. These include 382 elite Upland cotton germplasm (DIV panel) (Tyagi et al. 2014), 185 tropical landrace accessions (TLA panel) (Kaur et al. 2017), and a set of 96 Upland cotton accessions from the cotton breeding program (FB panel) at the University of Arkansas. The DIV panel represents the major portion of genetic diversity of the US and consists of released Upland cultivars and breeding lines from over 13 different states of the USA from the 1900s to 2005 ( Supplementary Fig. 1a, b). ...
... The high IBS similarity of 0.80 in FB panel accessions could be attributable to common parentages in the pedigree of Dr. Bourland's Upland breeding program. Nei's genetic distance estimated in the DIV panel of the current study using SNPs (0.195) was similar to the previous estimates using SSR markers (Tyagi et al. 2014;Zhang et al. 2005). However, the landraces panel showed significantly higher Nei's genetic distance value (0.23). ...
Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton.
Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of Gossypium hirsutum L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (FST) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest FST values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including Transcription factor Vascular Plant One-Zinc Finger 1 (VOZ1) and Protein Photoperiod-Independent Early Flowering 1 (PIE1) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.
... Among the various marker systems presently available, microsatellite or simple sequence repeat(SSR) markers have become more valuable and reliable tool for genetic diversity analysis of crop varieties [11] owing to their reproducibility, co-dominant inheritance, genome-wide presence, robustness, higher polymorphism and analytical simplicity. "Molecular data generated from SSR markers has also been utilized for QTL mapping, DNA fingerprinting and genetic purity testing" [12,13]. ...
Genetic diversity was assessed for 2 popular varieties and 5 promising lines of rabi sorghum by using11 SSR markers. The marker Xiabt312 reported 100% polymorphism rate followed by Xtxp15 (85.70%) and mSbCIR300 (85.71%). The sorghum varieties studied for this analysis showed the polymorphism information content (PIC) ranged from 0.25 to 0.87 with a mean of 0.67 indicates higher diversity within them. Clustering analysis based on the genetic dissimilarity grouped the 7 lines into 2 major and 4 sub clusters and grouping was in good agreement with pedigree. Cluster II was the largest cluster with 4 genotypes followed by cluster I with 3 genotypes. The rabi sorghum genotypes viz., M35-1, RSV-1876 and RSLG-2422 were placed in cluster I and Phule Anuradha, RSV-2371, RSV-1910 and RSV-1988 placed in cluster II. Clustering based on SSR molecular profile of the genotypes shows that there is a distinct variability among the genotypes under this study. The selected markers have great potential in DNA fingerprinting in sorghum which in future could be integrated with DUS data descriptors for effective cultivar identification and differentiation.
... This may even cause a loss of time for subsequent studies [16]. The solution is to record genetic diversity using genetic markers, which are not affected by space and time and can measure allele frequencies directly [17][18][19]. Molecular markers are used extensively in determining genetic diversity. ...
... Of the 47 cotton genotypes used, only 30 were identified as pure in this case. According to the number in Table 1, genotypes 1, 3,5,6,7,9,10,11,13,15,17,18,19,20,21,22,23,24,25,27,29,30,31,32,33,34,36,38,40 and 41 were considered pure. ...
... Of the 47 cotton genotypes used, only 30 were identified as pure in this case. According to the number in Table 1, genotypes 1, 3,5,6,7,9,10,11,13,15,17,18,19,20,21,22,23,24,25,27,29,30,31,32,33,34,36,38,40 and 41 were considered pure. The groupings according to the blotting technique are also shown in Figure 4. ...
Cotton is a major source of natural fibre for the global textile industry and is also an important oilseed crop. Cotton fibre is the main source of textiles, the seeds are used for oil and the remaining bagasse is used as high-protein animal feed. In addition, cotton’s so-called short fibre is used in more than 50 industries. Cotton breeding is generally based on crossing the best yielding and fibre quality genotypes. However, cotton breeding programmes are negatively affected by the narrow genetic diversity of varieties. It is for this reason that the identification of genetic resources and the disclosure of genetic diversity are so important. Here, the genetic diversity of G. hirsutum and G. barbadense genotypes was determined using high-resolution capillary gel electrophoresis. Using 19 EST-SSR markers, a total of 47 genotypes were screened. The PIC values of the markers used ranged from 0.268 to 0.889. The mean PIC value was calculated to be 0.603. In terms of clustering, PCoA and population structure analyses gave similar results, and the genotypes could be divided into three main groups. Genetic admixture with G. hirsutum was found in some genotypes of the G. barbadense species. We can conclude that (i) the EST-SSR markers used in this study are effective in the determination of genetic diversity, (ii) the genetic diversity should be increased through the collection of genetic resources and (iii) the genetic EST-SSR markers in this study should be considered in breeding programmes by using them in QTL studies.
... Given these challenges, cotton cultivars with an annual/determinate growth habit, optimal flowering time, and compact architecture are needed to minimize yield and economic losses. To dissect the genetics of these interrelated traits, i.e., perennial vs. annual growth habit, determinate vs. indeterminate growth, and regrowth after defoliation, we evaluated the Upland cotton mini-core collection of 44 genotypes [44] for the expression pattern of five floral induction and meristem identity genes, FT, SOC1, LFY, API, and FUL. ...
... We performed population structure analysis to estimate the genetic diversity among 44 Upland cotton genotypes of the mini-core collection and used the marker data set to investigate the relationship of the mini-core collection with the core collection of 382 accessions [44]. The analysis revealed seven population groups indicating that the mini-core collection had genes from seven different populations, reflecting the level of diversity among 44 Upland cotton genotypes. ...
... investigate the relationship of the mini-core collection with the core collection of 382 accessions [44]. The analysis revealed seven population groups indicating that the mini-core collection had genes from seven different populations, reflecting the level of diversity among 44 Upland cotton genotypes. ...
Cotton (Gossypium spp.) is the primary source of natural textile fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an Upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time, and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified molecular markers associated with the gene expression traits via genome-wide association analysis using a 63 K SNP Array. Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed associations with expression traits. Of these 396 markers, 159 were mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated.
