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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. [ABSTRACT FROM AUTHOR]

The Turkestan region is a cotton-growing zone in South Kazakhstan, but also the northernmost cotton-growing area in the world. Annually, medium-staple cotton (Gossypium hirsutum L.) cultivation occurs on 115,000-125,000 ha, with 80,000-85,000 ha grown in the Districts of Maktaaral and Zhetysay, Kazakhstan. This region is highly susceptible to salinity, drought, invasion of dangerous pests (cotton budworm, beet borer, spider mites, and aphids), and diseases (fusarium blight [wilt] and gummosis). An extremely high salt content and aridity in the arable soil are the main limiting factors of that region, hence, genotype selection through genetic principles is the most effective and economical way to reduce their negative impacts on vegetation. Therefore, the research on developing resistant cotton cultivars suitable for such soil and climatic conditions is most relevant. Considering the above situation, assessment of newly developed high-yielding cotton cultivars with fiber quality of types III-IV for tolerance to heat and drought, salinization, and pests and diseases ensued during 2019, 2020, and 2021 at the Agricultural Experimental Station of Cotton and Melon Growing, Atakent, Kazakhstan. Their promising cotton genotypes resulted from strains developed through intraspecific and interspecific diallel hybridization. The newly developed eight cotton cultivars, grown on more than 92% of the hectarage in the Southern region of Kazakhstan, are PA-3031, PA-3044, M-4005, M-4007, M-4011, Bereke-07, Myrzashol-80, and M-4017. [ABSTRACT FROM AUTHOR]

Four yield traits and five fiber quality traits of their 298 varieties (lines) and their 884 F2 crosses of upland cotton were analyzed for their additive and dominance effects by a genetic model with additive, dominance, and their interaction effects with the environment in two successive years in Alar, South Xinjiang. To explore the potential of the breeding and utilization value of varieties, all varieties were clustered using cluster analysis of the R software package based on the additive and dominance effects. The results indicated that under the high-density planting mode of "low plant growth (plant height: 0.8-1.0 m), high density (225,000-300,000 plant hm-2), early ripe and film cover" in southern Xinjiang province, the additive effects of 298 parents were divided into 12 groups. The average additive effects of yield and fiber quality traits of 23 varieties (lines) in the sixth group were in a good level. It was easy to obtain offspring with both yield (except lint percentage) and fiber quality traits through crossing between these varieties (lines). The eighth group had a better average additive effect on fiber quality traits, while the fourth group had a higher average additive effect on yield traits. The progeny with complementary yield and fiber quality traits could be obtained by crossing these two kinds of varieties. The dominance effects of 298 parents were divided into nine groups. The eighth group included eight varieties (lines) and their yield traits and fiber quality traits (except micronaire) were all at a better average level in dominance effect, indicating that could be used as parents for hybrid utilization of both yield traits and fiber quality traits. The average dominance effect of yield traits was higher in the eighth category, and the average value of dominance effect of fiber quality traits in the third group was higher. [ABSTRACT FROM AUTHOR]

Background: Cotton is a vital fiber crop fulfilling global demands for raw materials in the textile sector. Therefore, high-yielding cultivars with superior-quality traits are desired at regional scales. The high-yielding cultivars can be selected by determining their responses to various environmental conditions at different locations over a short or long period. Genotypes, environment, and year significantly alter seed cotton yield and fiber quality. Therefore, determining the response to various environmental conditions is necessary for selecting high-yielding cultivars with superior fiber quality. Methods: This study determined the yield and fiber quality traits of 3 cotton cultivars (i.e., ‘DP396′, ‘BA440′ and ‘Teksa 415′) at five different locations (i.e., Tepe, Boztepe, Bozçalı, Köseli and GAP International Agricultural Research and Training Center) in southeastern Anatolia, Turkey for 3 years (2019, 2020, and 2021). Data relating to seed cotton yield and fiber quality traits were collected and relationships of these traits were determined by biplot analysis. Results: Cultivars × traits relationship indicated that ‘DP396′ was the most stable cultivar with the highest seed cotton yield. Similarly, ‘BA440′ cultivar was associated with quality characteristics. Sector analysis divided the yield and quality traits into three different groups. The locations × traits relationship indicated that the examined traits differed according to the locations. Tepe location was in the center in terms of quality and seed yield, whereas Bozçalı location had superior quality traits. Likewise, Boztepe location resulted in higher values ​​ of seed and fiber yield, and number of bolls per plant. The studied characteristics varied among the years, and higher values of seed and fiber yields, and the number of bolls per plant were recorded during 2019. On the other hand, superior fiber quality traits were noted during 2021. Conclusions: It is concluded that ‘DP396′ was the most stable cultivar for seed cotton yield, whereas ‘BA440′ was stable for quality traits. Therefore, these cultivars can be used in the studied locations to increase yield and fiber quality. Furthermore, these cultivars could be utilized in the breeding programs for developing high-yielding and better fiber quality producing genotypes in the future.

Understanding genotype-environment interactions and trait relationships is pivotal for guiding breeding efforts aimed at stabilizing cotton varieties across diverse environments while boosting yield and fiber quality. The study aimed to assess genotypic variability and stability in 10 agronomic and fiber quality traits across four environments (Anyang in 2020 and 2021 and Weixian in 2020 and 2021) for three parental lines (ZR014121, CCRI60, and EZ60) and their corresponding 498 recombinant inbred lines (RILs) populations. The results indicated that the analysis of variance showed significant genotype and genotype-by-environment effects for all measured traits. Analysis of correlation revealed highly significant positive correlations between seed cotton yield and each of boll weight (r = 0.95), lint yield (r = 0.90), and between boll weight and lint yield (r = 0.90), while highly significant negative correlations were noticed between fiber maturity and fiber elongation (r = −0.52) and between fiber length and lint percentage (r = −0.38). Furthermore, the weighted average of absolute scores (WAASB) was calculated for each trait, revealing moderate to high stability for some yield traits and fiber quality parameters. Also, the multi-trait stability index (MTSI) applied to these RILs populations identified G13 as the most stable line (MTSI = 5.5) and S23 as the least stable (MTSI = 12.1). Selecting 25 RILs with the lowest MTSI values (5.5–6.47) revealed elite stable lines with favorable trait values, providing a valuable genetic resource for developing high-performance cotton cultivars in diverse environments. • The stability of cotton varieties was revealed across diverse environments. • Seed cotton yield correlated positively with boll weight and lint yield. • WAASB and MTSI demonstrate robust analyses of genotypic variability and stability. • The study provides insights into stable line identification and trait interactions. [ABSTRACT FROM AUTHOR]

The recombinant inbred lines of inter-specific cross, Gossypium hirsutum cv. DS-28 × G. barbadense cv. SBYF-425 was evaluated in three consecutive rainy seasons of 2017–18 (F13), 2018–19 (F14) and 2019–20 (F15) in an augmented design. The preponderance of huge continuous variability for both productivity and fiber quality traits was recorded. The principal component analysis revealed that the mapping population was well suited for mapping of productivity and fiber quality traits. On the basis the Z-scores for skewness and kurtosis, 178 RILs with normal distribution were selected for genetic linkage mapping. A high-density saturated linkage map was constructed using SNP arrays of CottonSNP63K, an Illumina's infinium array and CottonSNP50K, CSIR-National Botanical Research Institute's Axiom array with a total spanned length of 2402.65 cM, an average marker density of 1.54 and with map coverage of 96.99% of the reference genome. The developed genetic map of inter specific cross of Indian cotton varieties is a highly saturated in terms of coverage and highly comparable to the published maps. In QTL analysis, altogether 99 QTLs were identified for productivity and fiber quality traits. Among those, eight were stable and 38 were major QTLs. Cluster 1, 4 and 6 respectively on chromosome AD_chr.03, AD_chr.14 and AD_chr.18 were the biggest QTL clusters each with four QTLs and cluster 4 and 6 were QTL hotspots for fiber quality traits. [ABSTRACT FROM AUTHOR]

Abstract Background Upland cotton (Gossypium hirsutum) accounts for more than 90% of the annual world cotton output because of its high yield potential. However, yield and fiber quality traits often show negative correlations. We constructed four F2 populations of upland cotton, using two normal lines (4133B and SGK9708) with high yield potential but moderate fiber quality and two introgression lines (Suyuan04–3 and J02–247) with superior fiber quality, and used them to investigate the genetic basis underlying complex traits such as yield and fiber quality in upland cotton. We also phenotyped eight agronomic and economic traits and mapped quantitative trait loci (QTLs). Results Extensive phenotype variations and transgressive segregation were found across the segregation populations. We constructed four genetic maps of 585.97 centiMorgan (cM), 752.45 cM, 752.45 cM, and 1 163.66 cM, one for each of the four F2 populations. Fifty QTLs were identified across the four populations (7 for plant height, 27 for fiber quality and 16 for yield). The same QTLs were identified in different populations, including qBW4 and qBW2, which were linked to a common simple sequence repeat (SSR) marker, NAU1255. A QTL cluster containing eight QTLs for six different traits was characterized on linkage group 9 of the 4133B × Suyuan04–3 population. Conclusions These findings will provide insights into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding.

Abstract Background Meta-analysis of quantitative trait locus (QTL) is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies. The combination of meta-QTL intervals, significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants. Results In our study, 884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1, as a result, 74 meta-QTLs were identified, including 19 meta-QTLs for fiber length; 18 meta-QTLs for fiber strength; 11 meta-QTLs for fiber uniformity; 11 meta-QTLs for fiber elongation; and 15 meta-QTLs for micronaire. Combined with 8 589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies, 297 candidate genes were identified in the meta-QTL intervals, 20 of which showed high expression levels specifically in the developing fibers. According to the function annotations, some of the 20 key candidate genes are associated with the fiber development. Conclusions This study provides not only stable QTLs used for marker-assisted selection, but also candidate genes to uncover the molecular mechanisms for cotton fiber development.

Abstract Background Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Quantitative trait loci (QTL) mapping provides a powerful approach to dissect the molecular mechanism in fiber quality traits. In present study, F14 recombinant inbred line (RIL) population was backcrossed to paternal parent for a paternal backcross (BC/P) population, deriving from one upland cotton hybrid. Three repetitive BC/P field trials and one maternal backcross (BC/M) field trial were performed including both two BC populations and the original RIL population. Results In total, 24 novel QTLs are detected for fiber quality traits and among which 13 QTLs validated previous results. Thirty-five QTLs in BC/P populations explain 5.01%–22.09% of phenotype variation (PV). Among the 35 QTLs, 23 QTLs are detected in BC/P population alone. Present study provides novel alleles of male parent for fiber quality traits with positive genetic effects. Particularly, qFS-Chr3–1 explains 22.09% of PV in BC/P population, which increaseds 0.48 cN·tex− 1 for fiber strength. A total of 7, 2, 8, 2 and 6 QTLs explain over 10.00% of PV for fiber length, fiber uniformity, fiber strength, fiber elongation and fiber micronaire, respectively. In RIL population, six common QTLs are detected in more than one environment: qFL-Chr1–2, qFS-Chr5–1, qFS-Chr9–1, qFS-Chr21–1, qFM-Chr9–1 and qFM-Chr9–2. Two common QTLs of qFE-Chr2–2 (TMB2386-SWU12343) and qFM-Chr9–1 (NAU2873-CGR6771) explain 22.42% and 21.91% of PV. The region between NAU4034 and TMB1296 harbor 30 genes (379 kb) in A05 and 42 genes (49 kb) in D05 for fiber length along the QTL qFL-Chr5–1 in BC/P population, respectively. In addition, a total of 142 and 46 epistatic QTLs and QTL × environments (E-QTLs and QQEs) are identified in recombinant inbred lines in paternal backcross (RIL-P) and paternal backcross (BC/P) populations, respectively. Conclusions The present studies provide informative basis for improving cotton fiber quality in different populations.

Gene introgression from wild species has been shown to be a feasible approach for fiber quality improvement in Upland cotton. Previously, we developed an interspecific G. mustelinum × G. hirsutum advanced-backcross population and mapped over one hundred QTL for fiber quality traits. In the current study, a trait-based selective genotyping approach was utilized to prioritize a small subset of introgression lines with high phenotypic values for different fiber quality traits, to simultaneously validate multiple fiber quality QTL in a single experiment. A total of 75 QTL were detected by CIM and/or single-marker analysis, including 11 significant marker-trait associations (P < 0.001) and three putative associations (P < 0.005) also reported in earlier studies. The QTL that have been validated include three each for fiber length, micronaire, and elongation, and one each for fiber strength and uniformity. Collectively, about 10% of the QTL previously reported have been validated here, indicating that selective genotyping has the potential to validate multiple marker-trait associations for different traits, especially those with a moderate to large-effect detected simultaneously in one experimental population. The G. mustelinum alleles contributed to improved fiber quality for all validated loci. The results from this study will lay the foundation for further fine mapping, marker-assisted selection and map-based gene cloning.

Cotton is the most important fiber crop in the world. Asiatic cotton (Gossypium arboreum, genome A2) is a diploid cotton species producing spinnable fibers and important germplasm for cotton breeding and a significant model for fiber biology. However, the genetic map of Asiatic cotton has been lagging behind tetraploid cottons, as well as other stable crops. This study aimed to construct a high-density SNP genetic map and to map QTLs for important yield and fiber quality traits. Using a recombinant inbred line (RIL) population and genome resequencing technology, we constructed a high-density genetic map that covered 1980.17 cM with an average distance of 0.61 cM between adjacent markers. QTL analysis revealed a total of 297 QTLs for 13 yield and fiber quality traits in three environments, explaining 5.0–37.4% of the phenotypic variance, among which 75 were stably detected in two or three environments. Besides, 47 QTL clusters, comprising 131 QTLs for representative traits, were identified. Our works laid solid foundation for fine mapping and cloning of QTL for yield and fiber quality traits in Asiatic cotton. [ABSTRACT FROM AUTHOR]

Cotton is a valuable fiber crop which supplies raw material to more than 50 industries and is produced in more than 70 countries worldwide. The superiority of cotton fiber over other crops is primarily dependent on its quality. However, further improvements in fiber length and strength are required for modern processing technology and for cotton to maintain its position in the global market. Association mapping enables identification of QTLs controlling fiber quality-related traits which can be useful in cotton breeding. In the present study, we performed genetic diversity, linkage disequilibrium and association mapping analyses in 157 G. hirsutum multi-parent recombinant inbred lines using a total of 102 SSR markers. The population had depressed genetic variability (14%), a result of inbreeding of modern cotton genotypes. Despite this, we identified 11 significant and stable marker-trait associations for seed cotton yield, lint percentage, fiber length and fiber strength (p < 0.005). We also detected QTL co-localizations with positive and negative marker additive effects. Our results indicate that selection against negative alleles may be as important as selection for positive alleles. Analysis of the effects of allelic combinations at different QTLs revealed significant and stable marker clusters that can be selected for or against to provide maximum quality gains in cotton fiber quality. [ABSTRACT FROM AUTHOR]

Fiber length, fiber strength, and fiber micronaire are the main fiber quality parameters in cotton. Thus, mining the elite and stable loci/alleles related to fiber quality traits and elucidating the relationship between the two may accelerate genetic improvement of fiber quality in cotton. Here, genome-wide association analysis (GWAS) was performed for fiber quality parameters based on phenotypic data, and 56,010 high-quality single nucleotide polymorphisms (SNPs) using 242 upland cotton accessions under 12 field environments were obtained. Phenotypic analysis exhibited that fiber length (FL) had a positive correlation with fiber strength (FS) and had a negative correlation with fiber micronaire (Mic). Genetic analysis also indicated that FL, FS, and Mic had high heritability of more than 80%. A total of 67 stable quantitative trait loci (QTLs) were identified through GWAS analysis, including 31 for FL, 21 for FS, and 22 for Mic. Of them, three pairs homologous QTLs were detected between A and D subgenomes, and seven co-located QTLs with two fiber quality parameters were found. Compared with the reported QTLs, 34 co-located with previous studies, and 33 were newly revealed. Integrated with transcriptome analysis, we selected 256, 244, and 149 candidate genes for FL, FS, and Mic, respectively. Gene Ontology (GO) analysis showed that most of the genes located in QTLs interval of the three fiber quality traits were involved in sugar biosynthesis, sugar metabolism, microtubule, and cytoskeleton organization, which played crucial roles in fiber development. Through correlation analysis between haplotypes and phenotypes, three genes (GH_A05G1494, GH_D11G3097, and GH_A05G1082) predominately expressed in fiber development stages were indicated to be potentially responsible for FL, FS, and Mic, respectively. The GH_A05G1494 encoded a protein containing SGS-domain, which is related to tubulin-binding and ubiquitin-protein ligase binding. The GH_D11G3097 encoded 20S proteasome beta subunit G1, and was involved in the ubiquitin-dependent protein catabolic process. The GH_A05G1082 encoded RAN binding protein 1 with a molecular function of GTPase activator activity. These results provide new insights and candidate loci/genes for the improvement of fiber quality in cotton.

Fiber length, fiber strength, and fiber micronaire are the main fiber quality parameters in cotton. Thus, mining the elite and stable loci/alleles related to fiber quality traits and elucidating the relationship between the two may accelerate genetic improvement of fiber quality in cotton. Here, genome-wide association analysis (GWAS) was performed for fiber quality parameters based on phenotypic data, and 56,010 high-quality single nucleotide polymorphisms (SNPs) using 242 upland cotton accessions under 12 field environments were obtained. Phenotypic analysis exhibited that fiber length (FL) had a positive correlation with fiber strength (FS) and had a negative correlation with fiber micronaire (Mic). Genetic analysis also indicated that FL, FS, and Mic had high heritability of more than 80%. A total of 67 stable quantitative trait loci (QTLs) were identified through GWAS analysis, including 31 for FL, 21 for FS, and 22 for Mic. Of them, three pairs homologous QTLs were detected between A and D subgenomes, and seven co-located QTLs with two fiber quality parameters were found. Compared with the reported QTLs, 34 co-located with previous studies, and 33 were newly revealed. Integrated with transcriptome analysis, we selected 256, 244, and 149 candidate genes for FL, FS, and Mic, respectively. Gene Ontology (GO) analysis showed that most of the genes located in QTLs interval of the three fiber quality traits were involved in sugar biosynthesis, sugar metabolism, microtubule, and cytoskeleton organization, which played crucial roles in fiber development. Through correlation analysis between haplotypes and phenotypes, three genes (GH_A05G1494, GH_D11G3097 , and GH_A05G1082) predominately expressed in fiber development stages were indicated to be potentially responsible for FL, FS, and Mic, respectively. The GH_A05G1494 encoded a protein containing SGS-domain, which is related to tubulin-binding and ubiquitin-protein ligase binding. The GH_D11G3097 encoded 20S proteasome beta subunit G1, and was involved in the ubiquitin-dependent protein catabolic process. The GH_A05G1082 encoded RAN binding protein 1 with a molecular function of GTPase activator activity. These results provide new insights and candidate loci/genes for the improvement of fiber quality in cotton. [ABSTRACT FROM AUTHOR]

Abstract Background Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber. Recent advances in sequencing technologies provide powerful tools with which to explore the cotton genome for single nucleotide polymorphism marker identification and high density genetic map construction toward more reliable quantitative trait locus mapping. Results In the present study, a RIL population was developed by crossing a Chinese high fiber quality cultivar (Yumian 1) and an American high fiber quality line (CA3084), with distinct genetic backgrounds. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to discover SNPs, and a genetic map containing 6254 SNPs was constructed, covering 3141.72 cM with an average distance of 0.5 cM between markers. A total of 95 QTL were detected for fiber quality traits in three environments, explaining 5.5-24.6% of the phenotypic variance. Fifty-five QTL found in multiple environments were considered stable QTL. Nine of the stable QTL were found in all three environments. We identified 14 QTL clusters on 13 chromosomes, each containing one or more stable QTL. Conclusion A high-density genetic map of Gossypium hirsutum developed by using specific locus amplified fragment sequencing technology provides detailed mapping of fiber quality QTL, and identification of ‘stable QTL’ found in multiple environments. A marker-rich genetic map provides a foundation for fine mapping, candidate gene identification and marker-assisted selection of favorable alleles at stable QTL in breeding programs.

Abstract Background Gossypium barbadense (Sea Island, Egyptian or Pima cotton) cotton has high fiber quality, however, few studies have investigated the genetic basis of its traits using molecular markers. Genome complexity reduction approaches such as genotyping-by-sequencing have been utilized to develop abundant markers for the construction of high-density genetic maps to locate quantitative trait loci (QTLs). Results The Chinese G. barbadense cultivar 5917 and American Pima S-7 were used to develop a recombinant inbred line (RIL) population with 143 lines. The 143 RILs together with their parents were tested in three replicated field tests for lint yield traits (boll weight and lint percentage) and fiber quality traits (fiber length, fiber elongation, fiber strength, fiber uniformity and micronaire) and then genotyped using GBS to develop single-nucleotide polymorphism (SNP) markers. A high-density genetic map with 26 linkage groups (LGs) was constructed using 3557 GBS SNPs spanning a total genetic distance of 3076.23 cM at an average density of 1.09 cM between adjacent markers. A total of 42 QTLs were identified, including 24 QTLs on 12 LGs for fiber quality and 18 QTLs on 7 LGs for lint yield traits, with LG1 (9 QTLs), LG10 (7 QTLs) and LG14 (6 QTLs) carrying more QTLs. Common QTLs for the same traits and overlapping QTLs for different traits were detected. Each individual QTLs explained 0.97 to 20.7% of the phenotypic variation. Conclusions This study represents one of the first genetic mapping studies on the fiber quality and lint yield traits in a RIL population of G. barbadense using GBS-SNPs. The results provide important information for the subsequent fine mapping of QTLs and the prediction of candidate genes towards map-based cloning and marker-assisted selection in cotton.

Tillage system is a critical factor that limits plant growth and production all over the globe. The current study was to evaluate the performance of cotton cultivars and appropriate planting system for higher crop production in Punjab, Pakistan. Two factors; cultivars and planting system were examined under RCBD along four repeats. “CIM-602 cultivar” had the highest yield traits i.e. plant height, number of bolls/ plant, boll weight, seed cotton yield, lint yield, biological yield and seed cotton harvest. The excellent increase was shown in yield and phenological attributes of cotton cultivars under bed sowing compared to all other studied planting systems. Regarding the cultivars, the higher fiber related attributes such as fiber fineness, fiber uniformity, fiber elongation, fiber strength and micronaire were measured in “CIM-602 cultivar” as compared to “CIM-678cultivar”. The bed sowing provides the best fiber quality as compared to other planting systems. Economic analysis confirmed that bed sowing is best planting system which provides higher output to farmers with little input. It has been concluded that from present study, “CIM-602” is good cultivar and provides higher production, while bed sowing is suitable planting system for cotton production. [ABSTRACT FROM AUTHOR]

The analysis of association between genotypic markers and phenotypic traits allows identification of quantitative trait loci (QTLs), which can be applied through marker-assisted selection in breeding programs to improve the quality of crops. However, success in these applications depends primarily on the stability and dominance of the QTL. We previously identified a significant fiber length (FL) QTL on chromosome (Chr.) D11 based on the genome-wide association study (GWAS) of a multi-parent advanced generation inter-cross (MAGIC) population in upland cotton. In this report, we conducted mapping studies with two bi-parental populations to confirm the stability of the FL QTL on Chr. D11 and determine the magnitude of its effect on the fiber length phenotype. One of the F2 populations was developed from a cross between the longest fiber and the shortest fiber recombinant inbred lines (RILs) of the MAGIC population originally used for GWAS, whereas the second F2 population was created from a cross between two cotton lines Acala 1517–80 and JJ1145ne, which were not among the eleven MAGIC parental lines. The populations were grown in different environmental conditions. Genetic mapping of these populations confirmed the stability of the FL QTL on Chr. D11. The highest LOD scores of association with fiber length in both populations showed three SNP markers that resided within 360 kb of the QTL region on Chr. D11. Ten genes possessing non synonymous SNPs (nsSNPs) in their protein coding regions were identified in this region. RNAseq analysis detected activity in developing fiber tissue for seven of these candidate genes. [ABSTRACT FROM AUTHOR]

It is of great importance to identify quantitative trait loci (QTL) controlling fiber quality traits and yield components for future marker-assisted selection (MAS) and candidate gene function identifications. In this study, two kinds of traits in 231 F6:8 recombinant inbred lines (RILs), derived from an intraspecific cross between Xinluzao24, a cultivar with elite fiber quality, and Lumianyan28, a cultivar with wide adaptability and high yield potential, were measured in nine environments. This RIL population was genotyped by 122 SSR and 4729 SNP markers, which were also used to construct the genetic map. The map covered 2477.99 cM of hirsutum genome, with an average marker interval of 0.51 cM between adjacent markers. As a result, a total of 134 QTLs for fiber quality traits and 122 QTLs for yield components were detected, with 2.18–24.45 and 1.68–28.27% proportions of the phenotypic variance explained by each QTL, respectively. Among these QTLs, 57 were detected in at least two environments, named stable QTLs. A total of 209 and 139 quantitative trait nucleotides (QTNs) were associated with fiber quality traits and yield components by four multilocus genome-wide association studies methods, respectively. Among these QTNs, 74 were detected by at least two algorithms or in two environments. The candidate genes harbored by 57 stable QTLs were compared with the ones associated with QTN, and 35 common candidate genes were found. Among these common candidate genes, four were possibly “pleiotropic.” This study provided important information for MAS and candidate gene functional studies.

Fiber length is one of the most important fiber quality traits in Upland cotton (Gossypium hirsutum L.), the most important fiber crop, and its improvement has been impeded in part by a lack of knowledge regarding its genetic basis. Introgressed backcross inbred lines (BILs) or near isogenic lines (NILs) differing in fiber length in the same genetic background, developed through advanced backcrossing between Upland cotton and extra-long staple cotton (G. barbadense L.), provide an important genomic resource for studying the molecular genetic basis of fiber length. In the present study, a long-fiber group and a short-fiber group, each with five BILs of Upland cotton, were selected from a BIL population between G. hirsutum and G. barbadense. Through a microarray-based comparative transcriptome analysis of developing fibers at 10 days postanthesis from the two groups, 1478 differentially expressed genes (DEGs) were identified. A total of 166 DEGs were then mapped to regions of fiber length quantitative trait loci (QTL), including 12 QTL hotspots and 2 QTL identified previously in the BIL population from which the two sets of BILs were selected. Several candidate genes possibly underlying the genetic control of fiber length differences between G. barbadense and G. hirsutum, including GhACX and GhKIF, were identified in this study. These results provide a list of positional candidate genes for the fine-scale mapping and map-based cloning of fiber length QTL, which will facilitate targeted gene transfer from G. barbadense to Upland cotton to further improve fiber quality. [ABSTRACT FROM AUTHOR]

Background: Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber. Recent advances in sequencing technologies provide powerful tools with which to explore the cotton genome for single nucleotide polymorphism marker identification and high density genetic map construction toward more reliable quantitative trait locus mapping. Results: In the present study, a RIL population was developed by crossing a Chinese high fiber quality cultivar (Yumian 1) and an American high fiber quality line (CA3084), with distinct genetic backgrounds. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to discover SNPs, and a genetic map containing 6254 SNPs was constructed, covering 3141.72 cM with an average distance of 0.5 cM between markers. A total of 95 QTL were detected for fiber quality traits in three environments, explaining 5.5-24.6% of the phenotypic variance. Fifty-five QTL found in multiple environments were considered stable QTL. Nine of the stable QTL were found in all three environments. We identified 14 QTL clusters on 13 chromosomes, each containing one or more stable QTL. Conclusion: A high-density genetic map of Gossypium hirsutum developed by using specific locus amplified fragment sequencing technology provides detailed mapping of fiber quality QTL, and identification of 'stable QTL' found in multiple environments. A marker-rich genetic map provides a foundation for fine mapping, candidate gene identification and marker-assisted selection of favorable alleles at stable QTL in breeding programs. [ABSTRACT FROM AUTHOR]

It is of great importance to identify quantitative trait loci (QTL) controlling fiber quality traits and yield components for future marker-assisted selection (MAS) and candidate gene function identifications. In this study, two kinds of traits in 231 F6:8 recombinant inbred lines (RILs), derived from an intraspecific cross between Xinluzao24, a cultivar with elite fiber quality, and Lumianyan28, a cultivar with wide adaptability and high yield potential, were measured in nine environments. This RIL population was genotyped by 122 SSR and 4729 SNP markers, which were also used to construct the genetic map. The map covered 2477.99 cM of hirsutum genome, with an average marker interval of 0.51 cM between adjacent markers. As a result, a total of 134 QTLs for fiber quality traits and 122 QTLs for yield components were detected, with 2.18–24.45 and 1.68–28.27% proportions of the phenotypic variance explained by each QTL, respectively. Among these QTLs, 57 were detected in at least two environments, named stable QTLs. A total of 209 and 139 quantitative trait nucleotides (QTNs) were associated with fiber quality traits and yield components by four multilocus genome-wide association studies methods, respectively. Among these QTNs, 74 were detected by at least two algorithms or in two environments. The candidate genes harbored by 57 stable QTLs were compared with the ones associated with QTN, and 35 common candidate genes were found. Among these common candidate genes, four were possibly “pleiotropic.” This study provided important information for MAS and candidate gene functional studies. [ABSTRACT FROM AUTHOR]

Gossypium hirsutum L. is the most important fiber crop worldwide and contributes to more than 95% of global cotton production. Marker-assisted selection (MAS) is an effective approach for improving fiber quality, and quantitative trait loci (QTL) mapping of fiber quality traits is important for cotton breeding. In this study, a permanent intra-specific recombinant inbred line (RIL) population containing 137 families was used for fiber quality testing. Based on a previously reported high-density genetic map with an average marker distance of 0.63 cM, 186 additive QTLs were obtained for five fiber quality traits over five consecutive years, including 39 for fiber length (FL), 36 for fiber strength (FS), 50 for fiber uniformity (FU), 33 for micronaire (MC) and 28 for fiber elongation (FE). Three stable QTLs, qMC-A4-1, qMC-D2-3 and qFS-D9-1, were detected in four datasets, and another eight stable QTLs, qMC-A4-2, qMC-D11-2, qFU-A9-1, qFU-A10-4, qFS-D11-1, qFL-D9-2, qFL-D11-1 and qFE-A3-2, were detected in three datasets. The annotated genes in these 11 stable QTLs were collected, and these genes included many transcription factors with functions during fiber development. 33 QTL coincidence regions were found, and these involved nearly half of the total QTLs. Four chromosome regions containing at least 6 QTLs were promising for fine mapping. In addition, 41 pairs of epistatic QTLs (e-QTLs) were screened, including 6 for FL, 30 for FS, 2 for FU and 3 for MC. The identification of stable QTLs adds valuable information for further QTL fine mapping and gene positional cloning for fiber quality genetic detection and provides useful markers for further molecular breeding in enhancing fiber quality. [ABSTRACT FROM AUTHOR]

Background: Gossypium barbadense (Sea Island, Egyptian or Pima cotton) cotton has high fiber quality, however, few studies have investigated the genetic basis of its traits using molecular markers. Genome complexity reduction approaches such as genotyping-by-sequencing have been utilized to develop abundant markers for the construction of high-density genetic maps to locate quantitative trait loci (QTLs). Results: The Chinese G. barbadense cultivar 5917 and American Pima S-7 were used to develop a recombinant inbred line (RIL) population with 143 lines. The 143 RILs together with their parents were tested in three replicated field tests for lint yield traits (boll weight and lint percentage) and fiber quality traits (fiber length, fiber elongation, fiber strength, fiber uniformity and micronaire) and then genotyped using GBS to develop single-nucleotide polymorphism (SNP) markers. A high-density genetic map with 26 linkage groups (LGs) was constructed using 3557 GBS SNPs spanning a total genetic distance of 3076.23 cM at an average density of 1.09 cM between adjacent markers. A total of 42 QTLs were identified, including 24 QTLs on 12 LGs for fiber quality and 18 QTLs on 7 LGs for lint yield traits, with LG1 (9 QTLs), LG10 (7 QTLs) and LG14 (6 QTLs) carrying more QTLs. Common QTLs for the same traits and overlapping QTLs for different traits were detected. Each individual QTLs explained 0.97 to 20.7% of the phenotypic variation. Conclusions: This study represents one of the first genetic mapping studies on the fiber quality and lint yield traits in a RIL population of G. barbadense using GBS-SNPs. The results provide important information for the subsequent fine mapping of QTLs and the prediction of candidate genes towards map-based cloning and marker-assisted selection in cotton. [ABSTRACT FROM AUTHOR]

Cotton fiber quality traits are controlled by multiple quantitative trait loci (QTL), and the improvement of these traits requires extensive germplasm. Herein, an Upland cotton cultivar from America, Acala Maxxa, was crossed with a local high fiber quality cultivar, Yumian 1, and 180 recombinant inbred lines (RILs) were obtained. In order to dissect the genetic basis of fiber quality differences between these parents, a genetic map containing 12116 SNP markers was constructed using the CottonSNP80K assay, which covered 3741.81 cM with an average distance of 0.31 cM between markers. Based on the genetic map and growouts in three environments, we detected a total of 104 QTL controlling fiber quality traits. Among these QTL, 25 were detected in all three environments and 35 in two environments. Meanwhile, 19 QTL clusters were also identified, and nine contained at least one stable QTL (detected in three environments for a given trait). These stable QTL or QTL clusters are priorities for fine mapping, identifying candidate genes, elaborating molecular mechanisms of fiber development, and application in cotton breeding programs by marker-assisted selection (MAS).

Cotton fiber quality traits are controlled by multiple quantitative trait loci (QTL), and the improvement of these traits requires extensive germplasm. Herein, an Upland cotton cultivar from America, Acala Maxxa, was crossed with a local high fiber quality cultivar, Yumian 1, and 180 recombinant inbred lines (RILs) were obtained. In order to dissect the genetic basis of fiber quality differences between these parents, a geneticmap containing 12116 SNP markers was constructed using the CottonSNP80K assay, which covered 3741.81 cM with an average distance of 0.31 cM between markers. Based on the genetic map and growouts in three environments, we detected a total of 104 QTL controlling fiber quality traits. Among these QTL, 25 were detected in all three environments and 35 in two environments. Meanwhile, 19 QTL clusters were also identified, and nine contained at least one stable QTL (detected in three environments for a given trait). These stable QTL or QTL clusters are priorities for fine mapping, identifying candidate genes, elaborating molecular mechanisms of fiber development, and application in cotton breeding programs by marker-assisted selection (MAS). [ABSTRACT FROM AUTHOR]

The tetraploid species Gossypium hirsutum is cultivated widely throughout the world with high yield and moderate fiber quality, but its genetic basis is narrow. A set of 107 introgression lines (ILs) was developed with an interspecific cross using G. hirsutum acc. 4105 as the recurrent parent and G. tomentosum as the donor parent. A specific locus amplified fragment sequencing (SLAF-seq) strategy was used to obtain high-throughput single nucleotide polymorphism (SNP) markers. In total, 3157 high-quality SNP markers were obtained and further used for identification of quantitative trait loci (QTLs) for fiber quality and yield traits evaluated in multiple environments. In total, 74 QTLs were detected that were associated with five fiber quality traits (30 QTLs) and eight yield traits (44 QTLs), with 2.02-30.15% of the phenotypic variance explained (PVE), and 69 markers were found to be associated with these thirteen traits. Eleven chromosomes in the A sub-genome (At) harbored 47 QTLs, and nine chromosomes in the D sub-genome (Dt) harbored 27 QTLs. More than half (44 QTLs = 59.45%) showed positive additive effects for fiber and yield traits. Five QTL clusters were identified, with three in the At, comprised of thirteen QTLs, and two in the Dt comprised of seven QTLs. The ILs developed in this study and the identified QTLs will facilitate further molecular breeding for improvement of Upland cotton in terms of higher yield with enhanced fiber quality. [ABSTRACT FROM AUTHOR]

Cotton is a vital fiber crop fulfilling global demands for raw materials in the textile sector. Therefore, high-yielding cultivars with superior-quality traits are desired at regional scales. The high-yielding cultivars can be selected by determining their responses to various environmental conditions at different locations over a short or long period. Genotypes, environment, and year significantly alter seed cotton yield and fiber quality. Therefore, determining the response to various environmental conditions is necessary for selecting high-yielding cultivars with superior fiber quality. This study determined the yield and fiber quality traits of 3 cotton cultivars (i.e., 'DP396′, 'BA440′ and 'Teksa 415′) at five different locations (i.e., Tepe, Boztepe, Bozçalı, Köseli and GAP International Agricultural Research and Training Center) in southeastern Anatolia, Turkey for 3 years (2019, 2020, and 2021). Data relating to seed cotton yield and fiber quality traits were collected and relationships of these traits were determined by biplot analysis. Cultivars × traits relationship indicated that 'DP396′ was the most stable cultivar with the highest seed cotton yield. Similarly, 'BA440′ cultivar was associated with quality characteristics. Sector analysis divided the yield and quality traits into three different groups. The locations × traits relationship indicated that the examined traits differed according to the locations. Tepe location was in the center in terms of quality and seed yield, whereas Bozçalı location had superior quality traits. Likewise, Boztepe location resulted in higher values ​​ of seed and fiber yield, and number of bolls per plant. The studied characteristics varied among the years, and higher values of seed and fiber yields, and the number of bolls per plant were recorded during 2019. On the other hand, superior fiber quality traits were noted during 2021. It is concluded that 'DP396′ was the most stable cultivar for seed cotton yield, whereas 'BA440′ was stable for quality traits. Therefore, these cultivars can be used in the studied locations to increase yield and fiber quality. Furthermore, these cultivars could be utilized in the breeding programs for developing high-yielding and better fiber quality producing genotypes in the future. [ABSTRACT FROM AUTHOR]

Gossypium hirsutum L. is a widely cultivated species characterized by its high yield and wide environmental adaptability, while Gossypium barbadense is well known for its superior fiber quality. In the present report, we, for the first time, developed G. hirsutum chromosome segment introgression lines (ILs) in a G. barbadense background (GhILs_Gb) and genetically dissected the inheritance of lint yield and fiber quality of G. hirsutum in G. barbadense background. The GhILs_Gb contains introgressed segments spanning 4121.20 cM, which represents 82.20% of the tetraploid cotton genome, with an average length of 18.65 cM. A total of 39 quantitative trait loci (QTLs) for six traits are identified in this IL population planted in Xinjiang. Four QTL clusters are detected. Of them, however, three clusters have deleterious effects on fiber length and strength and boll weight, and only one cluster on Chr. D9 can be used in marker-assisted selection (MAS) to increase lint percentage and decrease micronaire value in G. barbadense. QTL mapping showed that most of yield-related QTLs detected have positive effects and increase lint yield in G. barbadense, while most of fiber quality-related QTLs have deleterious effects except for micronaire. It suggested that G. hirsutum evolved to have a high lint yield. Several lines improved in lint percentage and boll size in G. barbadense by introgressed one fragment of G. hirsutum have been developed from the GhILs_Gb. The ILs developed, and the analyses presented here will enhance the understanding of the genetics of lint yield and fiber quality in G. hirsutum and facilitate further molecular breeding to improve lint yield in G. barbadense. [ABSTRACT FROM AUTHOR]

Background: Since upland cotton was introduced into China during the 1920s-1950s, hundreds of inbreed cultivars have been developed. To explore the molecular diversity, population structure and elite alleles, 503 inbred cultivars developed in China and some foreign cultivars from the United States and the Soviet Union were collected and analyzed by 494 genome-wide SSRs (Simple Sequence Repeats). Methods: Four hundred and ninety-four pairs of SSRs with high polymorphism and uniform distribution on 26 chromosomes were used to scan polymorphisms in 503 nation-wide upland cottons. The programming language R was used to make boxplots for the phenotypic traits in different environments. Molecular marker data and 6 fiber quality traits were analyzed by the method of MLM (mixed linear model) (P + G + Q + K) in the TASSEL software package on the basis of the population structure and linkage disequilibrium analysis. The loci of elite allelic variation and typical materials carrying elite alleles were identified based on phenotypic effect values. Results: A total of 179 markers were polymorphic and generated 426 allele loci; the population based on molecular diversity was classified into seven subpopulations corresponding to pedigree origin, ecological and geographical distribution. The attenuation distance of linkage disequilibrium dropped significantly up to 0-5 cM. Association mapping for fiber quality showed that 216 marker loci were associated with fiber quality traits (P < 0.05) explaining 0.58 % ~ 5.12 % of the phenotypic variation, with an average of 2.70 %. Thirteen marker loci were coincident with other studies, and three were detected for the same trait. Seven quantitative trait loci were related to known genes in fiber development. Based on phenotypic effects, 48 typical materials that contained the elite allele loci related to fiber quality traits were identified and are widely used in practical breeding. Conclusions: The molecular diversity and population structure of 503 nation-wide upland cottons in China were evaluated by 494 genome-wide SSRs, and association mapping for fiber quality revealed known and novel elite alleles. The molecular diversity provides a guide for parental mating in cotton breeding, and the association mapping results will aid in the fine-mapping genes related to fiber quality traits and facilitate further studies on candidate genes. [ABSTRACT FROM AUTHOR]

Cotton fiber is widely used as the raw materials for the textile industry. With the development in spinning technology, the improvement of cotton fiber quality is becoming more and more important. However, negative correlation between yield and fiber quality is an obstacle for cotton improvement. Molecular marker assisted selection provides a potential methodology to break the negative correlation. The main objective of this research was to construct a genetic linkage map and mapping QTL for fiber quality, further to facilitate marker assisted selection for fiber quality traits in Upland cotton ( Gossypium hirsutum L.). A genetic linkage map, consisting of 581 loci and spanning 3714.4 cM of the cotton genome, was constructed using recombinant inbred lines population derived from the cross GX1135 × GX100-2, with an average interval of 6.39 cM between adjacent loci. Fiber quality traits were investigated in recombinant inbred lines population sampled by lines from three environments respectively, and each followed a randomized complete block design with two replications. Twenty quantitative trait loci were detected for four fiber quality traits: eight for fiber length, three for fiber strength, five for fiber elongation, and four for fiber micronaire. Among these QTLs, qFL- chr5- 2 and qFL- chr10- 1 for fiber length, qFS- chr1- 1 for fiber strength, and qFM- chr19- 1 for fiber micronaire were detected again, which verified the previous results in F, F and F populations (four environments), therefore these major QTLs were stable and especially useful for marker assisted selection to improve fiber quality in Upland cotton. [ABSTRACT FROM AUTHOR]

Cotton is a leading natural fiber crop in the textile industry worldwide. The improvement of cotton fiber quality has become more important because of changes in spinning technology and ever-increasing demands. Mapping quantitative trait locus (QTL) for fiber quality traits will enable molecular marker-assisted selection (MAS) to improve fiber quality and provide an access to reveal the molecular mechanism of fiber development. A high-density intraspecific genetic map is constructed based on an upland cotton recombinant inbred line (RIL) population. A total of 25,313 SSR primer pairs were used and yielded 1,333 polymorphic markers, with a polymorphic ratio of 5.3 %, producing 1,382 polymorphic loci in the RIL population. The map comprised 1,274 loci and spanned 3,076.4 cM with an average distance of 2.41 cM between two adjacent markers. Based on the phenotypic data of fiber quality traits from five environments, a total of 59 QTL were detected. These QTL comprised 15 QTL for fiber upper half mean length, 10 QTL for fiber length uniformity, 9 QTL for fiber strength, 10 QTL for fiber elongation and 15 QTL for fiber micronaire, respectively. The genetic map constructed in this study is the most detailed upland cotton intraspecific map based on SSR markers to date, and could be used to construct consensus map or as reference genetic map for tetraploid cotton genome assembly. Stable QTL identified across multiple environments reflect some important and favorable alleles shaping fiber quality, and they are valuable candidate alleles for MAS breeding projects as well as for gene function research related to cotton fiber development and quality improvement. [ABSTRACT FROM AUTHOR]

Six short season cotton cultivars ( Gossypium hirsutum L.) were crossed in a dillalel crossing system to evaluate inheritance and interrelationship of phenotype and genotype of fiber quality traits (fiber length, uniformity index, fiber strength, micronaire and fiber elongation) and their correlation with earliness and yield traits. The study was carried out from year 2005 to 2008. The experiment design was a randomized complete block design with three replications. Additive, dominance and epistasis effects were analyzed with ADAA model. The results showed that fiber quality traits were mainly controlled by dominant genetic effects and also had a definitely proportion additive genetic effects. Micronaire, fiber length, fiber strength and fiber elongation had the highest broad sense heritability (H) and by environment interaction (H) estimates, 0.618 (H) and 0.267 (H) for micronaire, 0.510 (H) and 0.287 (H) for fiber length, 0.452 (H) and 0.316 (H) for fiber strength, 0.294 (H) and 0.494(H) for fiber elongation, respectively. Narrow sense heritability (H) was 0.258 for fiber elongation, 0.136 for fiber length, 0.127 for fiber strength and 0.110 for micronaire. Some F hybrids (A×B), (A×A) and (B×A) for fiber length, F (A×B) and (B×B) for fiber strength, F (B×A), (A×B), (A×B), (B×A), (B×A) and (B×B) for micronaire and F (A×A), (A×A), (A×B), (A×B) and (B×A) for fiber elongation had significant positive heterozygous dominance effects and affected by environment. Some F hybrids (A×A), (A×B), (A×B), (B×A) and (B×A) for fiber length, (A×A), (A×B) and (A×B) for fiber strength, (A×A), (A×B), (A×B) and (B×B) for micronaire and (A×A), (A×B), (A×B) and (B×B) for fiber elongation had significant positive epistatic effects. Among fiber quality traits, fiber length with fiber strength, uniformity index with fiber strength and micronaire, fiber strength with micronaire showed a positive and significant correlation. Only elongation had a significant negative correlation with fiber quality traits. Fiber quality traits had a negative correlation with earliness traits except micronaire. Fiber length and strength showed a significant negative correlation with lint yield, lint yield before frost, lint percentage and boll number. Uniformity index, micronaire and fiber elongation had a significant positive correlation with yield traits except boll weight and lint percentage. The results showed that the higher the yield and the earlier the maturing and the worse the fiber quality. Therefore, selections of fiber properties and integration of high yield, good fiber quality and early maturing traits should be performed in higher generations in short season cotton variety breeding program. [ABSTRACT FROM AUTHOR]

Cotton fiber quality traits are controlled by multiple genes of minor effect. Identification of significant and stable quantitative trait loci (QTL) across environments and populations lays foundation for marker-assisted selection for fiber quality improvement and studies of its molecular regulation. Here, a detailed genetic map is constructed and QTL are detected based on an intraspecific recombinant inbred line population derived from a cross between Upland cotton cultivar/line Yumian 1 and 7235. A total of 25,313 SSR primer pairs, including 5,000 developed from G. raimondii BAC-ends sequences, were used to construct the genetic map which finally contained 1,540 loci, spanning 2,842.06 cM, with an average of 1.85 cM between adjacent markers. With 4 year fiber quality traits data, variance analysis revealed that they were significantly affected by genetic and environmental factors. Significant correlations were also detected between them. A total of 62 QTL were identified with combined analysis and single environment analysis. These QTL explain phenotypic variation from 5.0 to 28.1 %. For each trait, favorable alleles were conferred by both parents. Seventeen QTL were detected in more than one environment. The genetic map and stable QTL are valuable for Upland cotton genome research and breeding projects to improve fiber quality. [ABSTRACT FROM AUTHOR]

Identification parents with yield as well as good fiber quality traits are essential for development hybrids in cotton. Combining ability is a powerful tool to discriminate between good and poor general combiners and for choosing appropriate parental lines to produce superior hybrids. Combining ability studies were carried out in cotton seed yield and fibre quality traits by utilizing 7 lines, 8 testers and their 56 hybrids obtained by line x tester analysis. The gca variance was greater than to sca variance for ginning percentage, 2.5% span length, micronaire value and seed cotton yield indicating the predominance of additive gene action whereas, uniformity ratio and bundle strength were predominantly under control of non-additive gene action. Parents Galama, CPD 420, BC 68-2, HAG 1055, LRA 5166 and LK 861 were found to be good general combiners for yield and at least one of the fiber quality traits. The crosses NA 1325 x L 604 and NA 1325 x 4084 were identified as good specific combiners for seed cotton yield and whereas the crosses IC 357063 x L 761, IC 357063 x LRA 5166, CPD 420 x L 761 and IC 357063 x JK 344 exhibited significant sca effects for fiber quality traits in desirable direction. [ABSTRACT FROM AUTHOR]

Background Upland cotton (Gossypium hirsutum L.) accounts for about 95% of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between yield and fiber quality is an obstacle for cotton improvement. Random-mating provides a potential methodology to break this correlation. The suite of fiber quality traits that affect the yarn quality includes the length, strength, maturity, fineness, elongation, uniformity and color. Identification of stable fiber quantitative trait loci (QTL) in Upland cotton is essential in order to improve cotton cultivars with superior quality using marker-assisted selection (MAS) strategy. Results Using 11 diverse Upland cotton cultivars as parents, a random-mated recombinant inbred (RI) population consisting of 550 RI lines was developed after 6 cycles of random-mating and 6 generations of self-pollination. The 550 RILs were planted in triplicates for two years in Mississippi State, MS, USA to obtain fiber quality data. After screening 15538 simple sequence repeat (SSR) markers, 2132 were polymorphic among the 11 parents. One thousand five hundred eighty-two markers covering 83% of cotton genome were used to genotype 275 RILs (Set 1). The marker-trait associations were analyzed using the software program TASSEL. At p < 0.01, 131 fiber QTLs and 37 QTL clusters were identified. These QTLs were responsible for the combined phenotypic variance ranging from 62.3% for short fiber content to 82.8% for elongation. The other 275 RILs (Set 2) were analyzed using a subset of 270 SSR markers, and the QTLs were confirmed. Two major QTL clusters were observed on chromosomes 7 and 16. Comparison of these 131 QTLs with the previously published QTLs indicated that 77 were identified before, and 54 appeared novel. Conclusions The 11 parents used in this study represent a diverse genetic pool of the US cultivated cotton, and 10 of them were elite commercial cultivars. The fiber QTLs, especially QTL clusters reported herein can be readily implemented in a cotton breeding program to improve fiber quality via MAS strategy. The consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying fiber development. [ABSTRACT FROM AUTHOR]

With the development in spinning technology, the improvement of cotton fiber quality is becoming more and more important. The main objective of this research was to construct a high-density genetic linkage map to facilitate marker assisted selection for fiber quality traits in upland cotton ( Gossypium hirsutum L.). A genetic linkage map comprising 421 loci and covering 3814.3 cM, accounting for approximately 73.35% of the cotton genome, was constructed using an F population derived from cross GX1135 (P)×GX100-2 (P). Forty-four of 49 linkage groups were assigned to the 26 chromosomes. Fiber quality traits were investigated in F population sampled from individuals, and in F, and F generations sampled by lines from two sites and one respectively, and each followed a randomized complete block design with two replications. Thirty-nine quantitative trait loci were detected for five fiber quality traits with data from single environments (separate analysis each): 12 for fiber length, five for fiber uniformity, nine for fiber strength, seven for fiber elongation, and six for fiber micronaire, whereas 15 QTLs were found in combined analysis (data from means of different environments in F generation). Among these QTLs, qFL-chr5-2 and qFL-chr14-2 for fiber length were detected simultaneously in three generations (four environments) and verified further by combined analysis, and these QTLs should be useful for marker assisted selection to improve fiber quality in upland cotton. [ABSTRACT FROM AUTHOR]

Improvement of fiber quality is one of the priority themes in cotton breeding programs. Therefore, aspect of genetic progress, their rate and determination of correlation among fiber quality traits have an important role for planning future cotton breeding strategies. In this study, forty four cotton (Gossypium hirsutum L.) cultivars, released between 1980 and 2009 in Turkey, were evaluated. High genetic variation was determined among cultivars for the investigated fiber quality traits. During the thirty years of cotton breeding studies, favorable genetic improvements were determined for 32,69 % spinning consistency index, 7,99 % fiber length, 2,96 % fiber uniformity, -39,66 % short fiber content, 21,07 % fiber strength and -12,59 % fiber fineness waits. Among the investigated traits, spinning consistency index, fiber length, fiber strength and fiber uniformity were positively correlated with each other. However, short fiber content and fiber fineness were negatively correlated with the above mentioned 4 fiber quality traits. This result indicated that aforesaid 6 fiber quality traits can be improved simultaneously. [ABSTRACT FROM AUTHOR]

Sticky cotton causes severe processing problems at textile mills and can be caused by plant sugars deposited directly from the plant to the lint in the absence of insects. A partial diallel design was used to investigate the combining ability of six upland cotton, Gossypium hirsutum L., genotypes in Lubbock, Texas. Sucrose and glucose on fibers were measured as well as more mechanical fiber properties including stickiness ratings. Variance component analysis indicated significant differences among genotypes for all fiber traits and for sugar content. The greatest differentiation occurred in samples taken from more immature fruiting forms. Moreover, significant GCA and SCA differences were determined among parental lines for fiber traits including stickiness ratings. Findings suggest that breeding efforts could be directed toward lines with a low likelihood of producing sticky cotton. [ABSTRACT FROM AUTHOR]

A genetic model with additive effect, dominant effect, additive × additive effect, and their interaction with environment effect (GE) was employed to analyze the 2-year data of F1 and F2 hybrids from 5 × 4 diallel cross, whose parents were Sea Island cotton with different fruit branch types. Unconditional and conditional genetic variances were analyzed to demonstrate genetic impacts of fiber sugar content on fiber characters. Results of unconditional genetic variances showed that dominance × environment interaction effect and additive × additive epistatic effects mainly controlled the genetic variation of fiber sugar content, and environment influenced the inheritance of fiber sugar content. Fiber uniformity, fiber elongation, and fiber micronaire were mainly controlled by dominance × environment effects. Fiber strength was mainly controlled by the interaction of additive × additive epistatic effects and the environment. Analysis of correlation coefficients indicated that the varieties or hybrids with high-fiber sugar content had short fiber, low-fiber uniformity, strength, and fineness, which indicated the close co-variation between fiber quality traits and fiber sugar content. Relatively better fiber quality traits could be obtained effectively through selecting parents with low-fiber sugar. Fiber sugar content of different parents had different genetic effect on fiber quality traits. [ABSTRACT FROM AUTHOR]

Gene flow patterns and the genetic structure of domesticated crops like cotton are not well understood. Furthermore, marker-assisted breeding of cotton has lagged far behind that of other major crops because the loci associated with cotton traits such as fiber yield and quality have scarcely been identified. In this study, we used 19 microsatellites to first determine the population genetic structure and patterns of gene flow of superior germplasm resources in upland cotton. We then used association analysis to identify which markers were associated with 15 agronomic traits (including ten yield and five fiber quality traits). The results showed that the upland cotton accessions have low levels of genetic diversity (polymorphism information content = 0.427), although extensive gene flow occurred among different ecological and geographic regions. Bayesian clustering analysis indicated that the cotton resources used in this study did not belong to obvious geographic populations, which may be the consequence of a single source of domestication followed by frequent genetic introgression mediated by human transference. A total of 82 maker-trait associations were examined in association analysis and the related ratios for phenotypic variations ranged from 3.04% to 47.14%. Interestingly, nine SSR markers were detected in more than one environmental condition. In addition, 14 SSR markers were co-associated with two or more different traits. It was noteworthy that NAU4860 and NAU5077 markers detected at least in two environments were simultaneously associated with three fiber quality traits (uniformity index, specific breaking strength and micronaire value). In conclusion, these findings provide new insights into the population structure and genetic exchange pattern of cultivated cotton accessions. The quantitative trait loci of domesticated cotton identified will also be very useful for improvement of yield and fiber quality of cotton in molecular breeding programs., Competing Interests: The authors declare that they have no conflict of interests., (© 2020 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.)