Genetic dissection and origin of pleiotropic loci underlying multilevel fiber quality traits in upland cotton(Gossypium hirsutum L.)

Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile products.However,the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity,fineness,and neps,which in turn has impeded the genetic improvement and industrial utilization of cotton fiber.Here,12 single fiber quality traits were measured using Advanced Fiber Information System(AFIS)equipment among 383 accessions of upland cotton(Gossypium hirsutum L.).In addition,eight conventional fiber quality traits were assessed by the High Volume Instrument(HVI)System.Genome-wide association study(GWAS),linkage disequilibrium(LD)block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality traits.As a result,the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this study.More importantly,three novel pleiotropic loci(FM_A03,FF_A05,and FN_A07)regulating fiber maturity,fineness and neps,respectively,were detected based on AFIS traits.Numerous highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses,including the reported GhKRP6 for fiber length,the newly identified GhMAP8 for maturity and GhDFR for fineness.The origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11,FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton landraces.These findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in G.hirsutum.

Genome-wide identification of the pectate lyase(PEL)gene family members in Malvaceae,and their contribution to cotton fiber quality

Pectin is a major constituent of the plant cell wall.Pectate lyase(PEL,EC 4.2.2.2)uses anti-β-elimination chemistry to cleave theα-1,4 glycosidic linkage in the homogalacturonan region of pectin.However,limited information is available on the comprehensive and evolutionary analysis of PELs in the Malvaceae.In this study,we identified 597PEL genes from 10 Malvaceae species.Phylogenetic and motif analyses revealed that these PELs are classified into six subfamilies:Clades I,II,III,IV,Va,and Vb.The two largest subfamilies,Clades I and II,contained 237 and222 PEL members,respectively.The members of Clades Va and Vb only contained four or five motifs,far fewer than the other subfamilies.Gene duplication analysis showed that segmental duplication played a crucial role in the expansion of the PEL gene family in Gossypium species.The PELs from Clades I,IV,Va,and Vb were expressed during the fiber elongation stage,but nearly all PEL genes from Clades II and III showed no expression in any of the investigated fiber developmental stages.We further performed single-gene haplotype association analysis in 2,001G.hirsutum accessions and 229 G.barbadense accessions.Interestingly,14 PELs were significantly associated with fiber length and strength traits in G.barbadense with superior fiber quality,while only eight GhPEL genes were found to be significantly associated with fiber quality traits in G.hirsutum.Our findings provide important information for further evolutionary and functional research on the PEL gene family members and their potential use for fiber quality improvement in cotton.

Identification of new cotton fiber-quality QTL by multiple genomic analyses and development of markers for genomic breeding

Cotton fiber is one of the main raw materials for the textile industry.In recent years,many cotton fiber quality QTL have been identified,but few were applied in breeding.In this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(GhBreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 QTL.Most of these QTL were ignored by only using GWAS.The CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain extent.Then these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in breeding.Additionally,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated currently.These findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

Exogenous application of bio-stimulants and growth retardants improve nutrient absorption and fiber quality in upland cotton

Background Natural and synthetic plant growth regulators are essential for plant health,likewise these regulators also play a role in increasing organic production productivity and improving quality and yield stability.In the present study,we have evaluated the effects of foliar applied plant growth regulators,i.e.,moringa leaf extract(MLE)and mepiquat chloride(MC)alone and in combination MC and MLE on the conventional cotton cultivar(CIM 573)and transgenic one(CIM 598).The growth regulators were applied at the start of bloom,45 and 90 days after blooming.Results The application of MC and MLE at 90 days after blooming significantly improved the relative growth rate,net assimilation rate,the number of bolls per plant,and seed cotton yield.Likewise,the combined application of MLE and MC at 90 days after blooming significantly boosted the nitrogen uptake in locules,as well as the phosphorus and potassium uptake in the leaves of both cotton cultivars.The application of MLE alone has considerably improved the nitrogen uptake in leaves,and phosphorus and potassium contents in locules of Bt and conventional cotton cultivars.Similarly,Bt cotton treated with MLE at 90 days after blooming produced significantly higher ginning out turn and oil contents.Treatment in combination(MLE+MC)at 90 days after blooming produced considerably higher micronaire value,fiber strength,and staple length in conventional cultivar.Conclusion The natural growth enhancer,MLE is a rich source of minerals and zeatin,improving the nutrient absorption and quality of cotton fiber in both conventional and Bt cotton cultivars.

Combining ability of Egyptian cotton(Gossypium barbadense L.)reveals genetic potential for improved yield and fiber quality

Background As the most widely cultivated fiber crop,cotton production depends on hybridization to unlock the yield potential of current varieties.A deep understanding of genetic dissection is crucial for the cultivation of enhanced hybrid plants with desired traits,such as high yield and fine fiber quality.In this study,the general combining ability(GCA)and specific combining ability(SCA)of yield and fiber quality of nine cotton parents(six lines and three testers)and eighteen F1 crosses produced using a line×tester mating design were analyzed.Results The results revealed significant effects of genotypes,parents,crosses,and interactions between parents and crosses for most of the studied traits.Moreover,the effects of both additive and non-additive gene actions played a notably significant role in the inheritance of most of the yield and fiber quality attributes.The F1 hybrids of(Giza 90×Aust)×Giza 86,Uzbekistan 1×Giza 97,and Giza 96×Giza 97 demonstrated superior performance due to their favorable integration of high yield attributes and premium fiber quality characteristics.Path analysis revealed that lint yield has the highest positive direct effect on seed cotton yield,while lint percentage showed the highest negative direct effect on seed cotton yield.Principal component analysis identified specific parents and hybrids associated with higher cotton yield,fiber quality,and other agronomic traits.Conclusion This study provides insights into identifying potential single-and three-way cross hybrids with superior cotton yield and fiber quality characteristics,laying a foundation for future research on improving fiber quality in cotton.

Deciphering the fiber quality of Gossypium barbadense L.var.brasiliensis in La Convención,Cusco,Perú

Background The quality of cotton fiber determines its value in the textile market,influencing agricultural profitability and the efficiency of textile processing.The selection of genotypes with superior fibers is a key factor for genetic improvement programs seeking adaptability and sustainability in the face of climate change.This demonstrates the strategic importance of this plant for sustainable agriculture and the global textile industry.The objective of this research was to decipher the fiber quality of Gossypium barbadense var.brasiliensis in the native Amazonian communities of La Convención,Cusco-Perú,and to evaluate other critical aspects of native cotton that have not yet been identified.The methodology included non-probability sampling for accessibility,qualitative and quantitative analyses,and multivariate analyses.The fiber length(mm),micronaire index(maturity/fineness),fiber strength(gf/tex),length uniformity index(%),fiber elongation(%),maturation index(%),and short fiber index(%)were the fiber characteristics evaluated using the HVI method in cotton genotypes.Results Cotton accessions collected from Koribeni(Gossypium spp.)and Shivankoreni(Gossypium barbadense var.brasiliensis)stood out for their fiber quality properties,especially length,strength,and uniformity,which highlights their relevance for advanced textile applications and potential for use in plant genetic improvement programs.Conclusion These findings reinforce the need to conserve and study these native cotton accessions from the Peruvian Amazon region,which can offer promising perspectives for the textile industry and agricultural biodiversity.

Transcriptome and QTL analyses reveal candidate genes for fiber quality in Upland cotton

With increasing demand for high-quality cotton,it is desirable to identify genes involved in fiber development for molecular improvement of cotton.In this study,780 differentially expressed genes(DEGs)were identified in developing fibers at 10 days post-anthesis(DPA)in Gossypium hirsutum acc.DH962 and G.hirsutum cv.Jimian 5 using RNA-seq.Of 15 stable QTL for fiber quality identified in the same two parents in previous studies,4,3,6,1,and 1 QTL were associated with fiber length(FL),fiber strength(FS),micronaire(MIC),fiber elongation(FE)and fiber length uniformity ratio(FU),respectively.Integration of DEGs and QTL allowed the identification of 31 genes in 9 QTL regions,of which 25 were highly expressed in fibers based on the transcriptome datasets and 9 were preferentially expressed in different stages of fiber development.Gh_A01G0453(GhDTX19),Gh_D07G1581 and Gh_D04G0942 were expressed specifically in 5 and 10 DPA fibers,with Gh_D04G0942 showing low expression in other tissues except pistil.Gh_D07G1799(GhGAUT9),Gh_D11G0326(GhVPS29),Gh_D11G0333(GhTCP14),and Gh_D11G0334(GhNRP2)were preferentially expressed in 5 or 10 DPA fibers;Gh_A01G0397(GhABCG10)and Gh_D07G1744 were expressed specifically in 20 and 25 DPA fibers.These results suggest candidate genes for molecular improvement of cotton fiber quality.

Expression Profiling Identifies Candidate Genes for Fiber Yield and Quality

Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls and which could play a role in controlling early fiber development.Chief among these was GhMYB25,a Mixta-like MYB gene.Transgenic GhMYB25-silenced cotton

QTL and genetic analysis controlling fiber quality traits using paternal backcross population in upland cotton

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.

QTL Mapping for Fiber Quality Traits Based on a Dense Genetic Linkage Map with SSR,TRAP,SRAP and AFLP Markers in Cultivated Tetraploid Cotton

Cotton is one of the most important economic crops in the world,and it provides natural fiber for the textile industry.With the advancement of the textile technology and increased consumption demands on cotton fiber,both cotton yield and quality should be enhanced.However,cotton yield

Comprehensive Characterization Model of Integrated Cotton Fiber Quality Index

An integrated cotton fiber quality index （ICFQI） model with cotton fiber qualities which can directly express cotton fiber integrated quality and spinning yarn quality was studied. The fiber length, strength, Micronalre （fiber fineness and fiber maturity）, uniformity of fiber length, and short fiber content are the pivotal indexes expressing ICFQI. All of the results above are the basic knowledge to build up the models of ICFQI. According to spinning consistency index （SCI）, spinning strength and spinning yarn integrated quality, ICFQI was the best choice. As the methods of ICFQI had quite a lot of advantages like explicit mechanism, few independent variables. The integrated fiber quality index had a significant positive correlation with yarn strength and spinning consistency, significant negative correlation with yarn evenness and yarn thin places. In additional, the model of the relationship between ICFQI and SCI was established as： SCI=0. 235 6·ICFQI ＋56.153. It was concluded that ICFQI value was the shared reference index for the testing of fiber inspection agency and the selection and distribution of raw cotton bales by textile mills.

Effects of planting dates and shading on carbohydrate content,yield,and fiber quality in cotton with respect to fruiting positions

Two cotton（Gossypium hirsutum L.） cultivars, Kemian 1（cool temperature-tolerant） and Sumian 15（cool temperaturesensitive） were used to study the effects of cool temperature on carbohydrates, yield, and fiber quality in cotton bolls located at different fruiting positions（FP）. Cool temperatures were created using late planting and low light. The experiment was conducted in 2010 and 2011 using two planting dates（OPD, the optimized planting date, 25 April; LPD, the late planting date, 10 June） and two shading levels of crop relative light rate（CRLR, 100 and 60%）. Compared with fruiting position 1（FP1）, cotton yield and yield components（fiber quality, leaf sucrose and starch content, and fiber cellulose） were all decreased on FP3 under all treatments. Compared with OPD-CRLR 100%, other treatments（OPD-CRLR 60%, LPD-CRLR 100%, and LPD-CRLR 60%） had significantly decreased lint yield at both FPs of both cultivars, but especially at FP3 and in Sumian 15; this decrease was mainly caused by a large decline in boll number. All fiber quality indices decreased under late planting and shading except fiber length at FP1 with OPD-CRLR 60%, and a greater reduction was observed at FP3 and in Sumian 15. Sucrose content of the subtending leaf and fiber increased under LPD compared to OPD, whereas it decreased under CRLR 60% compared to CRLR 100%, which led to decreased fiber cellulose content. Therefore, shading primarily decreased the ＂source＂ sucrose content in the subtending leaf whereas late planting diminished translocation of sucrose towards cotton fiber. Notably, as planting date was delayed and light was decreased, more carbohydrates were distributed to leaf and bolls at FP1 than those at FP3, resulting in higher yield and better fiber quality at FP1, and a higher proportion of bolls and carbohydrates allocated at FP3 of Kemian 1 compared to that of Sumian 15. In conclusion, cotton yield and fiber quality were reduced less at FP1 compared to those at FP3 under low temperature and low light conditions. Thus, reduced cotton yield and fiber quality loss can be minimized by selecting low temperature tolerant cultivars under both low temperature and light conditions.

Regional Distribution of Cotton Fiber Quality in China

The fiber quality status is very important for super quality cotton production and diverse requirements of textile industry in China.In this study,the quality of cotton fiber samples which are collected from 13 major cotton production provinces between 2001 to 2005 were analyzed.Eight quality

Effects of irrigation and planting geometry on cotton(Gossypium hirsutum L.)fiber quality and seed composition

Background:Cotton fiber quality and seed composition play vital roles in the economics of cotton production systems and the cottonseed meal industry.This research aimed to examine the effects of different irrigation levels and planting geometries on fiber quality and seed composition of cotton(Gossypium hirsutum L.).We conducted a 2-year study in 2018 and 2019 in a warm,humid area in the Southeast United States on Dundee silt loam soil.There were three irrigation treatments in the study.The treatments included irrigating every furrow,or full irrigation(FI),every alternate furrow,or half irrigation(HI),and no irrigation,or rain-fed(RF).Planting geometries were on ridges spaced 102 cm apart and either a single-row(SR)or twin-rows(TR).Results:The results of high-volume instrument(HVI),advanced fiber information systems(AFIS)and near-infrared reflectance spectroscopy(NIRS)showed that irrigation and planting treatments played a significant role in fiber quality and seed composition.Across irrigation treatments,significant differences were seen in fiber properties,including fineness,maturity ratio,micronaire,neps,short fiber,strength,uniformity,upper half mean length(UHML),upper quartile length by weight(UQLw),and yellowness(+b).Irrigation and planting geometry(PG)had a significant effect on micronaire,strength,and UHML while their interaction was significant only for micronaire.The micronaire was negatively affected by irrigation as FI-SR,FI-TR,HI-SR,and HI-TR recorded 11%~12%lower over the RF-SR and TR treatments.The PG played a minor role in determining fiber quality traits like micronaire and nep count.Irrigation treatments produced significantly lower(3%~4%)protein content than rain-fed,while oil content increased significantly(6%~10%).Conclusions:The study results indicate a potential for improving cotton fiber and seed qualities by managing irrigation and planting geometries in cotton production systems in the Mississippi(MS)Delta region.The HI-TR system appears promising for lint and seed quality.

Genotypic variation in root morphology, cotton subtending leaf physiology and fiber quality against nitrogen

Background:Nitrogen(N)is important for improving various morphological and physiological processes of cotton but their contribution to fiber quality is still lacking.Aims:The current study aimed to explore the relationship between root morphology,subtending leaf physiology,and fiber quality of contrasting N-efficient cotton genotypes in response to N.Methods:We analyzed the above parameters of CCRI 69(N-efficient)and Xinluzao-30(XLZ-30,N-inefficient)under control(2.5 mmol·L^(-1))and high N(5 mmol·L^(-1))conditions.Results:The results showed that root morphological traits were increased in CCRI-69 under control conditions than high N.Subtending leaf morphology,chlorophyll and carotenoid contents,free amino acids,and soluble proteins were higher under high N as compared with the control.However,soluble sugars,fructose,sucrose contents,and sucrose phosphate synthase were higher under control conditions than high N across the growth stages.Irrespective of the N conditions,all morphological and physiological traits of cotton subtending leaf were higher in CCRI-69 than XLZ-30.Except for fiber uniformity,fiber quality traits like fiber length,strength,micronaire,and elongation were improved under control conditions than high N.Between the genotypes,CCRI-69 had significantly higher fiber length,strength,micronaire,and elongation as compared with XLZ-30.Strong positive correlations were found between root morphology,soluble sugars,sucrose content,and sucrose phosphate synthase activity with fiber quality traits,respectively.Conclusions:These findings suggest that CCRI-69 performed better in terms of growth and fiber quality under relatively low N condition,which will help to reduce fertilizer use,the cost of production,and environmental pollution.

Irrigation's effect and applied selection on the fiber quality of Ethyl MethaneSulfonate(EMS)treated upland cotton(Gossypium hirsutum L.)

Background: Producing rainfed cotton(Gossypium hirsutum L.) with high fiber quality has been challenging in the Texas High Plains because of extended periods of insufficient rainfall during sensitive boll developmental stages.Genetic variation created by Ethyl MethaneSulfonate(EMS) mutagen has successfully improved fiber quality of cotton. However, little is known about the effect of water deficit environments on fiber quality. Three EMS treated populations were advanced from the first to the fourth generation(M1 to M4) as bulk harvested populations. In2014, single-plant divergent selection was applied based on perceived morphological and agronomic differences seen during and at the end of the season.Results: Analyses from these selections in 2014-2016 showed significant(P< 0.05) improvement between and within populations for fiber traits(micronaire, length, strength, uniformity, and elongation) when compared with the original non-treated EMS source; some selections were found to have excellent fiber quality under diverse irrigationregimes.Conclusions: Some of these selections are being considered for germplasm release and could be useful for improving the fiber quality of cotton under water limited conditions, thereby helping to ensure the long-term survival of the cotton industry on the Texas High Plains.

Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL,significant SNP and transcriptomic data

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 8589 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.

Improvement of Fiber Quality by Distant Hybridization in the Green Cotton

In order to improve fiber quality of green cotton,a wide hybrid was used between a green fiber cotton and Sea Island cotton.The results show that the hybrid F1 plants were stable,but F2

Relationship Between the N Concentration of the Leaf Subtending Boll and the Cotton Fiber Quality

This experiments were conducted in Nanjing （118~50＂E, 32~02＂N） and Xuzhou （117~11 ＂E, 34~15＂N）, Jiangsu Province, China, to study the response of fiber quality to the N concentration of the leaf subtending boll in cotton （Gossypium hirsutum L.）. Results suggested that the N dilution curve of the leaf subtending boll can accurately indicate the stage- specific plant N status for fiber development. Fiber strength is likely to be the most variable fiber quality index responding to the leaf N variation which is different in cultivars. Fiber length was the most stable index among strength, length, micronaire, and elongation. There existed an optimum leaf N concentration for fiber strength development in each stage. The optimum leaf N regression curve was very close to the N dilution curve in the middle positional fruiting branches under the 240 kg N ha-1 soil N application rate.

QTL Analysis of Fiber Yield and Quality and Resistance to Verticillium Wilt Using Gossypium hirsutum and G.barbadense Advanced Backcross Populations

To introgress elite QTL alleles of Gossypium barbadense L.for fiber yield and quality and resistance to Verticillium wilt into G.hirsutum L.,enlarge the genetic base of G.hirsutum,and