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 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

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.

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.

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

Developmental and hormonal regulation of fiber quality in two natural-colored cotton cultivars

Cotton cultivars with brown （Xiangcaimian 2）, green （Wanmian 39） and white （Sumian 9） fiber were investigated to study fiber developmental characteristics of natural-colored cotton and the effect of hormones on fiber quality at different stages after anthesis. Fiber lengths of both natural-colored cottons were lower than the white-fibered control, with brown-fibered cotton longer than green. Fiber strength, micronaire and maturation of natural-colored cotton were also lower than the control. The shorter fiber of the green cultivar was due to slower growth during 10 to 30 days post-anthesis （DPA）. Likewise, the lower fiber strength, micronaire and maturation of natured-colored cotton were also due to slower growth during this pivotal stage. Indole-3-acetic acid （IAA） content at 10 DPA, and abscisic acid （ABA） content at 30 to 40 DPA were lower in the fibers of the natural-colored than that of the white-fibered cotton. After applying 20 mg L-1 gibberellic acid （GA3）, the IAA content at 20 DPA in the brown and green-fibered cottons increased by 51.07 and 64.33%, fiber ABA content increased by 38.96 and 24.40%, and fiber length increased by 8.13 and 13.96%, respectively. Fiber strength, micronaire and maturation were also enhanced at boll opening stage. Those results suggest that the level of endogenous hormones affect fiber quality. Application of external hormones can increase hormone content in natural-colored cotton fiber, improving its quality.

Genetical Genomics Dissection of Cotton Fiber Quality

Cotton fiber is a commodity of key economic importance in both developed and developing countries.The two cultivated species,Gossypium hirsutum and G.barbadense,are

Molecular Markers in Improvement of Fiber Quality Traits in Cotton

Cotton is the worlds leading natural fiber crop,and it is the cornerstone of textile industries worldwide.The cotton industry is confronted with problems in cost of production and

Analysis of the Fiber Quality of Upland Cotton in China from 2005 to 2007

Upper-half-mean length(Len),uniformity index(UI),breaking tenacity(Str),and micronaire value(Mic) are the key quality parameters of cotton fiber.In this study,182 upland cotton

High day and night temperatures impact on cotton yield and quality——current status and future research direction

Heat waves,and an increased number of warm days and nights,have become more prevalent in major agricultural regions of the world.Although well adapted to semi-arid regions,cotton is vulnerable to high temperatures,particularly during flowering and boll development.To maintain lint yield potential without compromising its quality under high-temperature stress,it is essential to understand the effects of heat stress on various stages of plant growth and development,and associated tolerance mechanisms.Despite ongoing efforts to gather data on the effects of heat stress on cotton growth and development,there remains a critical gap in understanding the distinct influence of high temperatures during the day and night on cotton yield and quality.Also,identifying mechanisms and target traits that induce greater high day and night temperature tolerance is essential for breeding climate-resilient cotton for future uncertain climates.To bridge these knowledge gaps,we embarked on a rigorous and comprehensive review of published literature,delving into the impact of heat stress on cotton yields and the consequential losses in fiber quality.This review encompasses information on the effects of heat stress on growth,physiological,and biochemical responses,fertilization,cotton yield,and quality.Additionally,we discuss management options for minimizing heat stress-induced damage,and the benefits of integrating conventional and genomics-assisted breeding for developing heat-tolerant cotton cultivars.Finally,future research areas that need to be addressed to develop heat-resilient cotton are proposed.

Effect of Storage Time on Main Quality Indicators of Cotton

The quality indicators of cotton will change during storage.Taking the 5.89 million t of Xinjiang cotton from 2016 to 2021 as a sample,this paper analyzed the main fiber quality indicator data of warehouse-in and warehouse-out cotton for storage of 1.5,3.0,4.0,5.0,6.0,and 7.0 years.It was found that the color grade of cotton decreased with the extension of storage time.The cotton with storage time of 5.0 years mainly changed from white cotton grade 2 and white cotton grade 3 to light yellow stained cotton grade 1 and yellow stained cotton grade 1.Among them,the increase of light yellow stained cotton grade 1 was the largest,and the change to yellow stained cotton grade 1 was the largest at the storage 6.0-7.0 years.In addition,there were no significant changes in moisture regain,Micronaire value,upper half mean length,length uniformity index and fiber strength.

Modeling Fiber Fineness, Maturity, and Micronaire in Cotton (Gossypium hirsutum L.)

Crop performance is determined by the combined effects of the genotype of the crop and the environmental conditions of the production system. This study was undertaken to develop a dynamic model for simulating environmental （temperature and solar radiation） and N supply effects on fiber fineness, maturity and micronaire. Three different experiments involving genotypes, sowing dates, and N fertilization rates were conducted to support model development and model evaluation. The growth and development duration of fiber fineness, maturity, and micronaire were scaled by using physiological development time of secondary wall synthesis （PDT SWSP ）, which was determined based on the constant ratio of SWSP/ BMP. PTP （product of relative thermal effectiveness （RTE） and photosynthetically active radiation （PAR）, MJ m-2） and subtending leaf N content per unit area （N A , g m-2） and critical subtending leaf N content per unit area （CN A , g m-2） of cotton boll were calculated or simulated to evaluate effects of temperature and radiation, and N supply. Besides, the interactions among temperature, radiation and N supply were also explained by piecewise function. The overall performance of the model was calibrated and validated with independent data sets from three field experiments with two sowing dates, three or five flowering dates and three or four N fertilization rates for three subsequent years （2005, 2007, and 2009） at three ecological locations. The average RMSE and RE for fiber fineness, maturity, and micronaire predictions were 372 m g-1 and 5.0%, 0.11 m g-1 and 11.4%, 0.3 m g-1 and 12.3%, respectively, indicating a good fit between the simulated and observed data. It appears that the model can give a reliable prediction for fiber fineness, maturity and micronaire formation under various growing conditions.

Effects of chemical topping on cotton development,yield and quality in the Yellow River Valley of China

Topping is a cultivation method that is widely practiced due to the indeterminate growth character of cotton(Gossypium hirsutum L.). Among the different methods of accomplishing topping, manual topping is common in the Yellow River Valley of China, although it is time-and labor-intensive. The objective of this study was to characterize the responses of cotton to different topping treatments with respect to development, yield and quality. This study included field experiments from 2015 to 2016 with three different topping methods: manual topping(MT), chemical topping(CT) using mepiquat chloride,and a non-decapitation treatment(NT). We found that the plant height, the number of fruiting branches and the length of upper fruiting branches of cotton treated with CT were significantly lower than NT. The chlorophyll content of cotton treated with CT was not significantly different from NT, but was higher than that of MT in the later season. CT enhanced plant development with reduced endogenous gibberellic acid and abscisic acid contents, and the apical development of the main stem was inhibited. Compared with MT, CT significantly increased the biomass of the vegetative parts. Most importantly,there were no significant differences in the yield or fiber quality between MT and CT. These findings suggested that CT, a simplified and effective topping method, could be utilized as an alternative in the Yellow River Valley of China.