Identification of candidate genes for early-maturity traits by combining BSA-seq and QTL mapping in upland cotton(Gossypium hirsutum L.)

Cotton breeding for the development of early-maturing varieties is an effective way to improve multiple cropping indexes and alleviate the conflict between grains and cotton in the cultivated fields in China.In the present study,we aimed to identify upland cotton quantitative trait loci(QTLs)and candidate genes related to early-maturity traits,including whole growth period(WGP),flowering timing(FT),node of the first fruiting branch(NFFB),height of the node of the first fruiting branch(HNFFB),and plant height(PH).An early-maturing variety,CCRI50,and a latematuring variety,Guoxinmian 11,were crossed to obtain biparental populations.These populations were used to map QTLs for the early-maturity traits for two years(2020 and 2021).With BSA-seq analysis based on the data of population 2020,the candidate regions related to early maturity were found to be located on chromosome D03.We then developed 22 polymorphic insertions or deletions(InDel)markers to further narrow down the candidate regions,resulting in the detection of five and four QTLs in the 2020 and 2021 populations,respectively.According to the results of QTL mapping,two candidate regions(InDel_G286-InDel_G144 and InDel_G24-InDel_G43)were detected.In these regions,three genes(GH_D03G0451,GH_D03G0649,and GH_D03G1180)have nonsynonymous mutations in their exons and one gene(GH_D03G0450)has SNP variations in the upstream sequence between CCRI50 and Guoxinmian 11.These four genes also showed dominant expression in the floral organs.The expression levels of GH_D03G0451,GH_D03G0649 and GH_D03G1180 were significantly higher in CCRI50 than in Guoxinmian 11 during the bud differentiation stages,while GH_D03G0450 showed the opposite trend.Further functional verification of GH_D03G0451 indicated that the GH_D03G0451-silenced plants showed a delay in the flowering time.The results suggest that these are the candidate genes for cotton early maturity,and they may be used for breeding early-maturity cotton varieties.

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.

Breeding against mycorrhizal symbiosis:Modern cotton (Gossypium hirsutum L.) varieties perform more poorly than older varieties except at very high phosphorus supply levels

Cotton (Gossypium hirsutum L.) is an importantfiber cash crop,but its root traits related to phosphorus (P) acquisition,including mycorrhizal root traits,are poorly understood.Eight cotton varieties bred in northwestern China that were released between 1950 and 2013 were grown in pots with or without one arbuscular mycorrhizal fungal (AMF) species(Funneliformis mosseae) at three P supply levels (0,50 and 300 mg P as KH_(2)PO_(4)kg^(-1)).Eleven root traits were measured and calculated after 7 wk of growth.The more recent accessions had smaller root diameters,acquired less P and produced less biomass,indicating an (inadvertent) varietal selection for thinner roots that provided less cortical space for AMF,which then increased the need for a high P fertilizer level.At the two lower P levels,the mycorrhizal plants acquired more P and produced more biomass than non-mycorrhizal plants (3.2 vs.0.9 mg P per plant;1.8 vs.0.9 g biomass per plant at P_(0);14.5 vs.1.7 mg P per plant;and 4.7 vs.1.6 g biomass per plant at P_(50)).At the highest P level,the mycorrhizal plants acquired more P than non-mycorrhizal plants (18.8 vs.13.4 mg per P plant),but there was no difference in biomass (6.2 vs.6.3 g per plant).At the intermediate P level,root diameter was significantly positively correlated with shoot biomass,P concentration and the P content of mycorrhizal plants.The results of our study support the importance of the outsourcing model of P acquisition in the root economics space framework.Inadvertent varietal selection in the last decades,resulting in thinner roots and a lower benefit from AMF,has led to a lower productivity of cotton varieties at moderate P supply (i.e.,when mycorrhizal,the average biomass of older varieties 5.0 g per plant vs.biomass of newer varieties 4.4 g per plant),indicating the need to rethink cotton breeding efforts in order to achieve high yields without very high P input.One feasible way to solve the problem of inadvertent varietal selection for cotton is to be aware of the trade-offs between the root do-it-yourself strategy and the outsourcing towards AMF strategy,and to consider both morphological and mycorrhizal root traits when breeding cotton varieties.

Are yarn quality prediction tools useful in the breeding of high yielding and better fibre quality cotton(Gossypium hirsutum L.)?

Results The population had large variations for lint yield,fibre properties,predicted yarn properties,and composite fibre quality values.Lint yield with all fibre quality traits was not correlated.When the selection was conducted first to keep those with improved fibre quality,and followed for high yields,a large proportion in the resultant populations was the same between selections based on Cottonspec predicted yarn quality and HVI-measured fibre properties.They both exceeded the selection based on FQI and Background The approach of directly testing yarn quality to define fibre quality breeding objectives and progress the selection is attractive but difficult when considering the need for time and labour.The question remains whether yarn prediction tools from textile research can serve as an alternative.In this study,using a dataset from three seasons of field testing recombinant inbred line population,Cottonspec,a software developed by the Commonwealth Scientific and Industrial Research Organisation(CSIRO)for predicting ring spun yarn quality from fibre properties measured by High Volume Instrument(HVI),was used to select improved fibre quality and lint yield in the population.The population was derived from an advanced generation inter-crossing of four CSIRO conventional commercial varieties.The Cottonspec program was able to provide an integrated index of the fibre qualities affecting yarn properties.That was compared with selection based on HVI-measured fibre properties,and two composite fibre quality variables,namely,fibre quality index(FQI),and premium and discount(PD)points.The latter represents the net points of fibre length,strength,and micronaire based on the Premiums and Discounts Schedule used in the market while modified by the inclusion of elongation.PD points.Conclusions The population contained elite segregants with improved yield and fibre properties,and Cottonspec predicted yarn quality is useful to effectively capture these elites.There is a need to further develop yarn quality prediction tools through collaborative efforts with textile mills,to draw better connectedness between fibre and yarn quality.This connection will support the entire cotton value chain research and evolution.

Present Status, Problems and Prospects of Molecular Breeding of Cotton (Gossypium) with Resistance against Verticillium dahliae Kleb.

VerticiUium wilt is an important disease in cotton production, which seriously affects the production of cotton. The classification and pathogenesis of Yer-ticillium dahliae Kleb. , achievements in QTL mapping and molecular breeding were reviewed in the paper. Meanwhile, the current problems and future direction of resistance breeding against V. dahliae Kleb. were discussed so as to provide reference information for further research on resistance breeding against the pathogen.

Breeding of High Yield and Genetically Modified Hybrid Cotton-Sumian 29

Sumian 29, a genetically modified cotton variety, was approved by Autho- rized Committee of Crop Varieties of Jiangsu Province in 2013. Yield performance, cultivation characteristics of Sumian 29, and its selection and breeding process were introduced in the paper. Regional tests from 2010 to 2011 in Jiangsu Province showed that seed cotton yield and lint yield averaged 4 185 and 1 737 kg/hm2, and increased by 10.6% and 8.5% respectively, when compared with control （Siza 3）. In production test, seed cotton yield and lint yield of Sumian 29 averaged 4 176 and 1 744.5 kg/hm2, respectively. Sumian 29 had high resistance to cotton bollworm, and also resistance to Fusarium wilt and Verticillium wilt of cotton. All of its fiber qualities achieved National Standard III and above. Sumian 29 has good application prospects.

Advances in Cotton Breeding for Resistance to Fusarium and Verticillium Wilt in the Last Fifty Years in China

This review summarizes the main advances in cotton breeding for resistance to fusarium and verticillium wilt in the last fifty years in China. The topics discussed include main achievements, experiences, problems and countermeasures for solving.

Patent analysis provides insights into the history of cotton molecular breeding worldwide over the last 50 years

Cotton is a globally important natural fiber and oilseed crop of crucial economic significance. Molecular breeding has become a dominant method of cotton cultivation because it allows for a shorter breeding period and directional selection of high quality genes. Patent data are key resources and are the core competitiveness of agricultural development, as the world's largest and most reliable source of technical information. However, little attention has been paid to patent analysis of cotton molecular breeding. This study uses bibliometric analysis methodology and technical classification indexing to reveal global development trends of cotton molecular breeding, based on patents by retrieval methods and expert screening. The annual number of patents, the life-cycle of patent-based technology, patent portfolios of primary countries, and main patentees, as well as technical distribution of patents, were analyzed in this study. In addition, this study put emphasis on the comparative analysis of two important patentees through patent roadmaps based on the relationship among patent citations. Finally, in order to understand the trend of new molecular breeding technology, patents related to clustered regularly interspaced short palindromic repeats(CRISPR), RNA interference(RNAi), and gene chip were also analyzed, all of which apply to cotton but also to other crops. Results in this paper can provide references for cotton molecular breeding researchers and relevant management departments.

Genetics of biochemical attributes regulating morpho-physiology of upland cotton under high temperature conditions

Background Cotton is a strategically important fibre crop for global textile industry.It profoundly impacts several countries’industrial and agricultural sectors.Sustainable cotton production is continuously threatened by the unpre-dictable changes in climate,specifically high temperatures.Breeding heat-tolerant,high-yielding cotton cultivars with wide adaptability to be grown in the regions with rising temperatures is one of the primary objectives of modern cotton breeding programmes.Therefore,the main objective of the current study is to figure out the effective breed-ing approach to imparting heat tolerance as well as the judicious utilization of commercially significant and stress-tolerant attributes in cotton breeding.Initially,the two most notable heat-susceptible(FH-115 and NIAB Kiran)and tolerant(IUB-13 and GH-Mubarak)cotton cultivars were spotted to develop filial and backcross populations to accom-plish the preceding study objectives.The heat tolerant cultivars were screened on the basis of various morphological(seed cotton yield per plant,ginning turnout percentage),physiological(pollen viability,cell membrane thermostabil-ity)and biochemical(peroxidase activity,proline content,hydrogen peroxide content)parameters.Results The results clearly exhibited that heat stress consequently had a detrimental impact on every studied plant trait,as revealed by the ability of crossing and their backcross populations to tolerate high temperatures.However,when considering overall yield,biochemical,and physiological traits,the IUB-13×FH-115 cross went over particularly well at both normal and high temperature conditions.Moreover,overall seed cotton yield per plant exhibited a posi-tive correlation with both pollen viability and antioxidant levels(POD activity and proline content).Conclusions Selection from segregation population and criteria involving pollen viability and antioxidant levels concluded to be an effective strategy for the screening of heat-tolerant cotton germplasms.Therefore,understanding acquired from this study can assist breeders identifying traits that should be prioritized in order to develop climate resilient cotton cultivars.

Red fluorescent protein (DsRed2), an ideal reporter for cotton genetic transformation and molecular breeding

Genes encoding reporter proteins are used as visual marker-assisted tools in genetic transformation as well as plant breeding. In this study, the red fluorescent protein identified in Discosoma sp. coral(DsRed2) was successfully used as a visual marker for cotton genetic engineering. DsRed2 was successfully expressed in two cotton cultivars,JIN668 and YZ1, driven by the Ca MV-35 S promoter via the Agrobacterium-mediated transformation. Our results suggest that DsRed2 expression provides an early-stage selection tool for the transgenic calli via visual observation. Red fluorescence can be detected not only in callus and somatic embryos but also in most tissues and organs of mature plants. The transgenic line Yz-2-DsRed2 was crossed with four different cotton cultivars to assess the transgene heritability and stability in different genetic backgrounds.The heritability of the red color was highly stable when Yz-2-DsRed2 was used as a male parent. The DsRed2 gene expressed 100% in the F_1 hybrids. To investigate the relationship between DsRed2 transcription and DNA methylation, a methylation-specific PCR approach was applied to the Ca MV-35 S promoter region. The results showed a negative association between DNA methylation level in the promoter region and the transgene transcription.Taken together, these findings suggest DsRed2 a visual reporter gene for cotton genetic transformation and molecular breeding programs.

Cotton Breeding in Xinjiang and Its Intellectual Property Protection

In 2021,Xinjiang's cotton output was 5.129 million t,accounting for 89.50%of China's total.The autonomous region produces high-quality long-staple cotton,natural colored cotton,fine-staple cotton(upland cotton),organic cotton,etc.The southern Xinjiang cotton area is one of the three major long-staple cotton(island cotton)producing regions in the world.This paper introduced the history of cotton planting and breeding in Xinjiang from the aspects of cultural relics records,history of entering Xinjiang,historical achievements of breeding and breeding leaders.We studied the intellectual property protection of cotton breeding in the autonomous region from the aspects of biological genetic resources,invention patents,utility model patents and new plant varieties,analyzed the six main problems existing in cotton breeding and its intellectual property protection,and discussed the tactics for cotton breeding and its intellectual property protection in Xinjiang under the strategy of strengthening the country with intellectual property.Eight suggestions in response to the Xinjiang cotton incident were also put forward,including establishing a Xinjiang national cotton germplasm nursery,protecting biological genetic resources,and strengthening the protection of creative intellectual property rights in the field of breeding to escort technological innovation in the cotton seed industry.

Pyramiding Breeding by Marker-Assisted Recurrent Selection in Upland Cotton: Selected Effects on Resistance to Helicoverpa armigera

The coincidence rates were more than 96% among the instar-weighted average of bioassaysin the lab, the percentage of resistance to Km in the field and the percentage of plantscontaining Bt gene. So, the performance of resistance to Km in the field can be used torepresent the transgenic Bt gene for selecting the resistance to bollworm. The instar-weighted averages were 30.585, 24.182, 16.615, 10.601, 10.123, 7.440 and 7.215 for theC0, P1, M1, M2, MP1, P2 and MP2 populations, respectively. The variance analysisindicated that the instar-weighted average in C0 was greatly significantly higher thanthat in all other populations, i.e., the performance of resistance to bollworm in C0 washighly significantly lower than all other populations. And the resistance in P1 wasgreatly lower than that of M1, M2, MP1, P2 and MP2, and M1 greatly lower than that of M2,MP1, P2 and MP2. There were no significant differences among M2, MP1, P2 and MP2. Withinthe populations of the first cycle selection, MP1 and M1 were greatly significantlyhigher than P1, and MP1 significantly higher than M1. The populations of the second cycleselection were significantly higher than their initial population M1, but no significantdifference among them. The boll size, seed index, the percent of the first harvest yield,fiber length, strength and elongation of the resistant plants to bollworm were significantlylower than that of sensitive plants to bollworm. And the yield of seed and lint cottonof the resistant plant to bollworm were lower than that of the sensitive to bollworm, butno significant difference between them. The boll numbers per plant, lint percent andmicronaire of the resistant plants to bollworm were significantly higher than that of thesensitive plant to bollworm.

The Utilization of HB-red Flower in Hybrid Cotton Breeding

The HB-red flower trait came from the filial generation of the interspecific cross of upland cotton(Gossypium hirsutum L.) and G.bickii.It exhibits pink petals and filaments,with a large

Progress and perspective on cotton breeding in Pakistan

Cotton is the prime natural fiber with economic significance globally.Cotton farming and breeding have a long his-tory in Pakistan.The development of high yielding upland cotton(Gossypium hirsutum)varieties gradually replaced the cultivation of diploid Gossypium species.Climate change along with emergence of new epidemic diseases caused yield loss in recent years.The biotic stress considerably reduced the performance and yield potential of cotton.Suit-able breeding strategies are essential to generate useful genetic variations and to identify desired traits.Conventional breeding has remarkably increased cotton yield and fiber quality,which has cultivated the NIAB-78,S-12,MNH‐786,and FH‐Lalazar like cultivars.However,this phenotypic selection based breeding method has low efficiency to pro-duce stress resilient cotton.The efficiency of traditional breeding has significantly improved by the marker assisted selection technology.Breakthroughs in molecular genetics,bioinformatics analysis,genetic engineering,and genome sequencing have opened new technique routes for cotton breeding.In addition,genetic improvement through quantitative trait loci,transcriptome,and CRISPR/Cas9 mediated genomic editing can provide suitable platform to improve the resistance to stresses induced by bollworms,cotton leaf curl virus,heat,drought,and salt.The approval of transgenic lines harboring triple gene Cry1Ac+Cry2A+GTG are critical for cotton crop.This review has critically discussed the progress and limitations of cotton breeding in Pakistan,and reviewed the utilization of novel genetic variations and selection tools for sustainable cotton production.

Breeding of High Yield,High Quality and Disease-Resistant Hybrid Cotton Varieties Hanza 160 and Hanza 1692

The hybrid cotton varieties of Hanza 160 and Hanza 1692 were bred by reciprocal crosses between Han 5158 and Han 333 in Hainan and Hebei for several years. Both varieties had the characters of high yield, high quality and disease resistance. Hanza 160 and Hanza 1692 were approved by Hebei Crop Variety Approval Committee in 2013 and 2016, respectively.

Utilization of Cotton DNA Markers in Cotton Breeding

Informative,portable,and efficient DNA markers have the potential to accelerate genetic gain in cotton breeding.Discovery and widespread application of DNA markers to cotton has

Breeding of Good-quality High-yield Salt-tolerant and Drought-resistant Hybrid Cotton Variety Hengyou 12

Salt and drought tolerance, high yield and quality, disease and pest resistance of cotton varieties are new requirements for the current situation in cotton production. Hengyou 12 is a transgenic Bt cotton variety bred by hybridizing JD 28 （interspeciflc progeny of upland cotton, sea-island cotton, wild cotton species） as female parent with GK55 （transgenic Bt cotton variety） as male parent. The combining of parents was based on the complementary principle of parental traits. Hengyou 12 with strong heterosis was selected under disease stress, pest stress, salt stress and drought stress. This variety has many excellent characteristics, such as good resis- tance to diseases and pests, high yield, excellent quality, strong drought resistance and salt tolerance. ＇Hengyou12＇ was approved by Hebei Province in 2015, and is suitable for planting in middle and south areas of Hebei and similar ecological areas in the Yellow River basin.

Studies on Cotton Breeding Resistant to Fusarium and Verticillium wilt Diseases

Both Fusarium and Verticillium wilts are important soil-borne diseases,which can not be effectively controlled by chemical fungicides.The two diseases,especially Verticillium wilt,have

Genetic Resources for Cotton Breeders, The Current Status and Storms Ahead

The sources of germplasm for the cotton breederto use as parents are changing.There are severalfactors effecting this change.Public collectionsare available but are operating under some serverrestrictions.The United States public collectionavailable to breeders has broadened due toaccessions from the former Soviet Union.

In Vitro Mutagenesis-Alternate Approach to Breeding of Gossypium hirsutum L.

Mutations are possibly the only source ofcreating heritable variability in all biologicalsystem and,many useful mutants in plants havebeen released for commercial cultivation acrossthe world.To-date throughout the world about2252 mutants have been officially registered inthe FAO/IAEA mutant varieties data