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| 1 | Genetic variations in plant architecture traits in cotton(Gossypium hirsutum) revealed by a genomewide association study显示文摘Plant architecture traits influence crop yield. An understanding of the genetic basis of cotton plant architecture traits is beneficial for identifying favorable alleles and functional genes and breeding elite cultivars. We collected 121 cotton accessions including 100 brownfiber and 21 white-fiber accessions, genotyped them by whole-genome resequencing, and phenotyped them in multiple environments. This genome-wide association study(GWAS)identified 11 quantitative trait loci(QTL) for two plant architecture traits: plant height and fruit spur branch number. Negative-effect alleles were enriched in the elite cultivars. Based on these QTL, gene annotation information, and published QTL, candidate genes and natural genetic variations in four QTL were identified. Ghir_D02 G017510 and Ghir_D02 G017600 were identified as candidate genes for qD02-FSBN-1, and a premature start codon gain variation was found in Ghir_D02 G017510. Ghir_A12 G026570, the candidate gene of qA12-FSBN-2, belongs to the pectin lyase-like superfamily, and a significantly associated SNP, A12_105366045(T/C), in this gene represents an amino acid change. The QTL, candidate genes, and associated natural variations in this study are expected to lay a foundation for studying functional genes and developing breeding programs for desirable architecture in brown-fiber cotton. | Tianwang Wen Baosheng Dai Tao Wang Xinxin Liu Chunyuan You Zhongxu Lin | 2019 | The Crop Journal2019，7，2： | 4 |
| 2 | Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL,significant SNP and transcriptomic data显示文摘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. | XU Shudi PAN Zhenyuan YIN Feifan YANG Qingyong LIN Zhongxu WEN Tianwang ZHU Longfu ZHANG Dawei NIE Xinhui | 2020 | Journal of Cotton Research2020，3，4： | 1 |
| 3 | Effects of mepiquat chloride and plant population density on leaf photosynthesis and carbohydrate metabolism in upland cotton显示文摘Background Mepiquat chloride(MC)application and plant population density(PPD)increasing are required for modern cotton production.However,their interactive effects on leaf physiology and carbohydrate metabolism remain obscure.This study aimed to examine whether and how MC and PPD affect the leaf morpho-physiological characteristics,and thus final cotton yield.PPD of three levels(D1:2.25 plants·m^(-2),D2:4.5 plants·m^(-2),and D3:6.75 plants·m^(-2))and MC dosage of two levels(MC0:0 g·ha^(-2),MC1:82.5 g·ha^(-2))were combined to create six treatments.The dynamics of nonstructual carbohydrate concentration,carbon metabolism-related enzyme activity,and photosynthetic attributes in cotton leaves were examined during reproductive growth in 2019 and 2020.Results Among six treatments,the high PPD of 6.75 plants·m^(-2)combined with MC application(MC1D3)exhibited the greatest seed cotton yield and biological yield.The sucrose,hexose,starch,and total nonstructural carbohydrate(TNC)concentrations peaked at the first flowering(FF)stage and then declined to a minimum at the first boll opening(FBO)stage.Compared with other treatments,MC1D3 improved starch and TNC concentration by 5.4%~88.4%,7.8%~52.0% in 2019,and by 14.6%~55.9%,13.5%~39.7% in 2020 at the FF stage,respectively.Additionally,MC1D3 produced higher transformation rates of starch and TNC from the FF to FBO stages,indicating greater carbon production and utilization efficiency.MC1D3 displayed the maximal specific leaf weight(SLW)at the FBO stage,and the highest chlorophyll a(Chl a),Chl b,and Chl a+b concentration at the mid-late growth phase in both years.The Rubisco activity with MC1D3 was 2.6%~53.2% higher at the flowering and boll setting stages in both years,and 2.4%~52.7% higher at the FBO stage in 2020 than those in other treatments.These results provided a explanation of higher leaf senescence-resistant ability in MC1D3.Conclusion Increasing PPD coupled with MC application improves cotton yield by enhancing leaf carbohydrate production and utilization efficiency and delaying leaf senescence. | LUO Haihua ZHANG Zhengxian WU Jianfei WU Zhenjiang WEN Tianwang TANG Feiyu | 2023 | Journal of Cotton Research2023，6，4： | 0 |
| 4 | A case study of a micro-inversion event in dark brown fibre cotton(Gossypium hirsutum)显示文摘Structural variation is a major type of genetic variation that can potentially induce powerful genetic effects.In this study,we examined the Inv(A07)p1.09 p2.23 genetic inversion in brown fibre cotton at the individual and population genetics levels.A dark-brown fibre mutant that resulted from a distant hybridization between Gossypium barbadense and G.hirsutum,and a natural population including 30 dark-brown,70 light-brown and 21 white fibre cotton accessions were collected to perform a functional study of this micro-inversion.The results showed that Inv(A07)p1.09 p2.23 can be detected by high-throughput resequencing method,and induce micro-deletion,gene disruption(Ghir_A07 G000980)and abnormal gene expression in the breakpoint regions.Inv(A07)p1.09 p2.23 existed in only dark-brown fibre cotton,had undergone negative selection in elite brown fibre cultivars,and was significantly associated with fibre colour and nine fibre traits.In the Inv(A07)p1.09 p2.23 region,nucleotide diversity was lower,recombination was absent,and linkage disequilibrium was higher.Overall,this inversion event in dark-brown fibre cotton produced significant genetic effects,and this study will guide us to better understand the genetic effects of inversion events in dark-brown fibre cotton. | Tianwang Wen Tian Yao Chunyuan You Zhongxu Lin | 2020 | The Crop Journal2020，8，4： | 0 |
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