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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 | Phenylpropanoid metabolism and pigmentation show divergent patterns between brown color and green color cottons as revealed by metabolic and gene expression analyses显示文摘Background:Naturally-colored cotton has become increasingly popular because of their natural properties of coloration,UV protection,flame retardant,antibacterial activity and mildew resistance.But poor fiber quality and limited color choices are two key issues that have restricted the cultivation of naturally-colored cotton.To identify the possible pathways participating in fiber pigmentation in naturally-colored cottons,five colored cotton accessions in three different color types(with green,brown and white fiber)were chosen for a comprehensive analysis of phenylpropanoid metabolism during fiber development.Results:The expression levels of flavonoid biosynthesis pathway genes in brown cotton fibers were significantly higher than those in white and green cotton fibers.Total flavonoids and proanthocyanidin were higher in brown cotton fibers relative to those in white and green cotton fibers,which suggested that the flavonoid biosynthesis pathway might not participate in the pigmentation of green cotton fibers.Further expression analysis indicated that the genes encoding enzymes for the synthesis of caffeic acid derivatives,lignin and lignan were activated in the developing fibers of the green cotton at 10 and 15 days post-anthesis.Conclusions:Our results strengthen the understanding of phenylpropanoid metabolism and pigmentation in green and brown cotton fibers,and may improve the breeding of naturally-colored cottons. | LI Zhonghua SU Qian XU Mingqi YOU Jiaqi KHAN Anam Qadir LI Junyi ZHANG Xianlong TU Lili YOU Chunyuan | 2020 | Journal of Cotton Research2020，3，4： | 1 |
| 3 | 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 |
| 4 | Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China显示文摘Background: Cotton fiber yield is a complex trait,which can be influenced by multiple agronomic traits.Unravelling the genetic basis of cotton fiber yield-related traits contributes to genetic improvement of cotton.Results: In this study,503 upland cotton varieties covering the four breeding stages(BS1–BS4,1911–2011)in China were used for association mapping and domestication analysis.One hundred and forty SSR markers significantly associated with ten fiber yield-related traits were identified,among which,29 markers showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4,and 26 markers showed decreased trend effect.Four favorable alleles of 9 major loci(R^(2)≥3)were strongly selected during the breeding stages,and the candidate genes of the four strongly selected alleles were predicated according to the gene function annotation and tissue expression data.Conclusions :The study not only uncovers the genetic basis of 10 cotton yield-related traits but also provides genetic evidence for cotton improvement during the cotton breeding process in China. | GUO Chunping PAN Zhenyuan YOU Chunyuan ZHOU Xiaofeng HUANG Cong SHEN Chao ZHAO Ruihai YANG Qingyong ZHU Longfu SHAHZAD Raheel MENG Fande LIN Zhongxu NIE Xinhui | 2021 | Journal of Cotton Research2021，4，2： | 0 |
| 5 | Identification of candidate genes for aphid resistance in upland cotton by QTL mapping and expression analysis显示文摘Lignin is one of the main components of cell walls and is essential for resistance to insect pests in plants.Cotton plants are damaged by aphid(Aphis gossypii) worldwide but resistant breeding is undeveloped due to scarce knowledge on resistance genes and the mechanism. This study reported a lignin biosynthesisrelated gene identified in the F_(2) population derived from the cross between cotton cultivars Xinluzao 61(resistant to aphid) and Xinluzao 50(susceptible to aphid). A quantitative trait locus was mapped on chromosome D04 with a logarithm of odds(LOD) score of 5.99 and phenotypic effect of 27%. RNA-seq analysis of candidate intervals showed that the expression level of GH_D04G1418 was higher in the resistant cultivar than in the susceptible cultivar. This locus is close to AtLAC4 in the phylogenetic tree and contains a conserved laccase domain. Hence, it was designated GhLAC4-3. Silencing of GhLAC4-3 in Xinluzao 61 via virus-induced gene silencing(VIGS) resulted in decreased lignin content and increased susceptibility to aphids. These results suggest that GhLAC4-3 might enhance aphid resistance by regulating lignin biosynthesis in cotton. | Qiushuang An Zhenyuan Pan Nurimanguli Aini Peng Han Yuanlong Wu Chunyuan You Xinhui Nie | 2023 | The Crop Journal2023，11，5： | 0 |
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