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

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The Crop Journal 2020年第1期8卷 98-106页

作者： Hantao Wang Ruiting Zhang Chao Shen Ximei Li De Zhu zhongxu lin State Key Laboratory of Cotton Biology Institute of Cotton Research of CAASAnyang 455000HenanChina National Key Laboratory of Crop Genetic Improvement College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070HubeiChina cCollege of Agronomy and Plant Protection Qingdao Agricultural UniversityShandong Key Laboratory of Dryland Farming TechnologyQingdao 266109ShandongChina

With increasing demand for high-quality cotton,it is desirable to identify genes involved in fiber development for molecular improvement of *** this study,780 differentially expressed genes(DEGs)were identified in developing fibers at 10 days post-anthesis(DPA)in Gossypium hirsutum ***962 and *** *** 5 using *** 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),*** 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 ***_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 ***_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 *** results suggest candidate genes for molecular improvement of cotton fiber quality.

关键词： Upland cotton Fiber quality RNA-seq QTL Candidate genes

Genome-wide association mapping of stress-tolerance traits in cotton

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The Crop Journal 2019年第1期7卷 77-88页

作者： Heng Sun Minghui Meng Zhenhua Yan zhongxu lin Xinhui Nie Xiyan Yang National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan Agricultural College Shihezi University

Environmental stresses severely impair cotton production worldwide. To identify the genetic basis of, and molecular markers associated with, environmental stresses such as salt, cold and Verticillium wilt, association mapping of salt-, cold-, and disease-tolerance traits was performed in a population of 503 upland cotton accessions using 179 polymorphic SSR markers and 11,975 array-derived SNP markers. Salt and cold tolerance was evaluated via the relative germination rate(RGR) of the seeds under seven and four environments, respectively. The disease index of Verticillium wilt was investigated for two years in the field in Xinjiang. These three traits showed large variation across environments. A genome-wide association study revealed that 31, 19, and 15 SSR markers were associated with RGR-Salt(the relative germination rates of seeds under salt stress),RGR-Cold(the relative germination rates of seeds under cold stress), and DIV(the disease index of Verticillium wilt), respectively. Six SNPs in seven environments and two SNPs in BLUP(best linear unbiased prediction) results were associated with RGR-Salt, and the phenotypic variance explained ranged from 3.96 to 5.00%. Two SNPs(i02237 Gh, i02243 Gh)on D01 were concluded to be stable genetic loci associated with RGR-Salt. A total of 223 genes were found in a candidate gene interval(D01, 37771–1942912). Of these four genes,GhPIP3A, GhSAG29, GhTZF4, and GhTZF4a, showed expression changes in sensitive and tolerant genotype accessions under salt stress, and were assigned as candidate genes associated with RGR-Salt. This study revealed the genetic basis of stress resistance in upland cotton and will facilitate stress-resistance breeding in cotton.

关键词： Upland cotton Stress Relative germination rate SSR SNP Candidate gene

Genetic variations in plant architecture traits in cotton(Gossypium hirsutum) revealed by a genomewide association study

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The Crop Journal 2019年第2期7卷 209-216页

作者： Tianwang Wen Baosheng Dai Tao Wang Xinxin Liu Chunyuan You zhongxu lin National Key Laboratory of Crop Genetic Improvement College of Plant Science and Technology Huazhong Agricultural University Huanggang Academy of Agricultural Sciences Cotton Research Institute Shihezi Academy of Agriculture Science

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.

关键词： Brown-fiber cotton Plant architecture traits GWAS QTL Genetic variation

Studies of new EST-SSRs derived from Gossypium barbadense

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Chinese Science Bulletin 2007年第18期52卷 2522-2531页

作者： ZHANG YanXin lin zhongxu LI Wu TU LiLi NIE YiChun ZHANG XianLong National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan 430070 China

Existing cotton EST-SSR markers are mostly derived from Gossypium arboreum and Gossypium hir-sutum, but EST-SSR markers from Gossypium barbadense are scarce. One hundred and nineteen EST-SSRs were developed based on 98 unique ESTs from a cDNA library constructed in our laboratory using developing fibers from G. barbadense cv. Pima3-79. Among the SSRs, trinucleotide AAG appeared at a high frequency of 11.76%. 36 accessions (consisting of 13 diploids of the A genome, 11 diploids of the D genome and 12 allotetraploids of the AD genome) were employed to test new EST-SSRs. 76 EST-SSRs were successfully amplified, and 313 polymorphic fragments were yielded, with an average of 4.11 fragments per primer pair. The PIC ranged from 0.17 to 0.95 with an average of 0.53. Based on Jaccard’s genetic similarity coefficient, these 36 accessions were clustered into three groups. 21 EST-SSRs exhibited polymorphisms in BC1 population ((Emian22 × Pima3-79) × Emian22), 24 polymor- phic loci were generated, while 22 of the 24 polymorphic loci were integrated with our interspecific BC1 backbone genetic linkage map, and anchored in 12 chromosomes. This study effectively proved that EST-SSRs from G. barbadense are valuable for genetic diversity analysis and genetic mapping.

关键词：棉花基因表达基因序列分析遗传多样性基因图谱

Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors

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Journal of Integrative Plant Biology 2019年第1期61卷 45-59页

作者： Hua Cheng Gaofei Sun Shoupu He Wenfang Gong Zhen Peng Ruiping Wang zhongxu lin Xiongming Du Research Base Anyang Institute of TechnologyState Key Laboratory of Cotton BiologyInstitute of Cotton Researchthe Chinese Academy of Agricultural Science College of Plant Science & Technology of Huazhong Agricultural University Department of Computer Science and Information Engineering Anyang Institute of Technology

An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements(TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium *** was the most abundant TE type and most TEs were located $500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs(siRNAs) that targeted TEs. TEs,particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.

关键词： progenitors allopolyploidization

High-density linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers

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Journal of Integrative Plant Biology 2007年第5期49卷 716-724页

作者： Jiwen Yu Shuxun Yu Cairui Lu Wu Wang Shuli Fan Meizhen Song zhongxu lin Xianlong Zhang Jinfa Zhang National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan 430070 China Key Laboratory for Cotton Genetic Improvement Ministry of Agriculture Anyang 455004 China China Cotton Research Institute Chinese Academy of Agricultural Science Anyang 455004 China Department of Plant and Environmental Sciences New Mexico State University Las Cruces NM 88003 USA

A high-density linkage map was constructed for an F2 population derived from an Interspecific cross of cultivated allotetraploid species between Gossypium hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the Interspecific cross of ＂CRI 36 × Hal 7124＂ were genotyped at I 252 polymorphic loci Including a novel marker system, target region amplification polymorphism （TRAP）. The map consists of 1 097 markers, including 697 simple se- quence repeats （SSRs）, 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1 cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes were Identified In tetraploid cotton. This map will provide an essential resource for high resolution mapping of quantitative trait loci and molecular breeding in cotton.

关键词： cotton linkage map target region amplification polymorphism

Phenotypic plasticity and genetic variation of cotton yield and its related traits under water-limited conditions

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The Crop Journal 2020年第6期8卷 966-976页

作者： Baoqi Li Qin Tian Xuwen Wang Bei Han Li Liu Xianhui Kong Aijun Si Juan Wang zhongxu lin Xianlong Zhang Yu Yu Xiyan Yang National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070HubeiChina Cotton Institute Xinjiang Academy of Agriculture and Reclamation ScienceShihezi 832000XinjiangChina

Global warming is limiting availability of water resources in arid and semi-arid regions,and so understanding water use efficiency(WUE)is increasingly important for agricultural production in those *** China is the largest cotton producing area,the problem of balancing WUE and efficient cotton production is a major *** this study,we used a natural population of 517 Upland cotton accessions to conduct a water-controlled trial in south and north of Xinjiang over two years.A total of 18 traits including agronomic traits,fiber yield indices and fiber quality indices,were investigated for broad-sense heritability and coefficient of *** water limitation was found to promote the establishment of favorable agronomic traits in cotton,associated with an increased cotton yield of 8.46%in Xinjiang,at the expense of a certain degree of fiber quality,such as decreased fiber length and an over-higher micronaire *** detected 33 QTL related to response to water limitation using a drought resistance coefficient(DRC),and 6 QTL were found using a comprehensive indicator of CIDT(comprehensive index of drought tolerance)at the genetic level by integrating resequencing *** novel QTL-hotspots including six differentially expressed genes(DEGs)were further identified related to the drought response of *** findings not only suggested a new approach to irrigation of cotton fields in Xinjiang,but also provided abundant genetic evidence for genetic breeders to study drought improvement of crops.

关键词： Upland cotton Water-limited conditions Fiber yield Fiber quality QTL hotspot

Cotton ethylene response factor Gh ERF91 is involved in the defense against Verticillium dahliae

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Journal of Integrative Agriculture 2024年第10期23卷 3328-3342页

作者： Nurimanguli Aini Yuanlong Wu Zhenyuan Pan Yizan Ma Qiushuang An Guangling Shui Panxia Shao Dingyi Yang Hairong lin Binghui Tang Xin Wei Chunyuan You Longfu Zhu Dawei Zhang zhongxu lin Xinhui Nie Key Laboratory of Oasis Eco-agriculture Xinjiang Production and Construction Group/Agricultural CollegeShihezi UniversityShihezi 832003China National Key Laboratory of Crop Genetic Improvement/College of Plant Sciences&Technology Huazhong AgriculturalUniversityWuhan 430070China Cotton Research Institute Shihezi Academy of Agricultural ScienceShihezi 832011China Institute of Economic Crops Xinjiang Academy of Agricultural SciencesUrumqi 830091China

Verticillium dahliae causes significant losses in cotton *** reveal the mechanism of the defense response to *** in cotton,transcriptomic analyses were performed using cotton cultivars M138(***-resistant)and P2(***-susceptible).The results revealed 11,076 and 6,640 differentially expressed genes(DEGs)in response to ***,*** weighted gene co-expression network analysis of 4,633 transcription factors(TFs)indicated a“MEblue”module containing 654 TFs that strongly correlate with resistance to *** these TFs,the ethylene response factor Ghi_A05G10166(GhERF91)was identified as a putative hub gene with a defense response against ***.A virus-induced gene silencing assay and exogenous application of ethephon showed that GhERF91 is activated by ethylene and positively regulates the response to *** exposure in *** study provides fundamental transcriptome data and a putative causal gene(GhERF91)associated with resistance to ***,as well as genetic resources for breeding ***-resistant cotton.

关键词： cotton Verticillium wilt RNA-sequencing GhERF91 virus-induced gene silencing

Development of MAGIC population for association study offiber quality traits in upland cotton

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Development of MAGIC population for association study offibe...