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Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

Journal of Cotton Research 2024年第2期7卷 177-187页

作者： SHUI Guangling LIN Hairong MA Xiaomei ZHU Bo HAN Peng AINI Nurimanguli GUO Chunping WU Yuanlong PAN Zhenyuan YOU Chunyuan SONG Guoli nie xinhui Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan Agricultural CollegeShihezi UniversityShiheziXinjiang 832003China Cotton Institute Xinjiang Academy of Agriculture and Reclamation ScienceShiheziXinjiang 832000China Agricultural Science Research Institute of the 5th Division of Xinjiang Production and Construction Corps ShuangheXinjiang 833408China Modern Agricultural College Kashi UniversityKashiXinjiang 844000China National Key Laboratory of Crop Genetic Improvement College of Plant Sciences&TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China National Key Laboratory of Cotton Bio‑Breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan 455000China

Background Cotton is an economically important *** is crucial to find an effective method to improve cotton yield,and one approach is to decrease the abscission of cotton bolls and ***,the lack of knowledge of the genetic and molecular mechanisms underlying cotton boll abscission traits has hindered genetic *** Pearson’s correlation analysis revealed a significant positive correlation between boll abscission rates 1(AR1)and boll abscission rates 2(AR2).A genome-wide association study was conducted on 145 loci that exhibited high polymorphism and were uniformly distributed across 26 chromosomes(pair).The study revealed 18,46,and 62 markers that were significantly associated with boll abscission,fiber quality,and yield traits(P<0.05),explaining 1.75%–7.13%,1.16%–9.58%,and 1.40%–5.44%of the phenotypic variation,***,the marker MON_SHIN-1584b was associated with the cotton boll abscission trait,whereas MON_CGR5732a was associated with cotton boll abscission and fiber quality *** of the marker loci identified in this study had been previously *** on phenotypic effects,six typical cultivars with elite alleles related to cotton boll abscission,fiber quality,and yield traits were *** cultivars hold great promise for widespread utilization in breeding *** These results lay the foundation for understanding the molecular regulatory mechanism of cotton boll abscission and provide data for the future improvement of cotton breeding.

关键词： SSR Genome wide association studies Abscission Favorable alleles Cotton Genetic improvement

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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

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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 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 College Shihezi University National Key Laboratory of Crop Genetic Improvement/College of Plant Sciences & Technology Huazhong Agricultural University Cotton Research Institute Shihezi Academy of Agricultural Science Institute of Economic Crops Xinjiang Academy of Agricultural Sciences

Verticillium dahliae causes significant losses in cotton production. To reveal the mechanism of the defense response to V. dahliae in cotton, transcriptomic analyses were performed using cotton cultivars M138(V. dahliae-resistant)and P2(V. dahliae-susceptible). The results revealed 11,076 and 6,640 differentially expressed genes(DEGs)in response to V. dahliae, respectively. The 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 V. *** these TFs, the ethylene response factor Ghi＿A05G10166(GhERF91) was identified as a putative hub gene with a defense response against V. dahliae. A virus-induced gene silencing assay and exogenous application of ethephon showed that GhERF91 is activated by ethylene and positively regulates the response to V. dahliae exposure in cotton. This study provides fundamental transcriptome data and a putative causal gene(GhERF91)associated with resistance to V. dahliae, as well as genetic resources for breeding V. dahliae-resistant cotton.

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Correction:Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

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Journal of Cotton Research 2024年第2期7卷 219-222页

作者： SHUI Guangling LIN Hairong MA Xiaomei ZHU Bo HAN Peng AINI Nurimanguli GUO Chunping WU Yuanlong PAN Zhenyuan YOU Chunyuan SONG Guoli nie xinhui Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan Agricultural CollegeShihezi UniversityShiheziXinjiang 832003China Cotton Institute Xinjiang Academy of Agriculture and Reclamation ScienceShiheziXinjiang 832000China Agricultural Science Research Institute of the 5 Division of Xinjiang Production and Construction CorpsShuangheXinjiang 833408China Modern Agricultural College Kashi UniversityKashiXinjiang 844000China National Key Laboratory of Crop Genetic Improvement College of Plant Sciences&TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China National Key Laboratory of Cotton Bio‑Breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan 455000China

Correction:J Cotton Res 7,20(2024)https://***/10.1186/s42397-024-00180-3 Following publication of the original article(Shui et al.2024),the author found 5 errors in the published *** of the author’s name has been corrected from Gou Chunping to Guo *** reference(Zhao SQ.2016)in Table 2 has been updated to:Zhao *** on the major gene and multigene mixed inheritance and QTL mapping for early maturity traits in upland *** Acad Agric ***://***/10.3969/***.201600501.(in Chinese with English abstract).***’Results’part,’Phenotype analysis of 238 cotton boll abscission among cotton accessions’paragraph,the phenotype analysis of AR1 ranging from 19.27%–63.79%,which was wrongly written as 19.27%-63.97%.***‘2018KRL’is modified to‘2018KEL’in Table 1.

关键词： germplasm traits cotton

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Morphological and cytological assessments reveal pollen degradation causes pollen abortion in cotton cytoplasmic male sterility lines

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Journal of Cotton Research 2024年第03期 266-276页

作者： PEI Qingyu LIU Jinshan GUO Chunping MA Xiaomei LIU Xiaoyan YOU Chunyuan LIN Hairong LI Zhibo ZHAO Ruihai ZHU Bo WU Yuanlong PAN Zhenyuan nie xinhui Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps Agricultural College Shihezi University Seed Management Station of Xinjiang Production and Construction Corps Cotton Institute Xinjiang Academy of Agricultural and Reclamation Science Xinjiang Jinbo Seed Industry Co. Ltd National Key Laboratory of Crop Genetic Improvement College of Plant Sciences and Technology Huazhong Agricultural University Cotton Research Institute Shihezi Academy of Agriculture Science Agricultural Science Research Institute of the 5th Division of Xinjiang Production and Construction Corps

Background Understanding the mechanism of male sterility is crucial for producing hybrid seeds and developing sterile germplasm resources. However, only a few cytoplasmic male sterility（CMS） lines of cotton have been produced due to several challenges, like inadequate variation of agronomic traits, incomplete sterility, weak resilience of restorer lines, and difficulty in combining strong dominance. Therefore, the morphological and cytological identification of CMS in cotton will facilitate hybrid *** Two F2segregating populations of cotton were constructed from cytoplasmic male sterile lines（HaA and 01A, maternal） and restorer lines（HaR and 26R, paternal）. Genetic analysis of these populations revealed a segregation ratio of 3:1 for fertile to sterile plants. Phenotypic analysis indicated no significant differences in traits of flower bud development between sterile and fertile plants. However, sterile plants exhibited smaller floral organs, shortened filament lengths, and anther atrophy on the flowering day in comparison with the fertile plants. When performed scanning electron microscopy（SEM）, the two F2populations revealed morphological variations in the anther epidermis. Cellular analysis showed no significant differences in pollen development before pollen maturation. Interestingly, between the pollen maturation and flowering stages, the tapetum layer of sterile plants degenerated prematurely, resulting in abnormal pollen grains and gradual pollen *** The results of this study suggest that fertility-restoring genes are controlled by a single dominant gene. Sterile plants exhibit distinctive floral morphology, which is characterized by stamen atrophy and abnormal anthers. Pollen abortion occurs between pollen maturity and flowering, indicating that premature tapetum degradation may be the primary cause of pollen abortion. Overall, our study provides a theoretical basis for utilizing CMS in hybrid breeding and in-depth investigati

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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

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Identification of candidate genes for aphid resistance in upland cotton by QTL mapping and expression analysis

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作物学报:英文版 2023年第5期11卷 1600-1604页

作者： Qiushuang An Zhenyuan Pan Nurimanguli Aini Peng Han Yuanlong Wu Chunyuan You xinhui nie Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps Agricultural CollegeShihezi UniversityShihezi 832003XinjiangChina Cotton Research Institute of the Shihezi Academy of Agriculture Science Shihezi 832011XinjiangChina

Lignin is one of the main components of cell walls and is essential for resistance to insect pests in *** 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.

关键词： GhLAC4-3 Lignin Gossypium hirsutum Aphid resistance

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Advances and prospects of genetic mapping of Verticillium wilt resistance in cotton

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Journal of Cotton Research 2022年第1期5卷 48-58页

作者： AINI Nurimanguli JIBRIL Abdulaziz Nuhu LIU Shiming HAN Peng PAN Zhenyuan ZHU Longfu nie xinhui Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan Agricul-tural CollegeShihezi UniversityShihezi 832003XinjiangChina National Key Laboratory of Crop Genetic Improvement College of Plant Sciences and Tech-nologyHuazhong Agricultural UniversityWuhan 430070HubeiChina

Verticillium wilt is one of the most important diseases affecting cotton production in *** fungus,Verticillium dahliae,has a wide host range and a high degree of genetic *** resistance resources have been found in the available planting resources,thus presenting difficulties and challenges for our *** long-term production practice shows that selection of disease-resistant varieties is the most economical and effective measure to control Verticillium wilt of cotton to reduce the yield loss and quality decline of *** this paper,we summarized the genetic mapping population,the analysis method of genetic localization,the discovery,mining and cloning of disease-resistant quantitative trait loci/markers,and the analysis of their genetic functions,so as to provide information for the molecular breeding approach of disease-resistant cotton.

关键词： Cotton Verticillium wilt Genetic mapping QTL

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Attenuation of ethylene signaling increases cotton resistance to a defoliating strain of Verticillium dahliae

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作物学报：英文版 2023年第1期11卷 89-98页

作者： Tianyi Wang Muhammad Shaban Junhui Shi Weiran Wang Shiming Liu xinhui nie Yu Yu Jie Kong Steven J.Klosterman Xianlong Zhang Alifu Aierxi Longfu Zhu National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070HubeiChina Department of Plant Breeding and Genetics University of Agricu Institute of Economic Crops Xinjiang Academy of Agricultural SciencesKuqa 842000XinjiangChina Key Laboratory of Oasis Eco-agriculture of the Xinjiang Production and Construction Crops College of AgronomyShihezi UniversityShihezi 832000XinjiangChina Xinjiang Academy of Agricultural&Reclamation Sciences Shihezi 832000XinjiangChina United States Department of Agriculture Agricultural Research ServiceSalinasCA 93905USA

The severity of Verticillium wilt on cotton caused by defoliating strains of Verticillium dahliae has gradually increased and threatens production worldwide. Identification of the molecular components of leaf defoliation may increase cotton tolerance to V. dahliae. Ethylene, a major player in plant physiological processes, is often associated with senescence and defoliation of plants. We investigated the cotton–*** interaction with a focus on the role of ethylene in defoliation and defense against V. *** plants inoculated with V. dahliae isolate V991, a defoliating strain, accumulated more ethylene and showed increased disease symptoms than those inoculated with a non-defoliating strain. In cotton with a transiently silenced ethylene synthesis gene(GhACOs) and signaling gene(GhEINs) during cotton–V. dahliae interaction, ethylene produced was derived from cotton and more ethylene increased cotton susceptibility and defoliation rate. Overexpression of AtCTR1, a negative regulator in ethylene signaling, in cotton reduced sensitivity to ethylene and increased plant resistance to V. ***, the results indicated precise regulation of ethylene synthesis or signaling pathways improve cotton resistant to Verticillium wilt.

关键词： Cotton Verticillium dahilae Ethylene Defoliation

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Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL,significant SNP and transcriptomic data

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Journal of Cotton Research 2020年第4期3卷 324-335页

作者： XU Shudi PAN Zhenyuan YIN Feifan YANG Qingyong LIN Zhongxu WEN Tianwang ZHU Longfu ZHANG Dawei nie xinhui Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Coprs Agricultural CollegeShihezi UniversityShihezi 832000XinjiangChina Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070HubeiChina National Key Laboratory of Crop Genetic Improvement College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070HubeiChina Research Institute of Economic Crops Xinjiang Academy of Agricultural SciencesUrumqi 830091China

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 *** combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various ***: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 *** 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 *** to the function annotations,some of the 20 key candidate genes are associated with the fiber ***: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.

关键词： Fiber quality traits Meta-QTL Significant SNPs Candidate genes Transcriptomic data

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