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[学术文献 ] Identification of Elite Alleles and Candidate Genes for the Cotton Boll Opening Rate via a Genome-Wide Association Study 进入全文
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
The boll opening rate (BOR) is an early maturity trait that plays a crucial role in cotton production in China, as BOR has a significant effect on defoliant spraying and picking time of unginned cotton, ultimately determining yield and fiber quality. Therefore, elucidating the genetic basis of BOR and identifying stably associated loci, elite alleles, and potential candidate genes can effectively accelerate the molecular breeding process. In this study, we utilized the mixed linear model (MLM) algorithm to perform a genome-wide association study (GWAS) based on 4,452,629 single-nucleotide polymorphisms (SNPs) obtained through whole-genome resequencing of a natural population of 418 upland cotton accessions and phenotypic BOR data acquired from five environments. A total of 18 SNP loci were identified on chromosome D11 that are stable and significantly associated with BOR in multiple environments. Moreover, a significant SNP peak (23.703-23.826 Mb) was identified, and a GH-D11G2034 gene and favorable allelic variation (GG) related to BOR were found in this genomic region, significantly increasing cotton BOR. Evolutionary studies have shown that GH-D11G2034 may have been subjected to artificial selection throughout the variety selection process. This study provides valuable insights and suggests that the GH-D11G2034 gene and its favorable allelic variation (GG) could be potential targets for molecular breeding to improve BOR in upland cotton. However, further research is needed to validate the function of this gene and explore its potential applications in cotton breeding programs. Overall, this study contributes to the advancement of genetic improvement in early maturity and has important implications for the sustainable development of the cotton industry.
[前沿资讯 ] 新疆科研团队破解机采长绒棉生产加工技术瓶颈 进入全文
中国新闻网
曾几何时，新疆机采长绒棉杂质多，加工后品质下降的问题一直困扰着产业发展。如今，这一难题已被新疆科技创新领军人才田立文团队一步步成功破解。近日，该团队继获得中国、欧洲和优质棉生产国澳大利亚多件发明专利授权外，又联合阿瓦提新雅棉业有限公司研发的优质机采长绒棉生产方法，在美国获发明专利授权。这是中国首个在优质棉生产技术发明创造方面获国内、国际同时授权认可的棉花栽培研究团队，为新疆长绒棉产业发展注入新的活力。 突破机采长绒棉生产加工技术瓶颈 “过去，新疆机采长绒棉加工含杂率偏高、纤维损失大，以及品质不能满足产业需要的问题一直困扰着我们。”新疆农业科学院棉花研究所副所长孔杰说，新疆长绒棉具有纤维长、细、强等特点，在国际市场具有很高知名度，但近年来面临机采后籽棉含杂量高，以及受到地膜、滴灌带等异物污染，不易清理等难题。为了提高机采棉加工质量，满足市场对高性价比原棉的需求，通常采用提高籽棉清杂强度的做法，但对纤维造成了严重机械损伤，导致机采长绒棉推进始终未达预期。 面对这一问题，田立文团队没有退缩。“我们对长绒棉种植与加工全流程进行了梳理，系统优化品种选择、株行距配置、机采前准备、脱叶催熟、加工等相关技术与工艺。”新疆农业科学院棉花研究所研究员田立文说：“我们首次通过发明创新提出了适宜机采长绒棉加工的完整工艺，还对主要清杂设备关键部件及其作业参数重新设计。” 这套创新方案的核心在于，除在种植环节确保机采籽棉优质，并尽可能降低籽棉杂质，还提出整套工艺应包括在籽棉清理环节，选用双通道大直径缠绕辊结构的复合异纤清理机、倾斜式籽棉清理机和提净式籽棉清理机；在皮棉清理环节，选用气流清理机和皮棉梳理机，严控杂质清理道次。 同时，团队发现常规的锯齿式轧花机和皮清机不适合长绒棉皮棉加工与清理，而应选用皮辊轧花机、气流清理机和皮棉梳理机，防止对原棉的循环无序清理造成纤维机械损伤。经过不懈努力，团队成功突破技术瓶颈，为新疆机采长绒棉的发展带来转机。 国际专利授权带来深远影响 “新疆机采长绒棉生产方法获得美国专利授权，意义重大。”田立文说：“此前我们已经先后获得了中国、欧洲、澳大利亚多个发明专利授权，以这些发明创新为支撑，还获得德国纽伦堡和瑞士日内瓦等国际有影响的发明展金、银奖多枚。以上荣誉凸显出中国在优质棉生产，包括优质机采长绒棉生产加工领域的自主创新能力已达世界一流水平。它展示出新疆棉花产业的现代化、机械化程度高，在生产方式上与国际先进水平接轨。我们是依靠技术和装备提升产能。” 在产业竞争力提升方面，田立文表示，通过新技术的应用，包括适宜机采品种选育、棉田机采群体构建、机采棉田机艺融合与水肥药管理，以及机采棉纤维减损加工等技术，“我们通过一系列的新技术创新与应用确保生产的棉花产量高、品质优，同时用工少、生产成本低。实践表明这是提升中国全球优质棉市场竞争力的最有效措施。” 未来研发规划与产业推动 谈及未来团队在长绒棉技术研发中的规划，田立文说：“优质长绒棉生产涉及多个环节，既需要做好单个环节的技术攻关突破，如机采品种培育，关键加工技术参数敲定，又需要系统整体推进。我们将充分发挥已掌握的技术优势，把制定更加完善的优质机采长绒棉生产技术标准作为未来3至5年的工作重点。” 在进一步推动新疆高端棉纺织产业链发展上，田立文说：“从品种筛选及其配套种植技术方面系统研发，积极回应纺织企业对高品质长绒棉技术标准的诉求，更好地为提高新疆优质长绒棉市场竞争力提供技术支撑。我们希望通过不断努力，让新疆优质棉，包括长绒棉在高端棉纺织原料供给中占据更重要的地位，推动整个产业链的升级发展。”
[前沿资讯 ] 陆地棉端粒到端粒基因组图谱构建 为陆地棉短季适应机制提供了新见解 进入全文
科技日报
中国农业科学院棉花研究所（以下简称中棉所）马雄风研究员团队成功构建了陆地棉主栽品种“中棉113”的端粒到端粒基因组图谱，并利用该基因组揭示了陆地棉着丝粒演化和短季适应性遗传基础。相关研究成果17日在线发表在国际学术期刊《自然·遗传学》上。 棉花是重要的经济作物和纺织工业原料。以新疆为主的西北内陆棉区是我国最大产棉区，但是该地区的部分棉区，热量条件差、无霜期短，迫切需要既高产、优质又早熟的棉花品种，而早熟性、品质、产量等性状通常相互拮抗，协同提升难度很大，制约新疆等地的棉花生产。 为此，马雄风带领研究团队创新棉花早熟育种策略，育成早熟、优质、高衣分、高产新品种中棉113，实现了多个性状的协同改良。该品种连续3年成为农业农村部主推品种，从2022年起，推广面积持续居全国常规棉主要品种第三位。 尽管陆地棉参考基因组已被多次组装，但生产品种的基因组组装中仍存在大量缺口，尤其是着丝粒、端粒和核仁组织区等复杂重复区域的解析不足，制约了对目标农业性状的精准遗传解析。 着丝粒是真核生物染色体中重要的组成元件，在确保染色体正常分离及遗传物质在世代间准确传递过程中发挥了重要作用。据介绍，该研究运用PacBio HiFi测序、ONT超长读长测序、Hi-C（染色质构象捕捉）和Bionano（全基因组光学图谱）等先进技术，成功组装了中棉113的端粒到端粒基因组图谱，连续性和完整性得到显著提升，为陆地棉基因组研究提供了更精确的参考。对中棉113全部26条染色体着丝粒的准确定位和序列分析发现，区别于其他典型陆地棉着丝粒的反转录转座子构成，D08染色体着丝粒（D08CEN）呈现独特特征，出现串联重复序列；相对于其他异源四倍体棉种及二倍体祖先种中的D08染色体着丝粒，中棉113发生了特异性的着丝粒位移和构成序列替换，这一发现为棉花着丝粒功能及其演化机制研究提供了独特视角。 该研究的另一个创新发现是，鉴定出D03染色体上的一个与开花时间相关的特定单倍型，证实其是在早期驯化过程中，通过跨着丝粒的倒位变异固定下来，并与陆地棉早熟性密切相关。研究结果为陆地棉短季适应机制提供了新见解。 据悉，中棉所是该研究的第一单位和通讯单位，共同参加单位包括中国农业科学院农业基因组研究所、郑州大学、中国农业科学院西部农业研究中心、南通大学、甘肃农业大学等。
[学术文献 ] Spatial transcriptome and single-cell RNA sequencing reveal the molecular basis of cotton fiber initiation development 进入全文
PLANT JOURNAL
Recent advances in single-cell transcriptomics have greatly expanded our knowledge of plant development and cellular responses. However, analyzing fiber cell differentiation in plants, particularly in cotton, remains a complex challenge. A spatial transcriptomic map of ovule from -1 DPA, 0 DPA, and 1 DPA in cotton was successfully constructed, which helps to explain the important role of sucrose synthesis and lipid metabolism during early fiber development. Additionally, single-cell RNA sequencing (scRNA-seq) further highlighted the cellular heterogeneity and identified clusters of fiber developmental marker genes. Integration of spatial and scRNA-seq data unveiled key genes SVB and SVBL involved in fiber initiation, suggesting functional redundancy between them. These findings provide a detailed molecular landscape of cotton fiber development, offering valuable insights for enhancing lint yield.
[前沿资讯 ] Microbiota transplantation offers new hope against cotton leaf curl disease 进入全文
University of Glasgow
Researchers at the University of Glasgow and the Forman Christian College University, Pakistan, are pioneering an approach to combat the devastating cotton leaf curl disease (CLCuD) through microbiota transplantation. For decades, CLCuD has been devastating cotton crops across the world, especially Southeast Asia. Pakistan, a leading high-quality cotton-producing country, faces a severe challenge due to the biotic stresses encountered by the cotton crop. A consistent crop loss and yield reductions of up to 35% have placed Pakistan's textile industry on the verge of crashing. While the annual economic loss of $2 billion USD is a severe blow to the country's economy, it has also become a critical concern for sustainability scientists. Traditional methods, including chemical treatments and genetic modifications, have had limited success in tackling the disease. However, researchers are now exploring an innovative strategy—transplanting entire microbial communities from disease-resistant cotton species to susceptible ones. This research, "Microbiota transplantation for cotton leaf curl disease suppression—core microbiome and transcriptome dynamics," published in Communications Biology, focuses on transferring rhizospheric (root-associated) and phyllospheric (leaf-associated) microbiota from Gossypium arboreum—a naturally resistant cotton species but not useful for good fabric production—to Gossypium hirsutum, which is highly susceptible to CLCuD but highly valuable for fabric production. "Organ transplantation has always been mainstreamed in human health and our minds often jump to organ donations in humans. But what we thought of was, why not plants? What if plants can have their own version of transplants as well? Not of organs, but of something equally vital, and that is their microbiome," says Ayesha Badar, first author and Ph.D. researcher for the study. Preliminary results indicate that rhizospheric microbiota transplantation significantly reduces disease incidence, outperforming traditional treatments such as salicylic acid application. While the researchers have found that interspecies microbiota transplantation contributes to viral disease tolerance in cotton plants, their study also states, "The rhizosphere of CLCuD-resistant G. arboreum (Rhi.RMF) appeared to harbor selective beneficial bacterial genera which, when transplanted onto susceptible host species G. hirsutum, imparted not only disease suppression but enhanced growth rate as well." Dr. Umer Zeeshan Ijaz from the University of Glasgow's James Watt School of Engineering, a leading expert in bioinformatics, plays a key role in analyzing the complex microbial interactions involved in this process. "Using advanced sequencing techniques, we can decode the microbial communities responsible for disease suppression, paving the way for targeted microbiome-based interventions," he said. Dr. Kauser Abdulla Malik, Professor and Dean of Postgraduate Studies at Forman Christian College University, explains, "Due to the advent of CLCuD in the early 1990s, the cotton production drastically reduced. The National Institute of Biotechnology and Genetic Engineering (NIBGE), Pakistan, where I was Director at the time, pioneered CLCuV isolation and characterization. "Despite employing RNAi and other advanced techniques, viral mutations rendered resistance efforts unsuccessful. "After decades of battling with CLCuV in Pakistan, now, by leveraging the power of beneficial microbes, we are developing a sustainable, biological solution to improve crop resilience. This research marks a shift from conventional disease management to harnessing nature's own defense mechanisms." The findings of this research hold immense potential for sustainable agriculture. By reducing dependency on chemical pesticides and fostering natural plant defenses, microbiota transplantation could become a game-changer in managing plant diseases globally. The research team envisions future applications of this method in various crops, expanding the scope of microbiome-based disease management. This work highlights the power of interdisciplinary collaboration in addressing agricultural challenges and underscores Pakistan's contribution to cutting-edge scientific advancements in plant health.
[学术文献 ] GWAS and eQTL analyses reveal genetic components influencing the key fiber yield trait lint percentage in upland cotton 进入全文
PLANT JOURNAL
Lint percentage is an important component of cotton yield traits and an important economic indicator of cotton production. The initial stage of fiber development is a critical developmental period that affects the lint percentage trait, but the genetic regulation of the initial stage of fiber development needs to be resolved. In this study, we used a genomewide association study (GWAS) to identify 11 quantitative trait loci (QTLs) related to lint percentage and identified a total of 13 859 expression QTL (eQTLs) through transcriptome sequencing of 312 upland cotton accessions. Candidate genes for improving the lint percentage trait were identified through transcriptome-wide association study (TWAS), colocalization analysis, and differentially expressed gene analysis. We located nine candidate genes through the TWAS, and prioritized two key candidate genes (Ghir_A12G025980 and Ghir_A12G025990) related to lint percentage through colocalization and differential expression analysis. We showed that two eQTL hotspots (Hot26 and Hot28) synergistically participate in regulating the biological pathways of fiber initiation and development. Additionally, we unlocked the potential of genomic variants in improving the lint percentage by aggregating favorable alleles in accessions. New accessions suitable for improving lint percentage were excavated.
