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[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.
[前沿资讯 ] NBRI’s innovative chip to boost cotton cultivation 进入全文
THE TIMES OF INDIA
Lucknow: CSIR-National Botanical Research Institute (NBRI), Lucknow, has developed a special chip that will assist scientists and farmers in cultivating superior cotton plants. Upon insertion of this ‘90K SNP Cotton Chip' in special equipment, it will provide data about various cotton varieties and their characteristics. The chip facilitates the development of high-quality cotton plants through marker-assisted breeding (MAB), a DNA-based approach. This utilises molecular markers to identify and choose plants with specific traits, creating new varieties. "The chip contains data of around 90,000 cotton SNP markers, which can be used to crossbreed and create a new variety according to climatic, production or pest control needs. This is the first such chip in India, and its license was given to a Delhi-based company in the presence of CSIR director general N Kalaiselvi," said NBRI director Ajit Kumar Shasany. Explaining MAB or chip technology, Shasany said: "In agricultural production, we often aim to combine good traits from different plants to breed a new variety. Suppose we have a cotton plant with many seeds but fewer branches and is not drought or pest-resistant while another variety has fewer seeds but is drought and pest-resistant and has more branches. We can combine these two to breed a desirable variety." "This may sound easy, but it's a herculean task as suitable varieties must be identified from thousands before crossbreeding. It may take months and even years. It's tough to determine which one is the best. The agricultural performance of plants is usually linked to traits that are encoded by DNA," he said. Shasany added that this chip was prepared by sequencing 320 cotton genotypes found in India, which resulted in 40 lakh single nucleotide polymorphisms (SNP), a variation in the DNA sequence at a single base position. Out of these, 90K SNPs were shortlisted as the best markers. Lucknow: CSIR-National Botanical Research Institute (NBRI), Lucknow, has developed a special chip that will assist scientists and farmers in cultivating superior cotton plants. Upon insertion of this ‘90K SNP Cotton Chip' in special equipment, it will provide data about various cotton varieties and their characteristics. The chip facilitates the development of high-quality cotton plants through marker-assisted breeding (MAB), a DNA-based approach. This utilises molecular markers to identify and choose plants with specific traits, creating new varieties. "The chip contains data of around 90,000 cotton SNP markers, which can be used to crossbreed and create a new variety according to climatic, production or pest control needs. This is the first such chip in India, and its license was given to a Delhi-based company in the presence of CSIR director general N Kalaiselvi," said NBRI director Ajit Kumar Shasany. Explaining MAB or chip technology, Shasany said: "In agricultural production, we often aim to combine good traits from different plants to breed a new variety. Suppose we have a cotton plant with many seeds but fewer branches and is not drought or pest-resistant while another variety has fewer seeds but is drought and pest-resistant and has more branches. We can combine these two to breed a desirable variety." "This may sound easy, but it's a herculean task as suitable varieties must be identified from thousands before crossbreeding. It may take months and even years. It's tough to determine which one is the best. The agricultural performance of plants is usually linked to traits that are encoded by DNA," he said. Shasany added that this chip was prepared by sequencing 320 cotton genotypes found in India, which resulted in 40 lakh single nucleotide polymorphisms (SNP), a variation in the DNA sequence at a single base position. Out of these, 90K SNPs were shortlisted as the best markers.
[学术文献 ] Identification of salt-resilient cotton genotypes using integrated morpho-physiological and biochemical markers at the seedling stage 进入全文
Scientific Reports
Soil salinity drastically hinders cotton productivity (Gossypium hirsutum), and fiber quality. The current study evaluated morpho-physiological and biochemical responses of fifty cotton genotypes under different salinity levels (control, 12 dS/m, and 17 dS/m) at the seedling stage. The experiment was performed in a factorial complete randomized design with three replications. Significant genotype × treatment interactions were observed for most traits, including shoot length (SL), root length (RL), fresh and dry shoot weight (FSW, DSW), fresh and dry root weight (FRW, DRW), total soluble protein (TSP), proline content, and antioxidant enzymes. Severe salinity stress reduces shoot length (SL) and root length (RL) along with notable decreases in biomass and altered biochemical responses, including increased antioxidant activities and proline content, indicating stress adaptation. Moreover, PCA and Pearson’s correlation analyses unveiled strong positive and negative correlations among studied attributes while MGIDI analyses assist in determining the salt-resilient cotton genotypes under applied treatments. The best-performing genotypes under control conditions were G2, G8, and G12, while G7, G43, and G30 showed resilience under severe salinity stress. MGIDI effectively identified genotypes with outstanding salinity tolerance, such as G2, G43, G40, and G26, across all stress levels. This research assists in determining the salinity stress-tolerant cotton genotypes using morpho-physiological and biochemical parameters and MGIDI is used as a precise method for identifying salt-resilient cotton accessions.
