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[前沿资讯 ] Nature Communications | 浙江大学棉花精准育种团队首次绘制全球棉花功能基因变异的单倍型图谱 进入全文
浙江大学农业生物技术学院
近日，浙江大学农学院棉花精准育种团队在Nature Communications上发表了题为“Reveal genomic insights into cotton domestication and improvement using gene level functional haplotype-based GWAS”的研究论文，研究围绕基因这一关键生物学元件中的遗传变异，创新性地开发出基于基因水平的功能单倍型变异（Functional haplotype，FH）标记，首次绘制了全球棉花功能基因变异的单倍型图谱。研究结果为解析棉花驯化与改良的遗传机制提供了突破性的工具，对作物高效精准育种具有重要意义。 突破传统GWAS限制，精准定位功能基因。传统GWAS依赖单核苷酸多态性（SNP）标记，易受基因组复杂结构和连锁不平衡干扰，导致候选区间冗长、因果基因难以锁定。本研究提出的功能单倍型标记策略，通过整合基因内所有非同义突变信息，将离散的基因组变异转化为反映蛋白质序列及功能差异的“基因单倍型”，实现农艺性状与功能基因的直接关联。这一方法成功将遗传分析对象从单核苷酸多态性变异转变为基因类型变异，在3724份棉花种质中定位到532个具有显著育种潜力的关键基因（Quantitative trait genes，QTGs），极大提升了基因挖掘的精准度。基于FH的GWAS分析结果，通过CRISPR-Cas9基因编辑技术验证了关键基因GhFAH1的生物学功能，证实其缺失可显著改良包括纤维长度、强度、细度与伸长率在内的纤维品质表现。结合转录组数据，FH标记进一步揭示了基因表达与表型的动态关联，为多性状协同改良提供了理论依据。 跨群体高效解析，揭示作物驯化改良的遗传足迹。FH标记在基因水平精准追踪野生种、地方品种与现代品种间的基因流动与选择信号。研究通过分析全球3724份棉花种质（涵盖野生种、半野生种、地方品种及现代栽培品种），首次绘制了棉花基因多样性的全景图谱，揭示了人工选择对纤维品质、产量等性状的关键优异基因的定向驯化规律。此外，基于FH标记成功捕捉到美洲早期品种及现代棉花育种史上基因交流的“热点事件”，为追溯品种改良路径提供了分子证据。 多组学验证驱动育种应用，助力智能设计育种。基因功能单倍型分析策略可直接对接“育种5.0”智能设计体系，结合传统SNP-GWAS、FH-GWAS及相关组学验证，通过生物大数据与人工智能深度挖掘优势单倍型和优异基因，实现从基因到品种的精准设计优化。 浙江大学张天真教授为论文通讯作者，浙江大学博士研究生齐国安，博士后李宜谦，博士研究生张婉莹为论文共同第一作者，浙江大学农学院助理研究员韩泽刚，农学院胡艳教授，方磊教授，博士后玄丽莎，博士研究生陈锦文，陈瑞等参与了该研究。该项目得到新疆生产建设兵团重点研发项目，国家自然科学基金面上项目和中央高校基本科研业务自主创新重点项目支持。
[学术文献 ] Heatmap clustering and performance analysis of cotton genotypes in response to environmental conditions 进入全文
SCIENTIFIC REPORTS
Cotton (Gossypium hirsutum) is a crucial cash crop in China, with yield performance influenced by genotype, environmental conditions, and management practices. The aim of this study was to assess the yield performance, biomass accumulation, and growth of nine cotton genotypes in Henan Province during three growing seasons (2017-2019) with different climates. Field experiments were conducted using a randomized complete block design (RCBD) at the Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang, China. Plant height, true leaf number, and boll number per plant were among the morphological characteristics that showed the most variance across years and genotypes. Reproductive biomass, leaf area index (LAI), and biomass accumulation followed distinct seasonal trends, with LAI rising during boll formation and flowering. Yield parameters such as seed cotton yield, lint percentage, and boll weight vary by genotype and year, with the highest yields recorded in 2019. According to correlation study, temperature and precipitation had a negative impact on seed cotton production and final biomass, whereas climatic parameters had a favorable correlation with the harvest index. The genotypes were divided into distinct categories according to growth and yield characteristics using heatmap clustering. These findings provide insight into the best cotton genotypes for increased productivity and resilience in a variety of climates, allowing breeders and farmers to make more informed cultivar selections.
[学术文献 ] Optimal drip irrigation leaching amount and timing enhanced cotton fiber yield, quality and nitrogen uptake by regulating soil salinity and nitrate nitrogen in saline-alkaline fields 进入全文
JOURNAL OF INTEGRATIVE AGRICULTURE
Improving cotton fiber quality can increase the economic income of cotton farmers, but achieving high fiber quality without decreasing cotton fiber yield remains a major challenge in saline-alkaline cotton fields. A field experiment was conducted in 2020 and 2021 on saline-alkaline soil with cotton under drip irrigation to examine how amount and timing of leaching affected soils salinity, cotton fiber yield and quality. There were five leaching amounts (CK: 0 mm, W1: 75 mm, W2: 150 mm, W3: 225 mm and W4: 300 mm) and three leaching timings (T1: once at the seedling stage, T2: twice at the seedling and budding stages, and T3: thrice at the seedling, budding and pollen-setting stages). Soil salinity, soil nitrate nitrogen (NO3-N), cotton nitrogen (N) uptake, irrigation water and fiber quality index (FQI) were investigated. The results indicated that soil salinity and NO3-N reduced with increasing leaching amount. The N uptake of cotton bolls was greater than in cotton leaves, stems and roots, and total N accumulation increased with increasing leaching amount. The optimal cotton fiber yield and IWP occurred in treatment W3T2, and were 3,199 and 2,771 kg ha-1, and 0.5482 and 0.4912 kg m-3 in 2020 and while there was a negative relationship between fiber micronaire and leaching amount. Soil salinity, NO3-N and fiber micronaire were negatively correlated with fiber quality (i.e., length, strength, elongation and uniformity) and yield, nitrogen uptake of various organs (i.e., root, stems and leaves) and whole plant nitrogen uptake. Pearson correlation analysis revealed that fiber elongation was most sensitive to soil salinity. The method of Entropy-Order Preference by Similarity to Ideal Solution (EM-TOPSIS) indicated that leaching of 300 mm of water applied equally at the seedling and budding periods was the optimal treatment to maintain soil salinity and nutrient levels and achieve high cotton fiber yield and quality. In conclusion, the optimal level of leaching treatment decreased soil salinity and improved nitrogen uptake and was beneficial to achieve high fiber yield and quality. Our results will be significant for guiding drip irrigation practice of leaching on saline-alkaline soils for sustainable cotton fiber production.
[前沿资讯 ] Nature Communications | 海岛棉高质量图泛基因组首发 进入全文
华中农业大学植物科学技术学院
近日，华中农业大学作物遗传改良全国重点实验室张献龙院士团队联合国内外多家科研机构，在国际权威期刊 Nature Communications 上发表了题为“Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L.”的研究论文。该研究通过从头组装12个野生-驯化连续体的海岛棉基因组，构建了首个海岛棉高质量泛基因组，并解析了其纤维品质和产量相关性状的遗传变异及种间渐渗现象。研究成果鉴定出棉花纤维产量与品质遗传改良的关键基因位点，提供了丰富的遗传资源，为海岛棉同步提升产量与纤维品质提供了新思路。 海岛棉（Gossypium barbadense L.）拥有世界顶级的纤维品质，其纤维以长度长、韧性强、光泽度高、垂感好等特点著称，是纺制精、细、薄高端棉纺织品的必备原料。然而，海岛棉因适应性差且产量低，导致市场长期供不应求，我国优质棉长期依赖进口。为破解这一瓶颈问题，团队前期已构建了海岛棉基因组草图（Yuan et al., 2015）和参考基因组（Wang et al., 2019），并解析了其变异图谱（Yuan et al., 2021）。为进一步探究海岛棉的遗传多样性并鉴定其优异纤维品质的遗传位点，本研究在前期构建的四倍体棉花系统发生树（Yuan et al., 2021）基础上，筛选出12份涵盖野生-驯化连续体的海岛棉种质资源，包括7份源自起源地附近的原始种质、2份来自加勒比海地区的农家种及3份广泛种植的栽培种。利用HiFi测序技术，研究团队完成了这12份海岛棉高质量基因组的从头组装。 研究团队对12个从头组装的和5个先前发表的海岛棉基因组开展泛基因组研究。泛基因组的尺寸大小排列组合数据显示，14个基因组就包含99%以上的基因家族，且基因家族数量增长曲线几乎趋于平稳。这表明这17个海岛棉材料不仅具有代表性，而且在总体上较为完整。 高质量的基因组为识别大尺寸结构变异提供遗传资源。通过比较基因组共鉴定到129,673个海岛棉的非冗余结构变异和350,995个四倍体棉花的非冗余结构变异。利用结构变异解析海岛棉的种间渐渗发现，海岛棉在加勒比海地区与陆地棉发生了广泛的种间渐渗，但仅有少量的渐渗保留到海岛棉的栽培种中。例如，一个位于开花基因FLK下游的结构变异起源于陆地棉，在加勒比海地区渐渗到海岛棉农家种，并遗传至现代海岛棉栽培种。该结构变异为“海岛棉在加勒比海地区通过与陆地棉种间杂交获得光周期中性性状”的猜测提供了证据。 该研究通过构建图形泛基因组和开展SV-GWAS分析，鉴定到4个纤维长度、3个纤维强度和7个衣分的海岛棉遗传位点。在探究这些位点优异等位变异的起源时发现，三个纤维品质的有利等位变异组合(FL2/FS1+FL4/FS2+FS3)通过选择和种间渐渗的方式结合在新疆新海棉中，改良了新海棉的纤维品质；三个衣分的有利等位变异组合(LP1+LP2+LP3)通过种间杂交聚合在Pima S1，并遗传给美国皮马棉，这是皮马棉产量高的原因之一。通过解析海岛棉纤维品质和产量的遗传构成发现，所有衣分位点的有利等位变异均与纤维品质显著负相关，这表明海岛棉的衣分和纤维品质间存在权衡关系；相反，三个与纤维品质相关位点的优异等位变异(FL1、FL3和FL4/FS2)可在不影响海岛棉衣分的前提下进一步改良纤维品质，其中FL4/FS2已经被应用于新海棉的纤维品质改良，而FL3的优异等位变异在海岛棉群体的频率较低，尚未被充分利用。因此，未来可以通过种间杂交方式将FL3的优异等位变异整合至新海棉中，实现海岛棉纤维产量和纤维品质的同步改良。 华中农业大学作物遗传改良全国重点实验室博士生孟庆营为该论文的第一作者，袁道军副教授为通讯作者。华中农业大学棉花团队张献龙院士、金双侠教授、林忠旭教授和王茂军教授，新疆农业大学陈全家教授，新疆农业科学院棉花研究所孔杰研究员，石河子大学聂新辉教授，美国爱荷华州立大学Jonathan F. Wendel教授和美国农业部作物种质资源研究中心主任Joshua A. Udall等参与了该研究。该研究得到了国家重点研发计划、新疆自治区杰出青年基金、国家科技创新2030重大项目、华中农业大学自主创新基金和新疆人才发展基金XL等的资助。
[学术文献 ] Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L. 进入全文
NATURE COMMUNICATIONS
Gossypium barbadense is renowned for its superior fiber quality, particularly its extra-long fibers, although its fiber yield is lower compared to G. hirsutum. Here, to further reveal fiber-related genomic variants of G. barbadense, we de novo assemble 12 genomes of G. barbadense that span the wild-to-domesticated continuum, and construct a graph-based pangenome by integrating these assemblies and 17 publicly available tetraploid cotton genome assemblies. We uncover the divergent evolutionary trajectories and subsequent exchanges between G. barbadense and G. hirsutum through investigation of structural variants (SVs). We perform the SV-based GWAS analysis in G. barbadense and identify four, three, and seven candidate SVs for fiber length, fiber strength, and lint percentage, respectively. Furthermore, we detect the underlying candidate genes and uncover the origin and distribution of favorable alleles, and reveal the tradeoff between lint percentage and fiber quality. These pangenome and trait-associated SVs provide insights into and resources for improving cotton fiber.
[前沿资讯 ] Cotton virus circulated undetected for nearly 20 years, study finds：Discovery reshapes understanding of disease emergence and highlights new opportunities for virus surveillance in U.S. agriculture 进入全文
EurekAlert!
A virus responsible for damaging cotton crops across the southern United States has been lurking in U.S. fields for nearly 20 years – undetected. According to new research, cotton leafroll dwarf virus (CLRDV), long believed to be a recent arrival, was infecting plants in cotton-growing states as early as 2006. The findings, published in Plant Disease by USDA Agricultural Research Service researchers and cooperators at Cornell University, challenge long-standing assumptions about when and how the virus emerged in U.S. cotton. They also demonstrate how modern data-mining tools can uncover hidden threats in samples collected well before the virus was on anyone’s radar. “CLRDV was officially detected in 2017, so the assumption was that it had only recently entered the U.S.,” said Alejandro Olmedo-Velarde, formerly a Cornell postdoctoral associate and now Assistant Professor in the Department of Plant Pathology, Entomology, and Microbiology at Iowa State. “Our study shows that this virus was actually present in the country’s Cotton Belt long before that. We found clear evidence of the virus in samples from 2006 in Mississippi, 2015 in Louisiana, and 2018 in California.” To confirm the findings, the team conducted field surveys in 2023, collecting fresh cotton samples in Southern California. Lab testing confirmed that CLRDV is currently present in California—marking the state’s first official report of the virus. The team’s approach relied heavily on reanalyzing existing data in public genetic databases. By mining these datasets, the researchers uncovered viral sequences that closely matched current U.S. strains, offering a more complete picture of CLRDV’s spread over time and geography. The study underscores the importance of maintaining easily accessible, publicly available databases for improving future disease surveillance and preparedness. In an unexpected twist, the researchers also identified traces of the virus in an unusual location: a sample from the gut of a cow studied by researchers in California. Their data are consistent with the hypothesis that the cow ingested CLRDV-infected plant-based animal feed. While this does not suggest that animals are infected, it adds a new dimension to understanding the timeline and extent of CLRDV infection in the U.S. prior to the official first report. The study also reignites interest in an unresolved issue in cotton pathology: bronze wilt. The researchers propose a potential connection between CLRDV and bronze wilt symptoms, a topic that has sparked debate in the past. “Now, as more studies align with our findings, the idea is gaining traction,” said Olmedo-Velarde. “It could help explain long-standing crop losses and inform virus monitoring strategies moving forward.” Agricultural Research Service Scientist Dr. Michelle Heck explains, “For growers, the findings offer both a caution and a call to action. CLRDV has been in U.S. fields far longer than anyone realized, and it may be more widespread than current reports suggest. Understanding how and why the virus remained under the radar for so long – and why it’s becoming more of a problem now – will be critical for developing effective management strategies.” The research highlights the growing role of bioinformatics, plant pathology, and cross-disciplinary collaboration in modern agriculture – and shows that existing data may already contain the clues we need to detect emerging threats earlier.
