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[学术文献 ] Membrane Interactions of GET1 and GET2 Facilitate Fiber Cell Initiation through the Guided Entry of the TA Protein Pathway in Cotton 进入全文
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
The guided entry of TA proteins (GET) pathway, which is responsible for the post-translational targeting and insertion of the tail-anchored (TA) protein into the endoplasmic reticulum (ER), plays an important role in physiological processes such as protein sorting, vesicle trafficking, cell apoptosis, and enzymatic reactions in which the GET1/2 complex is indispensable. However, a comprehensive study of the GET1 and GET2 genes and the GET pathway in cotton has not yet been carried out. Here, 12 GET1 and 21 GET2 genes were identified in nine representative plant species, and the phylogenetic relationships, gene structures, protein motifs, cis-regulatory elements (CREs), and temporal and spatial expression profiles were analyzed thoroughly. Our study indicated that GhGET1s and GhGET2s might be localized on ER membranes. According to expression profiling and CREs analysis, GhGET2-A02 was identified as a promising candidate for fiber cell development, interacting with two GhGET1s in the membrane, with a binding bias toward GhGET1-A06. Silencing of GhGET1-A06 or GhGET2-A02 reduced fiber initiation and elongation. In summary, our research provides important evidence for understanding the gene families and functions of GET1 and GET2 in cotton and provides clues for molecular breeding of high-quality cotton fiber varieties.
[前沿资讯 ] Breeding, digitalization boost Xinjiang's cotton output, quality 进入全文
CGTN
The breeding of superior cotton varieties, along with digitalization and mechanization in cotton cultivation, has significantly boosted cotton output and quality in northwest China's Xinjiang Uygur Autonomous Region. A major cotton production area in the country, Xinjiang supplies exceptional raw materials for the textile and apparel industry. On October 9, Li Xueyuan, chief expert of Xinjiang's technological system for the cotton industry, announced that the per-unit output at a high-yield cotton demonstration field in Jinghe County, Bortala Mongolian Autonomous Prefecture, has set a national record for calculated yield over a large harvest area. Since superior varieties are crucial for achieving high cotton yields, Li and his team have independently developed over 20 high-quality cotton varieties in recent years to boost yields in Xinjiang. "Initially, our goal in breeding new varieties focused solely on increasing cotton yields. Later, we expanded our objectives to achieve early maturity, premium quality, disease resistance, and suitability for mechanical harvesting. Now, most of these objectives have been achieved," Li said. In addition to cotton breeding efforts, the Xinjiang Department of Agriculture and Rural Affairs has established a technology system for cotton production, with the chief expert bearing ultimate responsibility. Demonstration fields have been set up in major cotton-growing counties to promote balanced growth in cotton production across the region. Now, digital farming supports cotton farmers in the meticulous management of their fields. For instance, field practices such as watering and fertilization can be controlled via mobile phone. "You see, the cotton crops we grow have robust stalks and abundant bolls. It's easy for one person to manage nearly 500 mu (about 33.3 hectares) of land," said Dong Chenglong, a cotton farmer in Jinghe County. Mechanized harvesting further eases Dong's work. A cotton picker can harvest an average of 500 mu of cotton per day, equivalent to the work of 2,000 laborers. "In the past, cotton scattered on the ground would become contaminated upon contact with soil. Now, with the cotton being baled by the cotton picker, contamination is eliminated. We use loaders and forklifts, making transportation simple with just one lift. This method also ensures high cotton quality," Dong said. This year, the mechanization rate for cotton plowing, planting, and harvesting in Xinjiang has reached 97 percent. In China, 90 percent of the cotton is used in the textile and apparel industry. Xinjiang's long-staple cotton, known for its long fibers, softness, and absorbency, is an excellent raw material for high-end textile products. "When we simulate sweating in the lining, there's no visible sweat stain from the outside. This solves the issue of sweat stains for people who wear shirts in summer. It's similar to coating the cotton with a membrane, and since we use long-staple cotton from Xinjiang, the fabric's breathability is excellent," said Cai Wei, general manager of a clothing brand in Xinjiang. Xinjiang's total cotton output has remained steady at over 5 million tonnes for five consecutive years, with its planting area and total production ranking first in China for 30 consecutive years.
[学术文献 ] Daily glycome and transcriptome profiling reveals polysaccharide structures and correlated glycosyltransferases critical for cotton fiber growth 进入全文
PLANT JOURNAL
Cotton fiber is the most valuable naturally available material for the textile industry and the fiber length and strength are key determinants of its quality. Dynamic changes in the pectin, xyloglucan, xylan, and cellulose polysaccharide epitope content during fiber growth contribute to complex remodeling of fiber cell wall (CW) and quality. Detailed knowledge about polysaccharide compositional and structural alteration in the fiber during fiber elongation and strengthening is important to understand the molecular dynamics of fiber development and improve its quality. Here, large-scale glycome profiling coupled with fiber phenotype and transcriptome profiling was conducted on fiber collected daily covering the most critical window of fiber development. The profiling studies with high temporal resolution allowed us to identify specific polysaccharide epitopes associated with distinct fiber phenotypes that might contribute to fiber quality. This study revealed the critical role of highly branched RG-I pectin epitopes such as beta-1,4-linked-galactans, beta-1,6-linked-galactans, and arabinogalactans, in addition to earlier reported homogalacturonans and xyloglucans in the formation of cotton fiber middle lamella and contributing to fiber plasticity and elongation. We also propose the essential role of heteroxylans (Xyl-MeGlcA and Xyl-3Ar), as a guiding factor for secondary CW cellulose microfibril arrangement, thus contributing to fiber strength. Correlation analysis of profiles of polysaccharide epitopes from glycome data and expression profiles of glycosyltransferase-encoding genes from transcriptome data identified several key putative glycosyltransferases that are potentially involved in synthesizing the critical polysaccharide epitopes. The findings of this study provide a foundation to identify molecular factors that dictate important fiber traits.
[学术文献 ] Genetic Dissection of Flowering and Plant Architectural Traits to Develop Early Maturing Compact Upland Cotton Genotypes for High-Density Planting 进入全文
TROPICAL PLANT BIOLOGY
Earliness in cotton is a highly valued trait that allows the crop to dodge late-season stress and facilitates efficient harvesting, ultimately benefiting farmers with optimal yield. Understanding the genetics of these complex traits is a prelude to designing extra-early maturing cotton genotypes. Two crosses with six generations (ESS-20 x FLT-25 and S-32 x FLT-25: P1, P2, F1, F2, BC1P1, and BC1P2) and one cross with five generations (NNDC-30 x NNDC-47: P1, P2, F1, F2, and F2:3) were field-evaluated for ten earliness and plant architecture traits in cotton. ANOVA presented significant generational differences for most traits. The inadequacy of the Additive-Dominance (A-D) model in explaining trait inheritance using scaling and joint-scaling tests highlighted the presence of epistatic gene actions. Further, the analysis of gene action unveiled the predominance of dominance effect [h] and dominance x dominance [l] epistatic effect, influencing the expression of most traits. Contrasting signs of [h] and [l] effects for these traits suggested the occurrence of duplicate epistasis across crosses. Therefore, population improvement strategies and heterosis breeding could be effective in designing extra-early maturing genotypes. All traits exhibited quantitative inheritance, with partial and overdominance favouring early maturity. Notably, days to flowering and boll opening, exhibited negative heterosis, suggesting the efficient development of short-duration cotton hybrids. Besides, the study also predicted less than one gene block for the majority of traits, suggesting a significant role of complex non-allelic interaction in trait expression. These findings offer valuable insights for strategizing efficient breeding methods to develop early-maturing cotton genotypes.
[前沿资讯 ] 华中农大学者找到棉花纤维品质形成的关键“钥匙” 进入全文
华中农业大学
10月29日，华中农大棉花遗传改良团队在Nature Genetics上发表了题为“Convergence and divergence of diploid and tetraploid cotton genomes”的研究论文，构建了二倍体亚洲棉和四倍体陆地棉图形泛基因组，解析了不同棉种纤维品质形成的遗传调控共性和分歧模块，推动了开辟棉花生物育种优异遗传资源精准创制的新途径，为通过种间靶向渗入实现纤维品质改良提供了支撑，为在不同倍性植物中解析同一性状形成的遗传调控机制提供了参考。 本研究根据216份亚洲棉材料挑选了15份进行了PacBio测序，根据3606份陆地棉材料的进化树、表型变异、地理分布挑选了23份半野生种质和37份栽培种品种进行了PacBio和ONT的三代测序，精细组装了15份亚洲棉和35份陆地棉材料（包括半野生种系20份、栽培种系15份）的基因组，分别构建了基于基因和结构变异的泛基因组。该研究确定了阔叶棉（Gh latifolium）是陆地棉栽培种最近的半野生种系，解析了陆地棉半野生种系到栽培种镶嵌(Mosaic)的基因组结构图谱，鉴定出半野生种系向栽培种高可变渐渗热点区域（图1）。进一步，发现优异农艺性状的遗传位点供体来源与Mosaic区块相关，例如纤维长度相关的位点与帕默尔棉（Gh palmeri）共享最多。 本研究首次提出二倍体与四倍体图形泛基因组的比较方法，鉴定了A基因组中1150Mb 同线区（SYN）和520Mb 高分歧区（HYD）（图2）。HYD相较于SYN展现出更高的存在/缺失变异（PAV）多样性水平，进而导致了种质间变异增加。在高分歧区中LTR反转录转座子比例远高于同线区，而DNA转座子在同线区高于高分歧区，表明在高分歧区中含有大量扩张的LTR 。所有材料间同线区和高分歧区LTR序列分析表明多倍化后At-Dt之间较A2-D5之间更为相似。A2中高分歧区的LTR爆发约0.6MYA，D5约1.9MYA，At约0.6MYA，Dt约0.4 MYA，表明At与Dt中的LTR爆发呈现协同模式。进一步，发现A2和D5基因组中着丝粒在同线区高于高分歧区，而多倍化后高分歧区远高于同线区。这些结果表明，多倍化后陆地棉的两个亚基因组呈现趋同演化特征。 研究者将结构变异与1005个亚洲棉和2215个陆地棉的纤维转录组相结合，鉴定出在育种选择下，两种倍性水平间保守的调控模式（图3）。亚洲棉和陆地棉的eQTL-eGene 的微共线性分析表明，57% (A2)或 63% (At) 的eQTL-eGene位于各自基因组的共线性区域；20% (A2)或22% (At) 的eQTL-eGene序列在另一个基因组中丢失，但是eGene存在；此外，还有23% (A2)或15% (At) 的eGene发生了丢失，A2 和At 之间只有 28 个eQTL-eGene的共享调控关系。为了研究种间调控差异，进而比较了二倍体和四倍体直系同源基因的表达模式，在A2和At中，发现9258个非冗余的种间PAV与4573 个直系同源基因的表达模式分歧有关。这些结果表明二倍体和四倍体之间基因组结构变异影响了基因表达调控。 本研究利用亚洲棉群体鉴定了34个纤维品质相关的PAV-QTL, 其中21个为新的QTL ，利用陆地棉群体鉴定了40个纤维品质相关的PAV-QTL，其中24个为新的QTL（图4）。在这些QTL中，亚洲棉与陆地棉存在6个与纤维品质选择的保守QTL，分别位于1号、6号和12号染色体。6个保守QTL内显著的PAV与PAV-eQTL共定位，共同调控44个eGene的表达。例如在1号染色体上，A2和Dt中直系同源的候选基因（GA2OX4），受到非同源PAV-eQTL的调控，且PAV-eQTL在陆地棉驯化和改良中同时受到选择。研究发现，大多数控制纤维品质的遗传位点在亚洲棉和陆地棉是独立存在的，说明控制二者纤维品质的遗传位点差异很大，为未来利用亚洲棉中独特的优异变异改良陆地棉的纤维品质提供了靶点。 本研究构建了二倍体和四倍体棉花图形泛基因组，解析了基因组结构变异从陆地棉半野生种系向栽培种渐渗的图谱，创新了多倍化驱动的祖先基因组结构演化规律；鉴定了纤维品质形成的遗传调控共性和分歧模块，推动了开辟棉花生物育种优异遗传资源精准创制的新途径，为通过种间渗入实现纤维品质的基因组靶向改良提供了支撑。这项研究加强了对于不同倍性物种重要性状平行选择的理解，为在其他植物不同种间泛基因组比较和同一性状形成的遗传机制研究提供了参考。
[前沿资讯 ] 浙江大学棉花精准育种团队等用AI破译棉花品种改良“密码本” 进入全文
中国科学报
棉花产量与纤维品质如何受到DNA甲基化调控？在人工智能（AI）的帮助下，中国棉花育种专家成功破译这一“密码本”，并从中找出有望改良棉花品种的关键基因位点。 近日，由浙江大学棉花精准育种团队、中国农业科学院生物技术研究所和湖畔实验室智慧育种团队组成的联合科研团队，综合运用遗传学、生物大数据和AI技术，构建了涵盖207个品种的棉花全基因组DNA甲基化图谱，鉴定了2.87亿个单甲基化多态性（SMP）位点，规模为目前所有作物之最。联合团队从中发现43个潜在参与纤维发育的eQTM基因，为棉花育种提供重要的候选基因列表。相关论文发表在国际期刊《细胞研究》（Cell Research）。 棉花是全球最大的天然纺织纤维来源，需要通过不断聚合优异的基因组遗传位点，进行品种改良。在AI、大数据等技术加持下，农业正在步入“智慧育种”时代，通过综合作物基因型数据、表型数据和环境数据，预测作物性状，精准筛选出优异基因。 此次，联合科研团队聚焦于DNA甲基化对作物的影响。DNA甲基化可以在不改变棉花DNA序列的情况下，影响棉花产量、纤维品质等农艺性状，并通过自然进化和人工选择传递。团队收集了207个品种的棉花全基因组甲基化测序数据、基因组测序数据、转录组测序数据，再结合农艺性状的表型数据，进行关联分析，首次构建起群体尺度的棉花全基因组DNA甲基化图谱，涵盖2.87亿个单甲基化多态性（SMP）位点。其中，仅甲基化测序数据就达到17TB。 湖畔实验室融合AI、并行计算等技术开发了一套新型算法，加速海量遗传数据的分析处理。湖畔实验室智慧育种团队负责人顾斐表示：“相比起传统方法，AI加成的分析计算速度提升近100倍，有助于开展亿级序列对比、群体变异分析和多组学关联分析，在数百个遗传变异、数万个基因以及数亿个甲基化位点之间建立起复杂的映射关系。” 联合科研团队进而首次绘制出与棉花纤维发育相关、独立于遗传因素的表观调控网络，揭示了43个潜在参与纤维发育的eQTM基因。其中一个位点已通过基因编辑实验，证实其调控棉花纤维长度的作用。此外，研究人员研发了深度学习模型DeepFDML，基于DNA甲基化位点附近的序列，预测影响基因表达的甲基化位点，未来有望发现更多具有育种价值的信息。 “这项研究成果证明了DNA甲基化数据可作为育种资源，为棉花品种改良提供新的思路。”来自浙江大学棉花精准育种团队的方磊表示：“依托生命科学+AI，育种家们将持续挖掘关键基因、预测农艺性状，加速培育‘超级’作物。” 据悉，湖畔实验室（数据科学与应用浙江省实验室）成立于2020年7月，依托阿里巴巴达摩院建设，聚焦数据科学领域的“数据智能”和“新型计算”两大方向。在智慧育种领域，湖畔实验室牵头研发全流程智慧育种平台，为育种家们提供包含育种数据管理和分析、计算加速、AI预测的“中央厨房”，大幅缩短培育新品种的周期。
