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[学术文献 ] Cell cycle-dependent kinase inhibitor GhKRP6, a direct target of GhBES1.4, participates in BR regulation of cell expansion in cotton 进入全文
PLANT JOURNAL
The steroidal hormone brassinosteroid (BR) has been shown to positively regulate cell expansion in plants. However, the specific mechanism by which BR controls this process has not been fully understood. In this study, RNA-seq and DAP-seq analysis of GhBES1.4 (a core transcription factor in BR signaling) were used to identify a cotton cell cycle-dependent kinase inhibitor called GhKRP6. The study found that GhKRP6 was significantly induced by the BR hormone and that GhBES1.4 directly promoted the expression of GhKRP6 by binding to the CACGTG motif in its promoter region. GhKRP6-silenced cotton plants had smaller leaves with more cells and reduced cell size. Furthermore, endoreduplication was inhibited, which affected cell expansion and ultimately decreased fiber length and seed size in GhKRP6-silenced plants compared with the control. The KEGG enrichment results of control and VIGS-GhKRP6 plants revealed differential expression of genes related to cell wall biosynthesis, MAPK, and plant hormone transduction pathways - all of which are related to cell expansion. Additionally, some cyclin-dependent kinase (CDK) genes were upregulated in the plants with silenced GhKRP6. Our study also found that GhKRP6 could interact directly with a cell cycle-dependent kinase called GhCDKG. Taken together, these results suggest that BR signaling influences cell expansion by directly modulating the expression of cell cycle-dependent kinase inhibitor GhKRP6 via GhBES1.4.
[学术文献 ] A cell wall-localized β-1,3-glucanase promotes fiber cell elongation and secondary cell wall deposition 进入全文
PLANT PHYSIOLOGY
A cell wall-localized & beta;-1,3-glucanase enhances polysaccharide metabolism and cell wall synthesis to promote fiber cell elongation and thickening. & beta;-1,3-glucanase functions in plant physiological and developmental processes. However, how & beta;-1,3-glucanase participates in cell wall development remains largely unknown. Here, we answered this question by examining the role of GhGLU18, a & beta;-1,3-glucanase, in cotton (Gossypium hirsutum) fibers, in which the content of & beta;-1,3-glucan changes dynamically from 10% of the cell wall mass at the onset of secondary wall deposition to <1% at maturation. GhGLU18 was specifically expressed in cotton fiber with higher expression in late fiber elongation and secondary cell wall (SCW) synthesis stages. GhGLU18 largely localized to the cell wall and was able to hydrolyze & beta;-1,3-glucan in vitro. Overexpression of GhGLU18 promoted polysaccharide accumulation, cell wall reconstruction, and cellulose synthesis, which led to increased fiber length and strength with thicker cell walls and shorter pitch of the fiber helix. However, GhGLU18-suppressed cotton resulted in opposite phenotypes. Additionally, GhGLU18 was directly activated by GhFSN1 (fiber SCW-related NAC1), a NAC transcription factor reported previously as the master regulator in SCW formation during fiber development. Our results demonstrate that cell wall-localized GhGLU18 promotes fiber elongation and SCW thickening by degrading callose and enhancing polysaccharide metabolism and cell wall synthesis.
[前沿资讯 ] 基因组水平解析陆地棉海南本土棉花—半野生棉种蓬蓬棉（G. purpurascens）的进化地位 进入全文
浙江在线-浙江日报
大约20万年前，一粒始发于中美洲西海岸的棉花种子一路向西漂流，在中国的海南岛登陆后生根发芽、繁衍生息。 直到2000~3000年前，海南岛的先民发现它的后代，开始了四倍体棉花的驯化栽培。 1月30日，浙江大学团队在Journal of Advanced Research(《先进研究期刊》)发表研究论文，文中还原了异源四倍体棉花这段数十万年的演化史。 研究团队从基因组水平解析陆地棉海南本土棉花—半野生棉种蓬蓬棉（G. purpurascens）的进化地位，发现中国是四倍体棉花最早驯化栽培的国家之一。 2019年，原新疆闫氏种业公司老总闫有发在海南崖城野外采集到一株棉花，计划用作亲本杂交育种实验。 当其他棉花含芳吐蕊，这株却迟迟没有动静。 “为什么不开花呢？”面对这棵身形略为魁梧的棉花，他们专门请教了浙江大学张天真教授团队。 “这‘暴露’了它是真正野生的棉花。”课题组成员之一关雪莹教授说，“许多野生的棉花带有光周期敏感的基因，花期受光照时间的牵制，一到北方就不开花。” 这个性状会影响到棉花的产量与品质，因此当前全球大规模栽培的棉花，都是已经剔除了这个遗传特征的人工选育品种，更适合工业化大规模种植与采摘。 对长期从事作物遗传育种的张天真来说，野生品种是取之不尽的宝藏。它们一方面能帮助人类进一步了解作物在地球上的繁衍与驯化历史；另一方面，随着育种技术的不断发展，野生作物保留下来的各种遗传信息将会被进一步发掘。 为此，棉花研究团队将这株棉花的样本命名为HPF17，对其进行了全基因组测序。 基于现有的陆地棉全基因组重测序数据和11个陆地棉骨干亲本基因组，研究发现，以HPF17为代表的海南本土野生棉花（Hainan Island cotton, HIC）属于陆地棉中较原始的蓬蓬棉野生种系。 “异源四倍体陆地棉原产于中美洲。其多年生野生种在美国南部经过人工选择，驯化成栽培的陆地棉或美棉，18世纪中期以后引种传播到世界各地广泛栽培。”张天真简要介绍了世界棉花的栽培史，“我国早期栽培的棉种是南亚地区起源的二倍体棉种亚洲棉，1949年以后大规模栽培的四倍体棉花品种也是美棉全球性传播带来的。” 但令人困惑的是，数千年前，我国海南的黎族先民就已经掌握了利用棉纤维纺织的技术，所使用的是一种独特的本土棉花，这些本土蓬蓬棉是何时来到中国的，以及它在陆地棉中演化过程中的进化地位，一直未得到科学研究的确认。 通过全基因组测序，张天真团队确认了HIC的古老“身份”，它是20万年前原产于中美洲的异源四倍体陆地棉的“直系”后代。“我们的研究表明，早在20万年前，它就和原产于中美洲的异源四倍体陆地棉分家了。”张天真说。 它是如何到达中国海南的？ 研究团队认为，随着太平洋洋流，它从中美洲西海岸逐渐西进到达中国南海诸岛（海南岛）。 对此他们提供了两个证据。一是洋流分布，海南本土棉花的种子小而坚硬，带绒毛的棉籽能够在水中浮半年以上，目前，人们所知的代表性的野生蓬蓬棉在太平洋岛屿上的分布，与太平洋洋流吻合度高；二是它极强的耐盐特性，能在盐水里存活半年以上。 海南岛登陆后，蓬蓬棉是“野生”状态，还是与人类的生产生活有交集？ 帮研究人员揭开这一谜团的是手工轧花机——一种给棉花脱籽的机器。 “徒手将纤维从种子上剥离非常费力，这是发展先民棉纺技术遇到的第一个难题。”论文的第一作者程宇介绍。 在研究了不同棉籽的纤维程度后，研究团队进一步确认，只有蓬蓬棉的棉纤维才需要用到轧棉机。“木棉的纤维非常短，无法取得用于纺织的纤维；而海岛棉和木棉，能够轻易脱籽。”从某种角度说，正是蓬蓬棉的棉籽特征才催生了轧棉机的诞生。 研究团队就此提出，在2000~3000年前左右，蓬蓬棉已经在海南岛被初步驯化和小规模栽培，并用于纺织“崖州布”。这个时间点，早在哥伦布时期前，美棉驯化栽培前。“三亚（崖州）可能是陆地棉最早驯化和栽培的地点之一，即中国是四倍体棉花最早驯化栽培的国家之一。”张天真说。
[学术文献 ] Acetylation of GhCaM7 enhances cotton resistance to Verticillium dahliae 进入全文
PLANT JOURNAL
Protein lysine acetylation is an important post-translational modification mechanism involved in cellular regulation in eukaryotes. Calmodulin (CaM) is a ubiquitous Ca2+ sensor in eukaryotes and is crucial for plant immunity, but it is so far unclear whether acetylation is involved in CaM-mediated plant immunity. Here, we found that GhCaM7 is acetylated upon Verticillium dahliae (V. dahliae) infection and a positive regulator of V. dahliae resistance. Overexpressing GhCaM7 in cotton and Arabidopsis enhances V. dahliae resistance and knocking-down GhCaM7 makes cotton more susceptible to V. dahliae. Transgenic Arabidopsis plants overexpressing GhCaM7 with mutation at the acetylation site are more susceptible to V. dahliae than transgenics overexpressing the wild-type GhCaM7, implying the importance of the acetylated GhCaM7 in response to V. dahliae infection. Yeast two-hybrid, bimolecular fluorescent complementation, luciferase complementation imaging, and coimmunoprecipitation assays demonstrated interaction between GhCaM7 and an osmotin protein GhOSM34 that was shown to have a positive role in V. dahliae resistance. GhCaM7 and GhOSM34 are co-localized in the cell membrane. Upon V. dahliae infection, the Ca2+ content reduces almost instantly in plants with downregulated GhCaM7 or GhOSM34. Down regulating GhOSM34 enhances accumulation of Na+ and increases cell osmotic pressure. Comparative transcriptomic analyses between cotton plants with an increased or reduced expression level of GhCaM7 and wild-type plants indicate the involvement of jasmonic acid signaling pathways and reactive oxygen species in GhCaM7-enabled disease resistance. Together, these results demonstrate the involvement of CaM protein in the interaction between cotton and V. dahliae, and more importantly, the involvement of the acetylated CaM in the interaction.
[前沿资讯 ] Gene grants powerful resistance to resurging plant disease 进入全文
EurekAlert
While wrapping oneself in 100% Egyptian cotton bedsheets is a delightful luxury on a warm summer night, cotton provides much more than breathable, soft fabric. In addition to textiles, the cotton plant is grown for food, fuel, and daily-use consumer products—such as coffee filters, currency, and moisturizers. However, a resurging plant disease called bacterial blight is currently threatening cotton production worldwide. Bacterial blight is best controlled through natural, genetic resistance. Although several genes for natural resistance to bacterial blight of cotton were discovered in northeast Africa during the mid-twentieth century, one of these genes, found in Egyptian cotton, had been overlooked until a team of researchers led by Margaret Essenberg from Oklahoma State University began studying the gene. One of their recent studies, published by the American Phytopathological Society in a special focus issue of its journal Phytopathology, unveiled that gene B5 confers powerful resistance to bacterial blight. Essenberg and colleagues observed puzzling behavior from gene B5 after it was crossed into the DNA of upland cotton—a variety used in most clothing fabrics—as it did not appear to follow typical Mendelian genetics. Further investigation revealed an explanation for this peculiarity: upland cotton (AcB5) appears to carry gene B5 at two locations in its genome versus the typical single location. Under Oklahoma field conditions, the gene at either location enabled strong resistance to bacterial blight. In the lab, AcB5 exhibited resistance to the predominant and widely virulent strain of the disease’s causal pathogen, race 18, in addition to nine other pathogen races. These findings have positive implications for bacterial blight resistance in agriculture. “Natural, heritable disease resistance is an economical and environmentally safe means of maintaining plant health,” corresponding author Melanie Bayles explains. “Resistance genes trigger synthesis of natural defense chemicals at sites of infection. AcB5 cotton is a champion in this activity; it accumulated at least ten-fold more defense chemicals than cotton lines with four other single resistance genes.” Because pathogens often evolve to overcome such resistance, relying only on a single gene for disease resistance is precarious. The researchers propose that plant breeders combine this valuable B5 gene with other strong, broadly specific genes, such as B12, to develop durable resistance to bacterial blight. In addition to plant breeding, Bayles states that this research can benefit disciplines such as molecular plant-microbe interactions and phytochemistry, since the “signal transduction pathways of five different major genes for bacterial disease resistance in cotton are shown to lead in part to production of the same set of defense chemicals.” AcB5 is available for other researchers to use, along with a near-isogenic susceptible parent line. Essenberg and colleagues’ new, quick method for estimating amounts of defense chemicals in cotton plants, reported in Phytopathology, offers a “blight bulb” idea for improving resistance to this prevalent disease. For further details, read Gene B5 in Cotton Confers High and Broad Resistance to Bacterial Blight and Conditions High Amounts of Sesquiterpenoid Phytoalexins, published in the Phytopathology Focus Issue “Plant Disease Resistance at the Dawn of the New Era”—Volume 113, Number 5 / May 2023.
[前沿资讯 ] Computer scientists sequence cotton genome 进入全文
DePaul University
Cotton is the primary source of natural fiber on Earth, yet only four of 50 known species are suitable for textile production. Computer scientists at DePaul University applied a bioinformatics workflow to reconstruct one of the most complete genomes of a top cotton species, African domesticated Gossypium herbaceum cultivar Wagad. Experts say the results give scientists a more complete picture of how wild cotton was domesticated over time and may help to strengthen and protect the crop for farmers in the U.S., Africa and beyond. The findings are published in the journal G3 Genes|Genomes|Genetics. Thiru Ramaraj, assistant professor of computer science in DePaul's Jarvis College of Computing and Digital Media, is lead author on the publication. Leaps in technological advancement in the past decade made it possible for Ramaraj to analyze the genome in his Chicago lab. "The power of this technology is it allows us to create high-quality genomes that supply a level of detail that simply wasn't possible before," says Ramaraj, who specializes in bioinformatics. "This opens up the possibility for more researchers to sequence many crops that are important to the global economy and to feeding the population." The work is part of a collaboration that includes Jonathan Wendel, distinguished professor in the Department of Ecology, Evolution, and Organismal Biology at Iowa State University; and Joshua Udall, research leader for the Crop Germplasm Research Unit at the U.S. Department of Agriculture Agricultural Research Service. According to Udall, Wagad cotton is a diploid strain grown predominantly in African countries. "This has the potential to provide a genetic map that could improve their cotton crop," Udall said. Advanced computational methodologies bring forward genome The team's work began with crunching DNA sequence data. They began reconstructing the Wagad genome by assembling high quality long DNA sequence data generated using Pacific Biosciences sequencing technology. As a next step, whole genome maps from Bionano genomics were used to order and orient the initial assembly. Lastly Hi-C sequence data from Phase genomics were used to construct chromosome level genome. Ramaraj then turned to Azalea Mendoza, a graduate student in computer science who also holds a bachelor's degree in environmental studies from DePaul. "Azalea had the biology background and knowledge to dive into this research," Ramaraj said. Mendoza began by researching the history of cotton to zoom out and understand "the big picture." No matter where cotton is grown, it's primarily used for fiber. Using comparative genomics, she looked for variations against its closet relative and to an outgroup. Mendoza also delved into annotated genes and noted their functions. "As we were studying the regions of the genome, we found many genes that were related to the content of fiber," Mendoza says. "It was incredible to see the real-life application of the work." Protecting crops in the U.S. and beyond The impact of cotton genomics on U.S. agriculture and economy are clear to Udall, who has worked with Ramaraj since 2015. Udall leads the Crop Germplasm Research Unit and examines some of the 10,000 accessions of various species that the USDA holds in its repository. Their goal is to maintain the country's genetic food and feed security, and part of that is understanding the resilience and weaknesses of crops from around the world. "When new diseases come to the U.S., or there's new invasive pests, one of the first things we do is screened the genetic diversity of cotton to see if any of the previous varieties are resistant to it," Udall says. This can give farmers a chance to cross breed those genes and improve modern varieties of cotton, potentially avoiding catastrophic loss of agriculture. Udall relies on computational biologists like Ramaraj to further this work. While the cost of sequencing genomes has come down, this study still took nearly two years of work across disciplines. "This is a good step in identifying future cotton genomes to sequence," Udall says. Ramaraj hopes the project will inspire other faculty and student collaborators to approach CDM with ideas for bioinformatics projects. For Mendoza, now an alumna working as a data analyst, the experience working in bioinformatics at DePaul is inspiring her career goals. "I love research and work that helps me grow on multiple levels," Mendoza says. "This is the kind of work that is going to affect humans and sustainability into the future."
