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[前沿资讯 ] Building resistance one plant at a time——Fred Bourland tracks plant bug resistance in breeding lines of cotton 进入全文
FarmProgress
Fred Bourland has been evaluating tarnished plant bug resistance in cotton breeding lines at the Northeast Research and Extension Center near Keiser, Ark., since before 2003. That’s a lot of cotton and plant bugs. When Bourland says varieties containing the ThryvOn technology “were very impressive” in their performance in his trials at the Northeast Research Center in 2023 and 2024, it’s based on years of experience. ThryvOn varieties But Bourland had a caveat: In 2024, the test had 16 ThryvOn varieties. Twelve of those ranked in the top varieties for boll loads in the tarnished plant bug tests. Of the other four, some were ranked considerably lower in the test. “So ThryvOn is not a silver bullet,” said Bourland. “But some of the varieties have stayed very consistent.” Bourland’s work with developing improved cotton varieties goes back more than the 20 years included in the presentation to include testing them for resistance to both tarnished plant bugs and boll weevils. He remembers the work of researchers including Bill Meredith with USDA’s Agricultural Research Service and Marion L. Laster with Mississippi State University at the Delta Research and Extension Center in Stoneville, Miss., in the 1960s, 70s and 80s. “They would take different lines and put them in large plots, side-by-side, treated and untreated, and see which ones in the untreated would do well,” he said. “Typically, they would use buffers planted with mustard in between those to serve as host plants for plant bugs. Then they would terminate the mustard to force the insects to move to cotton. Related:Supply and demand shifts leave cotton farms grasping for traction “I remember Bill Meredith presenting a paper at the Beltwide Cotton Conferences one year where he talked about being able to really cut the mustard, a reference to this tarnished plant bug work where they encouraged the plant bugs to move to the cotton.” Large plots Using large plots may still be the defining way to identify resistance to tarnished plant bugs, he said. “But how many varieties can you test at a time with these larger plots? With 20 or so entries that’s a big commitment. We’ve averaged looking at close to 100 different varieties or breeding line a year in our small plot work.” In the early days of his research, scientists had to be able to distinguish between insect damage caused by boll weevils and by tarnished plant bugs. “The first two years we used mustard, similar to what they did at Stoneville,” he said. “But mustard is a species that is difficult to manage out in a cotton field. So, we went to an early maturing frego-bract cotton, instead.” Frego bract, a mutant trait where the bracts surrounding the flower buds and bolls are long, narrow, twisted and tend to curl outward, exposing the square or boll, is another bit of cotton history associated with northeast Arkansas. It was discovered by a farmer named Frego, who observed it in a field of Stoneville 2B cotton on his farm about 20 miles from Keiser in the 1940s. He picked the cotton from the boll, ginned it by hand and planted the seed in his garden. The cotton that came up retained the trait, and Mr. Frego grew more of it. He told a county agent about it, and it eventually made its way to USDA researchers at Stoneville. “One thing we’ve learned is you don’t have to encourage the plant bugs in our area to get them to move to the plots,” Bourland noted. “They are there. And, really, the mustard was used back before boll weevil eradication. They were spraying for boll weevils and bollworms and controlling plant bugs with those sprays. They had to do something to encourage them, but we don’t have to do that. “I still plant the buffer of frego-bract – it helps separate the test. We like to plant it and three or four weeks earlier than we plant the plant bug test plots. We typically don’t use any insecticides for tarnished plant bugs. We did make one application this past year because they were just overwhelming our whole test.” Pest control Boll weevil eradication meant that farmers and researchers no longer had to contend with the pest. But it also meant the elimination of some of the boll weevil sprays that had helped control tarnished plant bugs. When Bourland began looking at cotton varieties for resistance solely to tarnished plant bugs in 2003, he started slowly because of the amount of manhours involved in plant sampling and determining boll loads to gauge the impact of the pest. “In 2006, Cotton Incorporated started supporting some of this work, and we expanded to variety tests and regional tests,” he said, “And, over the years, we have looked at a total of 2,724 lines in 102 tests. If you multiply that, that’s over 26,000 plots. So, it has been a large effort. “One lesson we have learned is we don’t have to have large plots. We can separate lines based on their performance in these short one-row plots. And I think that by using boll load ratings we can go to less than eight replications.”
[学术文献 ] Identification of favorable alleles from exotic Upland cotton lines for fiber quality improvement using multiple association models 进入全文
Frontiers in Plant Science
Upland cotton (Gossypium hirsutum) faces the challenge of limited genetic diversity in the elite or improved gene pool. To address this issue, we explored alleles contributed by five ‘converted’ exotic lines sampling most of the undomesticated botanical races of G. hirsutum, in BC1F2 and F3 populations. Joint analysis of all populations along with population-specific analyses identified 38 unique QTL for six different fiber quality traits. At 15 of these loci, DES56 or the elite allele improved upon all the exotics. For another 15, only a single of the five exotics improved upon the elite allele, suggesting the rare alleles that may not have been sampled in the cotton domestication or improvement. At the remaining 8 QTL, multiple exotic lines contributed the superior allele, suggesting that DES56 (and by extension the elite gene pool) has chronically poor alleles at these loci. Converted strains T1046, T326, and T063 showed the highest potential for contributions to cotton fiber quality breeding programs. Upper Half Mean Length and Fiber Strength showed multiple QTL regions affecting both traits simultaneously, while the Uniformity Index showed the smallest heritability values. The estimation of pairwise genetic distances for six parental lines indicates that DES56 has a higher genetic similarity with each exotic line than the exotic lines have with each other. Most of the detected QTL were ‘minor’ (explaining less than 10% of variance) supporting the implementation of genomic selection techniques to utilize the cumulative effects of most of these QTL distributed genome-wide. Finally, some regions were consistently unfavorable for exotic introgression such as on chromosomes A13 and D09, indicating the possible genome-wide haplotypes that may combine the benefits of a history of scientific breeding of the elite gene pool.
[学术文献 ] Differences in homologous and heterologous nucleocytoplasmic interactions of cytoplasmic male sterility lines in Gossypium barbadense 进入全文
scientific reports
The utilization of crop hybrids plays an important role in crop breeding and production, and the innovation of the male sterile germplasm is the basis for this utilization. Cotton has a very clear hybrid advantage, and the hybrid advantage in yield and quality has been widely utilized in cotton breeding. However, the exploitation of heterosis in cotton is currently dominated by cytoplasmic male sterility (CMS) lines. These CMS lines are found only in Harknessi cotton. They have a single cytoplasmic origin. Additionally, they exhibit a significant negative effect of cytoplasmic-nuclear interactions. To minimize this effect, it is necessary to select and breed CMS lines. In these CMS lines, both the cytoplasm and nucleus should originate from the same variety. However, no homologous cytoplasmic-nuclear CMS germplasm has been created, and its mechanism of occurrence has not been determined. In this study, two homologous cytoplasmic-nuclear CMS lines and two heterologous cytoplasmic-nuclear CMS lines were utilized, and the heterologous cytoplasmic-nuclear CMS lines were aborted at a relatively early stage. The physiological indexes related to reactive oxygen species ROS-mediated metabolic processes in the heterologous cytoplasmic-nuclear CMS lines were lower than those of the homologous cytoplasmic-nuclear CMS lines, including the enzyme activities of POD and CAT from tetrad to mature pollen grain, and the metabolite content of malondialdehyde (MDA) was inversely correlated with the enzyme activities of the heterologous cytoplasmic-nuclear CMS lines. Resequencing analysis of four cotton mitochondrial genomes (mt genomes) revealed that the heterologous cytoplasmic-nuclear CMS lines were more complex than the homologous cytoplasmic-nuclear CMS lines, and the homologous CMS lines showed a higher degree of collinearity with the maintainer lines. This indicates that heterologous cytoplasmic-nuclear interactions are more likely to lead to mtDNA structural variation. Taken together, the results showed that the cytoplasmic-nuclear homologous system was less affected by the cytoplasmic-nuclear interaction and was the best combination for the study of male sterility.
[前沿资讯 ] 陆地棉高清育种“地图”定位超级基因 进入全文
中国科学报
进入四月，一批早熟棉将被陆续播种在新疆广袤的棉田中。早熟棉“中棉113”的生长周期不到4个月，而破解其基因密码，需要整整四年。 近日，中国农业科学院棉花研究所研究员马雄风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的着丝粒演化和短季适应性遗传基础，为新疆棉业突破“早熟低产”困境、开启“设计育种”时代提供了关键钥匙。相关研究成果发表于《自然—遗传》（Nature Genetics）。 在中国工程院院士、中国农业科学院研究员万建民看来，该研究首次绘制了陆地棉端粒到端粒完整基因组图谱，填补了复杂重复区域的高精度序列空白，为目标性状遗传解析奠定了“精准坐标”。 中国工程院院士、华中农业大学教授张献龙指出，这项研究的一个重要创新发现是陆地棉谱系特异的D08着丝粒重定位到卫星重复区域的现象，改变了棉花着丝粒仅以转座子为主的传统认知，为后续棉花着丝粒多态性以及可能功能关联研究提供了新方向。 挑选优异性状突出的新品种作为“底盘” “我们现在以育种为目标，想要去解析棉花优异性状的遗传机制，那么找到一个特定的、更新的资源材料，才是实现研究目标的最佳路径。”论文通讯作者马雄风告诉《中国科学报》，对“中棉113”的选择，大有讲究。 马雄风介绍，以新疆为主的西北内陆棉区作为我国棉花生产的战略核心，其冷凉干旱的生态条件对品种早熟性提出了迫切需求。然而，传统早熟棉品种普遍面临“早熟低产”困境，早熟和高产两个性状协同提升难度很大，是制约新疆棉花生产的瓶颈。 为此，研究团队创新棉花早熟育种策略，通过分子聚合育种技术，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，特别符合新疆棉花生产的品种需求。 2019年，“中棉113”推出后，迅速得到广泛推广和应用。2022年至2024年连续3年入选农业农村部主导品种。 “有了‘中棉113’这样的优良早熟品种作为‘底盘’，育种工作者就能够进一步对其它迫切需要的生产性状进行改良。”马雄风说，比如让株型更适应高密度种植，同时减少荫蔽问题来提升光能利用率和机械化采收通过性；让棉铃吐絮更集中、叶片同步脱落，来降低机采籽棉杂质含量，以及提高脱叶剂使用效率等。 马雄风强调，育种是一个不断迭代更新、优中选优的动态过程。正因为“中棉113”是一个优异性状突出的新品种，和以往其它品种资源存在较大差异，进行参考基因组的组装才更加有意义和参考价值，才能为深入研究棉花遗传多样性、对目标性状进行遗传解析提供关键材料，为创新发现提供更大的空间和可能。“中棉113”作为深化品种改良选育的底盘品种，其基因组的参考价值面向未来长期育种实践的需要，将会被不断放大。 借助多项先进技术，他们完成了“中棉113”从端粒到端粒基因组的组装，实现了前所未有的基因组连续性和完整性。据了解，这是棉属物种中第一个作为现代生产品种的高质量组装，为陆地棉基因组研究提供了更为精确的参考。 高质量组装“放大”基因组细节 “高质量组装带来的惊喜是令人振奋的。”论文第一作者、中棉所研究员胡冠菁解释道，端粒到端粒（T2T）参考基因组组装，可定义为能够无缺口地覆盖所有染色体，包括对复杂的着丝粒、端粒、核糖体DNA区这些复杂“黑洞”区域的完整解析。 陆地棉是异源四倍体物种，基因组中含有A型和D型两个亚基因组，各有13对染色体，总计52条（2n=4x=52）。因为栽培棉花经历了长期的自交纯化，一对染色体之间的序列一致性很高，所以参考基因组组装出26条染色体。 胡冠菁介绍，在水稻、玉米等多种植物中，着丝粒主要由卫星重复序列组成，这是一类短而重复的DNA序列。而陆地棉的着丝粒比较特殊，主要由反转录转座子构成，这是一种可以自我复制并插入到基因组不同位置的DNA序列。 但是，当团队获得了高质量的基因组后却意外地发现，在陆地棉全部26条染色体中，D08这条染色体着丝粒并不是反转录转座子，而是和大多数植物一样由卫星重复序列组成——由重复元件以典型的高阶重复结构排布。 结合与其它近缘四倍体棉种的比较分析，团队最终确定其它棉种中依然存在常规的反转座子D08着丝粒，唯独陆地棉中发生了原本着丝粒的失活，并形成了新的重复序列着丝粒。 “实际上，最近陆地棉标准系TM-1的基因组研究也发现了D08着丝粒所在的位置，确认该位移事件发生于异源四倍化后。而我们的研究对该位移发生时间的尺度测量要更加精细，明确是在陆地棉从其他棉种中分化后发生的。高质量组装就像放大镜，让我们看清楚基因组里的更多细节。”胡冠菁说。 “这个现象在棉花中是首次被发现，在其它物种中也极少有两类不同类型着丝粒共存和相互动态变化的报道，可以说为着丝粒的起源、演化提供了新的研究视角。”马雄风说。 “超级基因”区段有望实现设计型品种快速创制 该研究的另一个创新发现，是锁定陆地棉D03染色体上一段长达11Mb的早熟关键区段，并揭示其独特的着丝粒横跨+染色体倒位双重复合结构。 胡冠菁解释，在遗传学研究中，主效位点通常指的是那些能够解释大量表型变异的基因或染色体区域。而这一次他们发现的调控棉花早熟的主效位点很大。 在D03染色体上的这个大型倒位区段的出现，能够追溯到陆地棉的早期驯化过程中的半野生地方品种，后续进一步发生变异并受到人工选择推动早熟性状的形成。 她说，这个区域中的大量基因，包括许多与开花相关基因，互相连锁着固定下来，能够以“超级基因”的形式整体遗传。传统的遗传学方法之所以无法将陆地棉的早熟“超级基因”拆开，是因为出现了倒位结构变异——区段序列倒置，使得其中所有基因被“打包”遗传、高度连锁。 “这个超级基因区域是深入研究早熟性分子遗传机制的重要资源。”胡冠菁说。 此外，棉花的一条纤维即为一个完整细胞，在整个植物界乃至生物界都是相当大型的单细胞结构。而棉纤维性状的改变，关系到整个细胞的生长，也就是说基本上所有基因都会参与到纤维性状改变的过程中，如同动用整个宇宙的“洪荒之力”一般。 “所以很难找到个别功能特别突出的基因，能够让棉花纤维一下子变得特别长，或特别坚韧，这是它的复杂性所在。”胡冠菁说，后续将进行的早熟与纤维性状的协同改良研究至关重要。 张献龙表示，该研究充分阐释了半野生棉来源的早熟单倍型在驯化中的稳定传递机制，丰富了棉花基因组结构的认知，并为早熟分子设计育种提供了精准坐标。 万建民强调，从功能基因研究视角看，棉花D03染色体区段内的基因资源发掘具有深远意义，需要通过进一步分子网络解析突破传统遗传定位瓶颈。同时，超级基因架构为分子设计育种提供了天然模块化工具——通过定向编辑该区段，有望实现早熟、高产与高衣分的“一因多效”协同改良。建议利用基因组编辑技术定向优化超级基因区段，实现“设计型品种”的快速创制。 相关论文信息：https://doi.org/10.1038/s41588-025-02130-4
[学术文献 ] Strigolactone promotes cotton fiber cell elongation by de-repressing DWARF53 on linolenic acid biosynthesis 进入全文
DEVELOPMENTAL CELL
Strigolactone (SL) is a plant hormone required for plant development. DWARF53 (D53) functions as a transcription repressor in SL signaling. However, the role of D53 in cotton (Gossypium hirsutum, Gh) fiber development remains unclear. Here, we identify that GhD53 suppresses fiber elongation by repressing transcription of GhFAD3 genes, which control linolenic acid (C18:3) biosynthesis. Mechanistically, GhD53 interacts with SL-related transcriptional activate factor (GhSLRF) to prevent its binding on Omega-3 fatty acid desaturase gene (GhFAD3) promoters, thereby inhibiting GhFAD3 transcription. Upon SL exposure, GhD53 is degraded and leads to GhSLRF activation. This activation further promotes GhFAD3 transcription, C18:3 biosynthesis, and fiber elongation. Our findings identify the molecular mechanism of how SL controls cell elongation via D53 and offer potential strategies to improve cotton quality through SL application.
[学术文献 ] Deciphering the role of small RNAs in the development of empurpled phenotypes in the Gossypium hirsutum mutant HS2 进入全文
PLANT GENE
Cotton fibers are among the most important natural fibers worldwide. Developing natural colored cotton (NCC) varieties is crucial for cotton fiber utilization due to their eco-friendly properties. Manipulation of anthocyanin synthesis is an effective strategy for creating novel NCCs. Our previous research revealed enhanced anthocyanin accumulation in an empurpled Gossypium hirsutum mutant, HS2, but the regulatory mechanism has not been fully elucidated. In this study, we employed an integrated analysis of RNA sequencing, small RNA (sRNA) sequencing, and degradome sequencing to assess the expression patterns and potential roles of sRNAs in the development of the empurpled phenotype in HS2. Our findings revealed that the expression profiles of sRNAs are highly similar between the wild type and the mutant, with only 11 miRNAs and 761 siRNAs showing significant expression variation. Eight miRNAs and one siRNA exhibited inverse regulation with their targets, which were not directly involved in regulating anthocyanin biosynthesis. Notably, degradome data analysis identified interactions between miR395 and ATP sulfurylase genes (APS1 and APS3). Further assessment determined down-regulation of miR395 and up-regulation ofAPS genes in HS2, as well as the enhanced biosynthesis of cysteine and glutathione. These results suggest that miRNA mediated post-transcriptional regulation might not be the primary mechanism driving anthocyanin enhancement in HS2. Instead, the miR395-APS modules are possibly involved in modulating cellular processes to cope with the increased anthocyanin levels. Overall, this study deepens our understanding of the molecular mechanisms underlying the empurpled phenotype in HS2 and facilitates its future use in NCC breeding.
