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Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis 拟南芥热胁迫期间蛋白质 SUMOylation 在 miRNA 转录调控中的功能表征
Pub Date : 2024-09-18 DOI: 10.1002/tpg2.20511
Simin Xia, Yue Chen, Jianbin Lai, Zhonghui Zhang, Chengwei Yang, Danlu Han
MicroRNAs (miRNAs) play an essential role as non‐coding‐RNA‐type epigenetic regulators in response to high‐temperature stress in plants. There are crucial roles for global transcriptional regulation under SUMO (small ubiquitin‐related MOdifier) stress response (SSR). However, the molecular mechanisms underlying its downstream regulation remain unclear. In this study, SUMO‐specific chromatin immunoprecipitation sequencing analysis detected specific binding in the promoter region of miRNAs under high‐temperature stress. A correlation analysis between this binding and miRNA profiling revealed that the location of SUMO on the chromosome was correlated with the expression pattern of miRNAs, particularly miR398a and miR824a. In contrast, knockout mutants of the SSR‐dependent SUMO E3 ligase SAP AND MIZ 1 in Arabidopsis exhibited opposing trends in target gene expression for the SUMO‐related miRNAs compared to the wild type. Multi‐omics correlation analyses identified 34 SUMO‐candidate proteins that might be involved in the regulation of miRNA response to high‐temperature stress. Therefore, we propose a potential model whereby high‐temperature exposure induces nuclear entry of SUMO molecules, modifying specific transcription factors that bind to miRNA gene promoters and potentially regulate miRNA expression.
微RNA(miRNA)作为非编码RNA类型的表观遗传调节因子,在植物应对高温胁迫的过程中发挥着重要作用。在 SUMO(小泛素相关修饰因子)胁迫响应(SSR)中,miRNAs 对全局转录调控起着至关重要的作用。然而,其下游调控的分子机制仍不清楚。在本研究中,SUMO 特异性染色质免疫沉淀测序分析检测到了高温胁迫下 miRNA 启动子区域的特异性结合。这种结合与 miRNA 图谱之间的相关性分析表明,SUMO 在染色体上的位置与 miRNA 的表达模式相关,尤其是 miR398a 和 miR824a。相比之下,拟南芥中依赖 SSR 的 SUMO E3 连接酶 SAP AND MIZ 1 的基因敲除突变体与野生型相比,在 SUMO 相关 miRNA 的靶基因表达方面表现出相反的趋势。多组学相关分析发现了 34 个可能参与调控 miRNA 对高温胁迫响应的 SUMO 候选蛋白。因此,我们提出了一个潜在的模型,即高温暴露诱导 SUMO 分子进入细胞核,从而修饰与 miRNA 基因启动子结合的特定转录因子,并可能调控 miRNA 的表达。
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引用次数: 0
Deciphering the genetic basis of novel traits that discriminate useful and non-useful biomass to enhance harvest index in wheat. 破译区分有用和无用生物量的新型性状的遗传基础,以提高小麦的收获指数。
Pub Date : 2024-09-18 DOI: 10.1002/tpg2.20512
Dipendra Shahi,Jia Guo,Md Ali Babar,Sumit Pradhan,Muhsin Avci,Naeem Khan,Jordan McBreen,Smita Rayamajhi,Zhao Liu,Guihua Bai,Paul St Amand,Amy Bernardo,Matthew Reynolds,Gemma Molero,Sivakumar Sukumaran,John Foulkes,Jahangir Khan
Wheat (Triticum aestivum L.) production must be doubled in the next 25 years to meet the global food demand. Harvest index (HI) is an important indicator of efficient partitioning of photosynthetic assimilates to grains. Reducing competition from alternative sinks, such as stems, and deviating assimilates toward grain increase grain number (GN), HI, and grain yield (GY). Novel partitioning traits have great potential to be utilized in wheat breeding programs to increase HI. In this study, we evaluated 236 US facultative soft wheat genotypes for multiple stem and spike partitioning traits at 7 days after anthesis, and for GN, HI, and GY in two locations of Florida in 2016-2017 and 2017-2018 wheat growing seasons. The panel was genotyped with 20,706 single nucleotide polymorphisms generated by genotype-by-sequencing approach. Spike partitioning index (SPI) showed negative significant correlations with lamina partitioning index and true stem partitioning index. Internode 2 and 3 lengths and partitioning indices had significant negative correlations with SPI and HI. The results indicate enhanced competition for assimilates between spikes and second and third internodes during stem elongation. Genome-wide association study (GWAS) identified 114 unique significant marker-trait associations (MTAs) for 12 traits, and 58 MTAs were found within genes that encode different proteins related to biotic/abiotic stress tolerance and other functions. Significant MTAs identified in the GWAS were converted into kompetitive allele specific PCR markers. Some of the markers were validated and can be effectively employed in marker-assisted selection to improve HI, GY, and GN.
小麦(Triticum aestivum L.)产量必须在未来 25 年内翻一番,才能满足全球粮食需求。收获指数(HI)是光合同化物有效分配到谷物的重要指标。减少来自茎等替代吸收汇的竞争,并将同化物偏向谷粒,可增加谷粒数(GN)、收获指数(HI)和谷粒产量(GY)。在小麦育种计划中,利用新的分配性状来提高 HI 有很大的潜力。在本研究中,我们在 2016-2017 年和 2017-2018 年小麦生长季节,在佛罗里达州的两个地方评估了 236 个美国面软小麦基因型在花后 7 天的多个茎秆和穗分化性状,以及 GN、HI 和 GY。通过逐基因型测序方法产生的 20706 个单核苷酸多态性对该面板进行了基因分型。穗分化指数(SPI)与叶片分化指数和真茎分化指数呈显著负相关。节间 2 和 3 长度及分区指数与 SPI 和 HI 呈显著负相关。结果表明,在茎伸长过程中,穗与第二和第三节间对同化物的竞争加剧。全基因组关联研究(GWAS)为 12 个性状确定了 114 个独特的显著标记-性状关联(MTAs),在编码与生物/非生物胁迫耐受性和其他功能相关的不同蛋白质的基因中发现了 58 个 MTAs。在 GWAS 中发现的重要 MTAs 被转化为竞争性等位基因特异性 PCR 标记。其中一些标记已通过验证,可有效用于标记辅助选择,以提高 HI、GY 和 GN。
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引用次数: 0
Genome‐wide association mapping reveals novel genes and genomic regions controlling root‐lesion nematode resistance in chickpea mini core collection 全基因组关联图谱揭示了控制鹰嘴豆小型核心集根瘤线虫抗性的新基因和基因组区域
Pub Date : 2024-09-13 DOI: 10.1002/tpg2.20508
Ashish Kumar, Yogesh Dashrath Naik, Vedant Gautam, Sunanda Patil, Vinod Valluri, Sonal Channale, Jayant Bhatt, Stuti Sharma, R. S. Ramakrishnan, Radheshyam Sharma, Himabindu Kudapa, Rebecca S. Zwart, Somashekhar M. Punnuri, Rajeev K. Varshney, Mahendar Thudi
Root‐lesion nematodes (RLN) pose a significant threat to chickpea (Cicer arietinum L.) by damaging the root system and causing up to 25% economic losses due to reduced yield. Worldwide commercially grown chickpea varieties lack significant genetic resistance to RLN, necessitating the identification of genetic variants contributing to natural resistance. This study identifies genomic loci responsible for resistance to the RLN, Pratylenchus thornei Sher & Allen, in chickpea by utilizing high‐quality single nucleotide polymorphisms from whole‐genome sequencing data of 202 chickpea accessions. Phenotypic evaluations of the genetically diverse set of chickpea accessions in India and Australia revealed a wide range of responses from resistant to susceptible. Genome‐wide association studies (GWAS) employing Fixed and Random Model Circulating Probability Unification (FarmCPU) and Bayesian‐Information and Linkage‐Disequilibrium Iteratively Nested Keyway (BLINK) models identified 44 marker‐trait associations distributed across all chromosomes except Ca1. Crucially, genomic regions on Ca2 and Ca5 consistently display significant associations across locations. Of 25 candidate genes identified, five genes were putatively involved in RLN resistance response (glucose‐6‐phosphate dehydrogenase, heat shock proteins, MYB‐like DNA‐binding protein, zinc finger FYVE protein and pathogenesis‐related thaumatin‐like protein). One notably identified gene (Ca_10016) presents four haplotypes, where haplotypes 1–3 confer moderate susceptibility, and haplotype 4 contributes to high susceptibility to RLN. This information provides potential targets for marker development to enhance breeding for RLN resistance in chickpea. Additionally, five potential resistant genotypes (ICC3512, ICC8855, ICC5337, ICC8950, and ICC6537) to P. thornei were identified based on their performance at a specific location. The study's significance lies in its comprehensive approach, integrating multiple‐location phenotypic evaluations, advanced GWAS models, and functional genomics to unravel the genetic basis of P. thornei resistance. The identified genomic regions, candidate genes, and haplotypes offer valuable insights for breeding strategies, paving the way for developing chickpea varieties resilient to P. thornei attack.
根线虫(RLN)对鹰嘴豆(Cicer arietinum L.)构成严重威胁,它会破坏根系,并因减产造成高达 25% 的经济损失。世界范围内商业种植的鹰嘴豆品种缺乏对 RLN 的显著遗传抗性,因此有必要鉴定天然抗性的遗传变异。本研究利用 202 个鹰嘴豆品种全基因组测序数据中的高质量单核苷酸多态性,确定了鹰嘴豆对 RLN(Pratylenchus thornei Sher & Allen)具有抗性的基因组位点。在印度和澳大利亚对不同基因的鹰嘴豆品种进行表型评估后发现,从抗性到易感性,鹰嘴豆的反应范围很广。全基因组关联研究(GWAS)采用了固定和随机模型循环概率统一(FarmCPU)以及贝叶斯信息和连锁-失衡迭代嵌套关键途径(BLINK)模型,确定了 44 个标记与性状的关联,分布在除 Ca1 以外的所有染色体上。最重要的是,Ca2 和 Ca5 上的基因组区域始终显示出不同位置的显著关联。在确定的 25 个候选基因中,有 5 个基因可能参与了 RLN 抗性反应(葡萄糖-6-磷酸脱氢酶、热休克蛋白、MYB 样 DNA 结合蛋白、锌指 FYVE 蛋白和致病相关的潮霉素样蛋白)。其中一个已发现的基因(Ca_10016)有四个单倍型,其中单倍型 1-3 具有中度易感性,而单倍型 4 则对 RLN 具有高度易感性。这些信息为标记开发提供了潜在目标,以提高鹰嘴豆抗 RLN 的育种能力。此外,根据其在特定地点的表现,确定了五种对 P. thornei 有潜在抗性的基因型(ICC3512、ICC8855、ICC5337、ICC8950 和 ICC6537)。这项研究的意义在于它采用了综合方法,整合了多地点表型评估、先进的 GWAS 模型和功能基因组学,以揭示荆条穗霉抗性的遗传基础。所确定的基因组区域、候选基因和单倍型为育种策略提供了宝贵的见解,为开发能抵抗 P. thornei 侵袭的鹰嘴豆品种铺平了道路。
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引用次数: 0
Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis 通过图像分析改进马铃薯(Solanum tuberosum)品质性状的基因组预测
Pub Date : 2024-09-11 DOI: 10.1002/tpg2.20507
Muyideen Yusuf, Michael D. Miller, Thomas R. Stefaniak, Darrin Haagenson, Jeffrey B. Endelman, Asunta L. Thompson, Laura M. Shannon
Potato (Solanum tuberosum L.) is the most widely grown vegetable in the world. Consumers and processors evaluate potatoes based on quality traits such as shape and skin color, making these traits important targets for breeders. Achieving and evaluating genetic gain is facilitated by precise and accurate trait measures. Historically, quality traits have been measured using visual rating scales, which are subject to human error and necessarily lump individuals with distinct characteristics into categories. Image analysis offers a method of generating quantitative measures of quality traits. In this study, we use TubAR, an image‐analysis R package, to generate quantitative measures of shape and skin color traits for use in genomic prediction. We developed and compared different genomic models based on additive and additive plus non‐additive relationship matrices for two aspects of skin color, redness, and lightness, and two aspects of shape, roundness, and length‐to‐width ratio for fresh market red and yellow potatoes grown in Minnesota between 2020 and 2022. Similarly, we used the much larger chipping potato population grown during the same time to develop a multi‐trait selection index including roundness, specific gravity, and yield. Traits ranged in heritability with shape traits falling between 0.23 and 0.85, and color traits falling between 0.34 and 0.91. Genetic effects were primarily additive with color traits showing the strongest effect (0.47), while shape traits varied based on market class. Modeling non‐additive effects did not significantly improve prediction models for quality traits. The combination of image analysis and genomic prediction presents a promising avenue for improving potato quality traits.
马铃薯(Solanum tuberosum L.)是世界上种植最广泛的蔬菜。消费者和加工商根据马铃薯的形状和皮色等质量性状对其进行评价,因此这些性状成为育种者的重要目标。精确和准确的性状测量有助于实现和评估遗传增益。一直以来,质量性状的测量都是采用目测评分法,这种方法容易出现人为误差,而且必然会将具有不同特征的个体归为一类。图像分析为质量性状的量化测量提供了一种方法。在本研究中,我们使用图像分析 R 软件包 TubAR 生成形状和肤色特征的定量测量值,用于基因组预测。我们针对 2020 年至 2022 年期间在明尼苏达州种植的新鲜上市红薯和黄薯,开发并比较了基于加性关系矩阵和加性加非加性关系矩阵的不同基因组模型,涉及皮色的两个方面--红度和亮度,以及形状的两个方面--圆度和长宽比。同样,我们利用同一时期种植的更大的削片马铃薯种群,制定了包括圆度、比重和产量在内的多性状选择指数。性状的遗传率各不相同,形状性状的遗传率介于 0.23 和 0.85 之间,颜色性状的遗传率介于 0.34 和 0.91 之间。遗传效应主要是加性效应,其中颜色性状的效应最强(0.47),而形状性状则因市场等级而异。建立非加成效应模型并不能明显改善质量性状的预测模型。图像分析与基因组预测的结合为改善马铃薯品质性状提供了一条很有前景的途径。
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引用次数: 0
Multi‐locus genome‐wide association study for grain yield and drought tolerance indices in sorghum accessions 高粱品种谷物产量和耐旱性指数的多焦点全基因组关联研究
Pub Date : 2024-09-11 DOI: 10.1002/tpg2.20505
Yirgalem Tsehaye, Temesgen M. Menamo, Fetien Abay, Taye Tadesse, Kassahun Bantte
Drought is a significant factor that causes yield loss in essential cereal crops such as sorghum [Sorghum bicolor (L.) Moench], necessitating the development of drought‐tolerant varieties adaptable to various water conditions. This study aimed to pinpoint drought‐tolerant sorghum lines and genomic regions for tolerance by utilizing 216 sorghum accessions in stressed and non‐stressed environments at two locations. Genetic diversity was evident among accessions in terms of grain yield under different watering regimes. Drought stress indices such as the stress tolerance index, mean productivity, geometric mean productivity, harmonic mean productivity, yield stability index, and yield index were identified as effective measures for selecting drought‐tolerant sorghum. Cluster analysis classified genotypes into four groups based on their association with grain yield, highlighting Acc. #28546 and Acc. #216739 as highly drought tolerant across environments. This study identified 32 and 22 quantitative trait nucleotides (QTNs) for drought indices and grain yield under stress and non‐stress conditions, respectively, at two locations, with five common QTNs linked to multiple drought indices. Colocation analysis revealed that these QTNs were associated with known stay‐green‐related quantitative trait loci (QTLs), and 47 putative genes near these QTNs potentially influenced drought tolerance traits. It is suggested that accession selection considers multiple indices for robust evaluation. Understanding the identified genes and their functions provides insights into the genetic mechanisms governing plant responses to drought stress, offering prospects for developing improved drought‐resistant sorghum varieties through further genetic research.
干旱是导致高粱(Sorghum bicolor (L.) Moench)等重要谷类作物减产的一个重要因素,因此有必要培育适应各种水分条件的耐旱品种。本研究旨在利用两地 216 个高粱品种在胁迫和非胁迫环境中的表现,确定耐旱高粱品系和耐旱基因组区域。结果表明,在不同的浇水条件下,高粱品种的粮食产量具有明显的遗传多样性。耐旱指数、平均生产力、几何平均生产力、调和平均生产力、产量稳定指数和产量指数等干旱胁迫指数被认为是筛选耐旱高粱的有效措施。聚类分析根据基因型与谷物产量的关系将基因型分为四组,突出了Acc.#28546和Acc.#218546号和216739号基因型在不同环境下都具有很强的抗旱性。这项研究在两个地点分别发现了 32 个和 22 个干旱指数和谷物产量的胁迫和非胁迫条件下的数量性状核苷酸(QTNs),其中五个共同的 QTNs 与多个干旱指数相关。同位分析表明,这些QTN与已知的留绿相关数量性状位点(QTL)有关,这些QTN附近的47个推测基因可能影响耐旱性状。建议入选者在选择时考虑多种指标,以进行稳健评估。通过对已鉴定基因及其功能的了解,可以深入了解植物对干旱胁迫反应的遗传机制,为进一步开展遗传学研究,培育抗旱高粱改良品种提供了前景。
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引用次数: 0
Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset 探索基因组特征选择:大规模大豆数据集中 GWAS 和机器学习算法的比较分析
Pub Date : 2024-09-10 DOI: 10.1002/tpg2.20503
Hawlader A. Al‐Mamun, Monica F. Danilevicz, Jacob I. Marsh, Cedric Gondro, David Edwards
The surge in high‐throughput technologies has empowered the acquisition of vast genomic datasets, prompting the search for genetic markers and biomarkers relevant to complex traits. However, grappling with the inherent complexities of high dimensionality and sparsity within these datasets poses formidable hurdles. The immense number of features and their potential redundancy demand efficient strategies for extracting pertinent information and identifying significant markers. Feature selection is important in large genomic data as it helps in enhancing interpretability and computational efficiency. This study focuses on addressing these challenges through a comprehensive investigation into genomic feature selection methodologies, employing a rich soybean (Glycine max L. Merr.) dataset comprising 966 lines with over 5.5 million single nucleotide polymorphisms. Emphasizing the “small n large p” dilemma prevalent in contemporary genomic studies, we compared the efficacy of traditional genome‐wide association studies (GWAS) with two prominent machine learning tools, random forest and extreme gradient boosting, in pinpointing predictive features. Utilizing the expansive soybean dataset, we assessed the performance of these methodologies in selecting features that optimize predictive modeling for various phenotypes. By constructing predictive models based on the selected features, we ascertain the comparative prediction accuracies, thereby illuminating the strengths and limitations of these feature selection methodologies in the realm of genomic data analysis.
高通量技术的迅猛发展为获取庞大的基因组数据集提供了可能,促使人们寻找与复杂性状相关的遗传标记和生物标志物。然而,要解决这些数据集固有的高维性和稀疏性等复杂问题,却面临着巨大的障碍。大量的特征及其潜在的冗余性要求采用高效的策略来提取相关信息并识别重要标记。特征选择在大型基因组数据中非常重要,因为它有助于提高可解释性和计算效率。本研究通过对基因组特征选择方法的全面调查,采用丰富的大豆(Glycine max L. Merr.)数据集,包括 966 个品系和 550 多万个单核苷酸多态性,重点解决这些挑战。我们强调了当代基因组研究中普遍存在的 "小 n 大 p "困境,比较了传统的全基因组关联研究(GWAS)与随机森林和极端梯度提升这两种著名的机器学习工具在确定预测特征方面的功效。利用广阔的大豆数据集,我们评估了这些方法在选择优化各种表型预测模型的特征方面的性能。通过基于所选特征构建预测模型,我们确定了预测准确率的比较,从而阐明了这些特征选择方法在基因组数据分析领域的优势和局限性。
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引用次数: 0
Exploring the role of FAT genes in Solanaceae species through genome‐wide analysis and genome editing 通过全基因组分析和基因组编辑探索茄科植物中 FAT 基因的作用
Pub Date : 2024-09-10 DOI: 10.1002/tpg2.20506
Sibel Bahadır, Mohamed Farah Abdulla, Karam Mostafa, Musa Kavas, Safa Hacıkamiloğlu, Orhan Kurt, Kubilay Yıldırım
Plants produce numerous fatty acid derivatives, and some of these compounds have significant regulatory functions, such as governing effector‐induced resistance, systemic resistance, and other defense pathways. This study systematically identified and characterized eight FAT genes (Acyl‐acyl carrier protein thioesterases), four in the Solanum lycopersicum and four in the Solanum tuberosum genome. Phylogenetic analysis classified these genes into four distinct groups, exhibiting conserved domain structures across different plant species. Promoter analysis revealed various cis‐acting elements, most of which are associated with stress responsiveness and growth and development. Micro‐RNA (miRNA) analysis identified specific miRNAs, notably miRNA166, targeting different FAT genes in both species. Utilizing clustered regularly interspaced short palindromic repeats/CRISPR‐associated protein 9 (CRISPR/Cas9)‐mediated knockout, mutant lines for SlFATB1 and SlFATB3 were successfully generated and exhibited diverse mutation types. Biochemical evaluation of selected mutant lines revealed significant changes in fatty acid composition, with linoleic and linolenic acid content variations. The study also explored the impact of FAT gene knockout on tomato leaf architecture through scanning electron microscopy, providing insights into potential morphological alterations. Knocking out of FAT genes resulted in a significant reduction in both trichome and stoma density. These findings contribute to a comprehensive understanding of FAT genes in Solanaceous species, encompassing genetic, functional, and phenotypic aspects.
植物会产生大量脂肪酸衍生物,其中一些化合物具有重要的调节功能,如调节效应器诱导的抗性、系统抗性和其他防御途径。这项研究系统地鉴定并描述了八个 FAT 基因(酰基载体蛋白硫酯酶),其中四个在茄属植物中,四个在块茎茄属植物基因组中。系统发育分析将这些基因分为四个不同的组,在不同植物物种中显示出保守的结构域。启动子分析揭示了各种顺式作用元件,其中大部分与胁迫响应性和生长发育有关。微 RNA(miRNA)分析发现了特定的 miRNA,特别是 miRNA166,它们在两个物种中都以不同的 FAT 基因为靶标。利用聚类规律性间隔短回文重复序列/CRISPR相关蛋白9(CRISPR/Cas9)介导的基因敲除,成功产生了SlFATB1和SlFATB3的突变株,并表现出不同的突变类型。对所选突变品系进行的生化评估显示,脂肪酸组成发生了显著变化,亚油酸和亚麻酸的含量发生了变化。研究还通过扫描电子显微镜探讨了 FAT 基因敲除对番茄叶片结构的影响,从而深入了解了潜在的形态学改变。敲除 FAT 基因会导致毛状体和气孔密度显著降低。这些发现有助于全面了解茄科植物的 FAT 基因,包括遗传、功能和表型等方面。
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引用次数: 0
Thanks to Reviewers, The Plant Genome, 2023 感谢审稿人,《植物基因组》,2023 年
Pub Date : 2024-05-31 DOI: 10.1002/tpg2.20472
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引用次数: 0
Evolutionary patterns of DNA base composition at polymorphic sites highlight the role of the environment in shaping barley and rice genomes 多态位点 DNA 碱基组成的进化模式凸显了环境在塑造大麦和水稻基因组中的作用
Pub Date : 2024-05-01 DOI: 10.1002/tpg2.20456
Xiangjian Gou, Yang Shao, Xiao Wang, Haoran Shi, Jianming Yu, Xianran Li, Tingting Guo
Insights into changes in genome base composition underlying crop domestication can be gained by using comparative genomics. With this approach, previous studies have reported that crop genomes during domestication accumulate more nucleotides adenine (A) and thymine (T) (termed as [AT]‐increase) across polymorphic sites. However, the potential influence of the environment or its factors, for example, solar ultraviolet (UV) radiation and temperature, on the [AT]‐increase has not been well elucidated. Here, we investigated the [AT]‐increase in barley (Hordeum vulgare L.) and rice (Oryza sativa L.) and the association with natural environments, where accessions are distributed. With 12,798,376 and 2,861,535 single‐nucleotide polymorphisms from 368 barley and 1375 rice accessions, respectively, we discovered that [AT] increases from wild accessions to improved cultivars, and genomic regions with larger [AT]‐increase tend to have higher UV‐related motif frequencies, suggesting solar UV radiation as a potential factor in driving genome variation. To link [AT] change with the geographic distribution, we gathered georeferenced accessions and examined their local environments. Interestingly, negative correlations between [AT] and environmental factors were observed (r = −0.39 ∼ −0.75) and modern accessions with higher [AT] values, as compared with wild relatives, are from the environments with lower solar UV radiation or lower temperature. With [AT] and environmental factors as phenotypes, genome‐wide association mapping identified three candidate genes that have the potential to contribute to [AT] variation under the effect of environmental conditions. Our findings provide genomic and environmental insights into evolutionary pattern of DNA base composition and underlying mechanisms.
利用比较基因组学可以深入了解作物驯化过程中基因组碱基组成的变化。利用这种方法,以往的研究报告指出,在驯化过程中,作物基因组在多态位点上积累了更多的腺嘌呤(A)和胸腺嘧啶(T)核苷酸(称为[AT]-increase)。然而,环境或环境因素(如太阳紫外线(UV)辐射和温度)对[AT]-增加的潜在影响尚未得到很好的阐明。在此,我们研究了大麦(Hordeum vulgare L.)和水稻(Oryza sativa L.)中[AT]-增加的情况以及与自然环境的关系,这些环境中分布着不同的品种。我们利用分别来自 368 个大麦和 1375 个水稻品种的 12,798,376 和 2,861,535 个单核苷酸多态性,发现从野生品种到改良栽培品种,[AT]都在增加,而且[AT]增加较多的基因组区域往往具有较高的紫外线相关图案频率,这表明太阳紫外线辐射是驱动基因组变异的潜在因素。为了将[AT]变化与地理分布联系起来,我们收集了有地理参照的入选品种,并考察了它们的当地环境。有趣的是,我们观察到[AT]与环境因素之间存在负相关(r = -0.39 ∼ -0.75),与野生近缘种相比,[AT]值较高的现代入选种来自太阳紫外线辐射较低或温度较低的环境。以[AT]和环境因素为表型,全基因组关联图谱发现了三个候选基因,它们有可能在环境条件的影响下导致[AT]变异。我们的研究结果为 DNA 碱基组成的进化模式及其内在机制提供了基因组和环境方面的见解。
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引用次数: 0
Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2. 全球部署的高粱蚜虫抗性基因 RMES1 很容易受到生物类型转变的影响,但 RMES2 却能增强其抗性。
Pub Date : 2024-04-23 DOI: 10.1002/tpg2.20452
Carl VanGessel, Brian Rice, Terry J. Felderhoff, Jean Rigaud Charles, G. Pressoir, V. Nalam, Geoffrey P. Morris
Durable host plant resistance (HPR) to insect pests is critical for sustainable agriculture. Natural variation exists for aphid HPR in sorghum (Sorghum bicolor), but the genetic architecture and phenotype have not been clarified and characterized for most sources. In order to assess the current threat of a sorghum aphid (Melanaphis sorghi) biotype shift, we characterized the phenotype of Resistance to Melanaphis sorghi 1 (RMES1) and additional HPR architecture in globally admixed populations selected under severe sorghum aphid infestation in Haiti. We found RMES1 reduces sorghum aphid fecundity but not bird cherry-oat aphid (Rhopalosiphum padi) fecundity, suggesting a discriminant HPR response typical of gene-for-gene interaction. A second resistant gene, Resistance to Melanaphis sorghi 2 (RMES2), was more frequent than RMES1 resistant alleles in landraces and historic breeding lines. RMES2 contributes early and mid-season aphid resistance in a segregating F2 population; however, RMES1 was only significant with mid-season fitness. In a fixed population with high sorghum aphid resistance, RMES1 and RMES2 were selected for demonstrating a lack of severe antagonistic pleiotropy. Associations with resistance colocated with cyanogenic glucoside biosynthesis genes support additional HPR sources. Globally, therefore, an HPR source vulnerable to biotype shift via selection pressure (RMES1) is bolstered by a second common source of resistance in breeding programs (RMES2), which may be staving off a biotype shift and is critical for sustainable sorghum production.
寄主植物对害虫的持久抗性(HPR)对于可持续农业至关重要。高粱(Sorghum bicolor)中的蚜虫 HPR 存在自然变异,但大多数来源的遗传结构和表型尚未明确和定性。为了评估当前高粱蚜虫(Melanaphis sorghi)生物型转变的威胁,我们在海地高粱蚜虫严重侵扰下筛选出的全球混交种群中鉴定了高粱蚜虫抗性 1(RMES1)的表型和其他 HPR 结构。我们发现 RMES1 能降低高粱蚜虫的繁殖力,但不能降低鸟樱桃-燕麦蚜虫(Rhopalosiphum padi)的繁殖力,这表明 HPR 反应具有典型的基因间相互作用的特征。在陆地品种和历史育种品系中,第二个抗性基因--抗黑穗蚜 2(RMES2)比抗 RMES1 的等位基因更为常见。在一个分离的 F2 群体中,RMES2 对早季和中季的蚜虫具有抗性;但 RMES1 只对中季的适应性有显著影响。在一个高抗高粱蚜虫的固定群体中,RMES1 和 RMES2 被选育出来,表现出缺乏严重的拮抗多效性。抗性与氰基葡糖苷生物合成基因的共位相关性支持了额外的 HPR 来源。因此,在全球范围内,通过选择压力容易发生生物型转变的 HPR 来源(RMES1)得到了育种计划中第二种常见抗性来源(RMES2)的支持,这可能避免了生物型的转变,对高粱的可持续生产至关重要。
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The Plant Genome
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