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Genetic diversity and genome-wide association study of partial resistance to Sclerotinia stem rot in a Canadian soybean germplasm panel. 加拿大大豆种质群对硬核菌茎腐病部分抗性的遗传多样性和全基因组关联研究。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-11 DOI: 10.1007/s00122-024-04708-8
Deus Mugabe, Mohsen Yoosefzadeh-Najafabadi, Istvan Rajcan

Key message: Developing genetically resistant soybean cultivars is key in controlling the destructive Sclerotinia Stem Rot (SSR) disease. Here, a GWAS study in Canadian soybeans identified potential marker-trait associations and candidate genes, paving the way for more efficient breeding methods for SSR. Sclerotinia stem rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is one of the most important diseases leading to significant soybean yield losses in Canada and worldwide. Developing soybean cultivars that are genetically resistant to the disease is the most inexpensive and reliable method to control the disease. However, breeding for resistance is hampered by the highly complex nature of genetic resistance to SSR in soybean. This study sought to understand the genetic basis underlying SSR resistance particularly in soybean grown in Canada. Consequently, a panel of 193 genotypes was assembled based on maturity group and genetic diversity as representative of Canadian soybean cultivars. Plants were inoculated and screened for SSR resistance in controlled environments, where variation for SSR phenotypic response was observed. The panel was also genotyped via genotyping-by-sequencing and the resulting genotypic data were imputed using BEAGLE v5 leading to a catalogue of 417 K SNPs. Through genome-wide association analyses (GWAS) using FarmCPU method with threshold of FDR-adjusted p-values < 0.1, we identified significant SNPs on chromosomes 2 and 9 with allele effects of 16.1 and 14.3, respectively. Further analysis identified three potential candidate genes linked to SSR disease resistance within a 100 Kb window surrounding each of the peak SNPs. Our results will be important in developing molecular markers that can speed up the breeding for SSR resistance in Canadian grown soybean.

关键信息:开发具有抗性基因的大豆栽培品种是控制具有破坏性的大豆茎腐病(SSR)的关键。在此,一项针对加拿大大豆的 GWAS 研究确定了潜在的标记-性状关联和候选基因,为更有效的 SSR 育种方法铺平了道路。由真菌病原体 Sclerotinia sclerotiorum 引起的茎腐病(SSR)是导致加拿大和全世界大豆产量大幅下降的最重要病害之一。培育具有抗病基因的大豆栽培品种是控制这种病害的最廉价、最可靠的方法。然而,由于大豆对 SSR 的遗传抗性非常复杂,抗性育种受到阻碍。本研究试图了解 SSR 抗性的遗传基础,尤其是加拿大大豆的 SSR 抗性。因此,根据加拿大大豆栽培品种的成熟度组和遗传多样性,组建了一个由 193 个基因型组成的小组。在受控环境中对植物进行接种并筛选 SSR 抗性,观察 SSR 表型反应的变化。此外,还通过基因分型测序对面板进行了基因分型,并使用 BEAGLE v5 对由此产生的基因型数据进行了估算,从而得到了 417 K SNPs 的目录。通过使用 FarmCPU 方法进行全基因组关联分析(GWAS),以 FDR 调整后的 p 值为阈值
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引用次数: 0
Agrobacterium-mediated transformation of B. juncea reveals that BjuLKP2 functions in plant yellowing. 农杆菌介导的君子兰转化揭示了 BjuLKP2 在植物黄化中的功能。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-09 DOI: 10.1007/s00122-024-04707-9
Jing Zeng, Liang Zhao, Yuanqing Lu, Tonghong Zuo, Baowen Huang, Diandong Wang, Yawen Zhou, Zhongxin Lei, Yanling Mo, Yihua Liu, Jian Gao

Key message: A stable Agrobacterium-mediated transformation system was constructed for B. juncea, and BjuLKP2 was overexpressed, leading to plant yellowing. A stable and efficient transformation system is necessary to verify gene functions in plants. To establish an Agrobacterium-mediated transformation system for B. juncea, various factors, including the explant types, hormone combination and concentration, infection time and concentration, were optimized. Eventually, a reliable system was established, and two BjuLKP2 overexpression (OE) lines, which displayed yellowing of cotyledons, shoot tips, leaves and flower buds, as well as a decrease in total chlorophyll content, were generated. qRT-PCR assays revealed significant upregulation of five chlorophyll synthesis genes and downregulation of one gene in the BjuLKP2 OE line. Furthermore, antioxidant capacity assays revealed reduced activities of APX, CAT and SOD, while POD activity increased in the BjuLKP2 OE26. Additionally, the kinetic determination of chlorophyll fluorescence induction suggested a decrease in the photosynthetic ability of BjuLKP2 OE26. GUS assays revealed the expression of BjuLKP2 in various tissues, including the roots, hypocotyls, cotyledons, leaf vasculature, trichomes, sepals, petals, filaments, styles and stigma bases, but not in seeds. Scanning electron revealed alterations in chloroplast ultrastructure in both the sponge and palisade tissue. Collectively, these findings indicate that BjuLKP2 plays a role in plant yellowing through a reduction in chlorophyll content and changes in chloroplasts structure.

关键信息:构建了一个稳定的农杆菌介导的君子兰转化系统,BjuLKP2 被过量表达,导致植株黄化。要验证基因在植物中的功能,需要一个稳定高效的转化系统。为了建立农杆菌介导的君子兰转化系统,我们优化了各种因素,包括外植体类型、激素组合和浓度、感染时间和浓度。通过 qRT-PCR 检测发现,在 BjuLKP2 OE 株系中,五个叶绿素合成基因显著上调,一个基因下调。此外,抗氧化能力测定显示,BjuLKP2 OE26 的 APX、CAT 和 SOD 活性降低,而 POD 活性提高。此外,叶绿素荧光诱导的动力学测定表明,BjuLKP2 OE26 的光合能力下降。GUS 检测表明,BjuLKP2 在不同组织中都有表达,包括根、下胚轴、子叶、叶脉、毛状体、萼片、花瓣、花丝、花柱和柱头基部,但在种子中没有表达。扫描电子显微镜显示,海绵和栅栏组织的叶绿体超微结构都发生了改变。总之,这些研究结果表明,BjuLKP2 通过降低叶绿素含量和改变叶绿体结构在植物黄化中发挥作用。
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引用次数: 0
Identification of stripe rust resistance gene YrBDT in Chinese landrace wheat Baidatou using BSE-seq and BSR-seq. 利用BSE-seq和BSR-seq鉴定中国陆地小麦白大头的条锈病抗性基因YrBDT。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-07 DOI: 10.1007/s00122-024-04704-y
Jingchun Wu, Yukun Cheng, Weihao Hao, Bin Bai, Luping Fu, Yan Ren, Yuanfeng Hao, Fengju Wang, Ruiming Lin, Hongqi Si, Chuanxi Ma, Zhonghu He, Jiansheng Chen, Can Chen, Xianchun Xia

Key message: A new stripe rust resistance gene YrBDT in Chinese landrace wheat Baidatou was mapped to a 943.6-kb interval on chromosome arm 6DS and co-segregated with a marker CAPS3 developed from candidate gene TraesCS6D03G0027300. Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a devastating foliar disease of wheat. Chinese landrace wheat Baidatou has shown high resistance to a broad spectrum of Pst races at both the seedling and adult-plant stages for decades in the Longnan region of Gansu province, a hot spot for stripe rust epidemics. Here, we report fine mapping and candidate gene analysis of stripe rust resistance gene YrBDT in Baidatou. Analysis of F1, F2 plants and F2:3 lines indicated that resistance in Baidatou to Pst race CYR31 was conferred by a single dominant gene, temporarily designated YrBDT. Bulked segregant exome capture sequencing (BSE-seq) analysis revealed 61 high-confidence polymorphic SNPs concentrated in a 5.4-Mb interval at the distal of chromosome arm 6DS. Several SNPs and InDels were also identified by genome mining of DNA sampled from the parents and contrasting bulks. The YrBDT locus was mapped to a 943.6-kb (4,658,322-5,601,880 bp) genomic region spanned by markers STS2 and STS3 based on IWGSC RefSeq v2.1, including five putative disease resistance genes. There was high collinearity of the target interval among Chinese Spring RefSeq v2.1, Ae. tauschii AL8/78 and Fielder genomes. The expression level of TraesCS6D03G0027300 showed significant association with Pst infection, and a gene-specific marker CAPS3 developed from TraesCS6D03G0027300 co-segregated with YrBDT suggesting this gene as a candidate of YrBDT. The resistance gene and flanking markers can be used in marker-assisted selection for improvement of stripe rust resistance.

关键信息中国陆地小麦白大头中一个新的条锈病抗性基因YrBDT被映射到染色体臂6DS上的943.6kb区间,并与从候选基因TraesCS6D03G0027300发展而来的标记CAPS3共分离。由条锈病菌 Puccinia striiformis f. sp. tritici(Pst)引起的条锈病是一种毁灭性的小麦叶面病害。在条锈病流行的热点地区--甘肃省陇南地区,中国陆地小麦白大头几十年来在幼苗期和成株期都表现出对广谱 Pst 株系的高抗性。在此,我们报告了白大头抗条锈病基因 YrBDT 的精细图谱和候选基因分析。对F1、F2植株和F2:3品系的分析表明,白塔头对Pst race CYR31的抗性是由一个单一显性基因赋予的,暂定为YrBDT。批量分离外显子组捕获测序(BSE-seq)分析显示,61 个高置信度多态性 SNPs 集中在染色体臂 6DS 远端的 5.4-Mb 区间。通过对亲本和对比群体的 DNA 进行基因组挖掘,还发现了几个 SNP 和 InDels。根据 IWGSC RefSeq v2.1,YrBDT 基因座被映射到标记 STS2 和 STS3 跨过的 943.6 kb(4,658,322-5,601,880 bp)基因组区域,其中包括五个假定的抗病基因。目标区间在华春RefSeq v2.1、Ae. tauschii AL8/78和Fielder基因组之间存在高度共线性。TraesCS6D03G0027300 的表达水平与 Pst 感染有显著相关性,从 TraesCS6D03G0027300 发展出的基因特异性标记 CAPS3 与 YrBDT 共分离,表明该基因是 YrBDT 的候选基因。该抗性基因和侧翼标记可用于标记辅助选择,以提高条锈病的抗性。
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引用次数: 0
Mapping of a novel locus Ra conferring extreme resistance against potato virus A in cultivated potato (Solanum tuberosum L.). 在栽培马铃薯(Solanum tuberosum L.)中绘制一个新基因座 Ra 的图谱,该基因座赋予马铃薯对马铃薯病毒 A 的极端抗性。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-06 DOI: 10.1007/s00122-024-04705-x
Wei Huang, Jie Zheng, Bihua Nie, Jiana Li, Ruhao Chen, Xianzhou Nie, Zhen Tu, Kyle Gardner, Jiaru Chen, Manhua Yang, Jingcai Li, Jianke Dong, Hui Ma, Botao Song

Key message: The Ra extreme resistance against potato virus A was mapped to the upper of chromosome 4 in tetraploid potato. Potato virus A (PVA) is one of the major viruses affecting potato worldwide and can cause serious disease symptoms and yield losses. Previously, we determined that potato cultivar Barbara harbors Rysto (genotype: Ryryryry) and Ra (genotype: Rararara) that each independently confer extreme resistance to PVA. In this study, employing a combination of next-generation sequencing and bulked-segregant analysis, we further located this novel Ra on chromosome 4 using a tetraploid BC1 potato population derived from a Ry-free progeny (Rararararyryryry) of Barbara (RarararaRyryryry) × F58050 (rararararyryryry). Using 29 insertion-deletion (InDel) markers spanning chromosome 4, Ra was delimited by the InDel markers M8-83 and M10-8 within a genetic interval of 1.46 cM, corresponding to a 1.86-Mb genomic region in the potato DM reference genome. The InDel marker M10-8, which is closely linked with the resistance against PVA in the Ry-free segregating populations, was then used to screen 43 selected Rysto-free tetraploid potato breeding clones. The phenotype to PVA was significantly correlated with the present/absent of the marker, albeit with a 9.3% false positive rate and a 14.0% false negative rate. These findings are of importance in furthering the cloning of Ra and employing the marker-assisted selection for PVA resistance.

关键信息:在四倍体马铃薯中,Ra 对马铃薯病毒 A 的极端抗性被映射到 4 号染色体的上部。马铃薯病毒 A(PVA)是影响全球马铃薯的主要病毒之一,可导致严重的病害症状和产量损失。此前,我们确定马铃薯栽培品种 Barbara 含有 Rysto(基因型:Rryryry)和 Ra(基因型:Rararara),这两个基因型各自独立地赋予马铃薯对 PVA 的极强抗性。在本研究中,我们结合使用下一代测序和大块分离分析,利用从 Barbara (RarararaRyryry) × F58050 (arrarararyryry)的无 Ry 后代 (Rararararyryry) 中获得的四倍体 BC1 马铃薯群体,进一步定位了 4 号染色体上的新型 Ra。利用横跨 4 号染色体的 29 个插入-缺失(InDel)标记,InDel 标记 M8-83 和 M10-8 将 Ra 限定在 1.46 cM 的遗传间隔内,相当于马铃薯 DM 参考基因组中 1.86-Mb 的基因组区域。InDel 标记 M10-8 与无 Ry 分离群体对 PVA 的抗性密切相关,因此被用来筛选 43 个精选的无 Rysto 四倍体马铃薯育种克隆。尽管假阳性率为 9.3%,假阴性率为 14.0%,但对 PVA 的表型与标记的存在/不存在显著相关。这些发现对进一步克隆 Ra 和采用标记辅助选择 PVA 抗性具有重要意义。
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引用次数: 0
A framework for simulating genotype-by-environment interaction using multiplicative models. 使用乘法模型模拟基因型与环境相互作用的框架。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-06 DOI: 10.1007/s00122-024-04644-7
J Bančič, G Gorjanc, D J Tolhurst

Key message: The simulation of genotype-by-environment interaction using multiplicative models provides a general and scalable framework to generate realistic multi-environment datasets and model plant breeding programmes. Plant breeding has been historically shaped by genotype-by-environment interaction (GEI). Despite its importance, however, many current simulations do not adequately capture the complexity of GEI inherent to plant breeding. The framework developed in this paper simulates GEI with desirable structure using multiplicative models. The framework can be used to simulate a hypothetical target population of environments (TPE), from which many different multi-environment trial (MET) datasets can be sampled. Measures of variance explained and expected accuracy are developed to tune the simulation of non-crossover and crossover GEI and quantify the MET-TPE alignment. The framework has been implemented within the R package FieldSimR, and is demonstrated here using two working examples supported by R code. The first example embeds the framework into a linear mixed model to generate MET datasets with low, moderate and high GEI, which are used to compare several popular statistical models applied to plant breeding. The prediction accuracy generally increases as the level of GEI decreases or the number of environments sampled in the MET increases. The second example integrates the framework into a breeding programme simulation to compare genomic and phenotypic selection strategies over time. Genomic selection outperforms phenotypic selection by 50-70% in the TPE, depending on the level of GEI. These examples demonstrate how the new framework can be used to generate realistic MET datasets and model plant breeding programmes that better reflect the complexity of real-world settings, making it a valuable tool for optimising a wide range of breeding methodologies.

关键信息:利用乘法模型模拟基因型与环境之间的相互作用为生成真实的多环境数据集和模拟植物育种计划提供了一个通用的、可扩展的框架。植物育种历来受基因型与环境相互作用(GEI)的影响。然而,尽管其重要性不言而喻,目前的许多模拟并不能充分反映植物育种所固有的 GEI 的复杂性。本文开发的框架利用乘法模型模拟了具有理想结构的 GEI。该框架可用于模拟假定的环境目标群(TPE),并从中抽取许多不同的多环境试验(MET)数据集。我们开发了解释方差和预期准确度的测量方法,以调整非交叉和交叉 GEI 的模拟,并量化 MET-TPE 的一致性。该框架已在 R 软件包 FieldSimR 中实现,并在此使用两个由 R 代码支持的工作示例进行演示。第一个示例将该框架嵌入线性混合模型,生成具有低、中和高 GEI 的 MET 数据集,用于比较应用于植物育种的几种流行统计模型。随着 GEI 水平的降低或 MET 中采样环境数量的增加,预测准确率普遍提高。第二个例子是将该框架集成到育种计划模拟中,以比较基因组和表型选择策略随时间的变化。在 TPE 中,基因组选择优于表型选择 50% 至 70%,具体取决于 GEI 水平。这些例子表明,新框架可用于生成现实的 MET 数据集和植物育种方案模型,从而更好地反映现实世界环境的复杂性,使其成为优化各种育种方法的宝贵工具。
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引用次数: 0
Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models. 利用双基因组预测模型预测抗药性、毒力和宿主与病原体之间的相互作用。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-06 DOI: 10.1007/s00122-024-04698-7
Owen Hudson, Marcio F R Resende, Charlie Messina, James Holland, Jeremy Brawner

Key message: Integrating disease screening data and genomic data for host and pathogen populations into prediction models provides breeders and pathologists with a unified framework to develop disease resistance. Developing disease resistance in crops typically consists of exposing breeding populations to a virulent strain of the pathogen that is causing disease. While including a diverse set of pathogens in the experiments would be desirable for developing broad and durable disease resistance, it is logistically complex and uncommon, and limits our capacity to implement dual (host-by-pathogen)-genome prediction models. Data from an alternative disease screening system that challenges a diverse sweet corn population with a diverse set of pathogen isolates are provided to demonstrate the changes in genetic parameter estimates that result from using genomic data to provide connectivity across sparsely tested experimental treatments. An inflation in genetic variance estimates was observed when among isolate relatedness estimates were included in prediction models, which was moderated when host-by-pathogen interaction effects were incorporated into models. The complete model that included genomic similarity matrices for host, pathogen, and interaction effects indicated that the proportion of phenotypic variation in lesion size that is attributable to host, pathogen, and interaction effects was similar. Estimates of the stability of lesion size predictions for host varieties inoculated with different isolates and the stability of isolates used to inoculate different hosts were also similar. In this pathosystem, genetic parameter estimates indicate that host, pathogen, and host-by-pathogen interaction predictions may be used to identify crop varieties that are resistant to specific virulence mechanisms and to guide the deployment of these sources of resistance into pathogen populations where they will be more effective.

关键信息:将宿主和病原体种群的病害筛选数据和基因组数据整合到预测模型中,可为育种者和病理学家提供开发抗病性的统一框架。培养作物的抗病性通常包括让育种群体接触致病病原体的毒株。虽然在实验中加入多种病原体是开发广泛而持久的抗病性的理想选择,但这在逻辑上非常复杂,而且并不常见,限制了我们实施双(宿主-病原体)基因组预测模型的能力。本研究提供了一个替代性病害筛选系统的数据,该系统用一组不同的病原体分离物对一个多样化的甜玉米群体进行挑战,以证明利用基因组数据提供稀疏试验处理间的连通性所导致的遗传参数估计的变化。当预测模型中包含分离株之间的亲缘关系估计值时,遗传变异估计值出现膨胀,而当模型中包含宿主与病原体之间的交互效应时,这种膨胀有所缓和。包含宿主、病原体和交互作用效应基因组相似性矩阵的完整模型表明,病斑大小表型变异中宿主、病原体和交互作用效应所占比例相似。对接种不同分离物的宿主品种的病斑大小预测的稳定性以及用于接种不同宿主的分离物的稳定性的估计也相似。在这一病理系统中,遗传参数估计表明,宿主、病原体和宿主与病原体之间的交互作用预测可用于确定对特定毒力机制具有抗性的作物品种,并指导将这些抗性来源部署到病原体种群中,使其更加有效。
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引用次数: 0
Advances in functional studies of plant MYC transcription factors. 植物 MYC 转录因子功能研究的进展。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-08-05 DOI: 10.1007/s00122-024-04697-8
Zewei Li, Yunshuai Huang, Zhiwei Shen, Meifang Wu, Mujun Huang, Seung-Beom Hong, Liai Xu, Yunxiang Zang

Myelocytomatosis (MYC) transcription factors (TFs) belong to the basic helix-loop-helix (bHLH) family in plants and play a central role in governing a wide range of physiological processes. These processes encompass plant growth, development, adaptation to biotic and abiotic stresses, as well as secondary metabolism. In recent decades, significant strides have been made in comprehending the multifaceted regulatory functions of MYCs. This advancement has been achieved through the cloning of MYCs and the characterization of plants with MYC deficiencies or overexpression, employing comprehensive genome-wide 'omics' and protein-protein interaction technologies. MYCs act as pivotal components in integrating signals from various phytohormones' transcriptional regulators to orchestrate genome-wide transcriptional reprogramming. In this review, we have compiled current research on the role of MYCs as molecular switches that modulate signal transduction pathways mediated by phytohormones and phytochromes. This comprehensive overview allows us to address lingering questions regarding the interplay of signals in response to environmental cues and developmental shift. It also sheds light on the potential implications for enhancing plant resistance to diverse biotic and abiotic stresses through genetic improvements achieved by plant breeding and synthetic biology efforts.

髓细胞瘤(MYC)转录因子(TFs)属于植物中的基本螺旋-环-螺旋(bHLH)家族,在调控一系列生理过程中发挥着核心作用。这些过程包括植物的生长、发育、对生物和非生物胁迫的适应以及次生代谢。近几十年来,人们在理解 MYCs 的多方面调控功能方面取得了长足进步。这一进展是通过克隆 MYCs 以及利用全面的全基因组 "组学 "和蛋白质-蛋白质相互作用技术分析 MYC 缺失或过表达植物的特征实现的。MYCs 是整合各种植物激素转录调控因子信号的关键元件,可协调全基因组转录重编程。在这篇综述中,我们汇编了目前有关 MYCs 作为分子开关调节由植物激素和植物色素介导的信号转导通路的作用的研究。这一全面综述使我们能够解决有关信号在响应环境线索和发育转变时的相互作用的未决问题。它还揭示了通过植物育种和合成生物学努力实现的遗传改良来增强植物对各种生物和非生物胁迫的抵抗力的潜在意义。
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引用次数: 0
Bud shapes dictate tiller-rhizome transition in African perennial rice (Oryza longistaminata). 芽的形状决定了非洲多年生水稻(Oryza longistaminata)的分蘖-根茎过渡。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-30 DOI: 10.1007/s00122-024-04699-6
Kai Wang, Yufei Lu, Suwen Jing, Ru Yang, Xianjie Xu, Yourong Fan, Jiangyi Yang

Key message: Rhizome formation of Oryza longistaminata was dependent on the bud shape. The loci qBS3.1, qBS3.2 and qBS3.3 for controlling rhizome formation were functional redundant under Oryza longistaminata background. The rhizome, a root-like underground stem, is the key organ for grasses to achieve perennial growth. Oryza longistaminata, the only rhizomatous wild Oryza species with the same AA genome as cultivated rice, is an important germplasm for developing perennial rice. Our study found that the rhizome formation of O. longistaminata was dependent on the bud shape: the dome-like axillary bud (dome bud) usually penetrated through the leaf sheaths, developing into rhizome (extravaginal branching), but the flat axillary bud (flat bud) wrapped by the leaf sheaths only developed into tiller (intravaginal branching). The genetic loci (QTL) controlling the bud shape (BS) were mapped by entire population genotyping method (F2 population from crossing O. longistaminata with Balilla (Oryza sativa) and selective genotyping mapping method (BC1F2 population from backcrossing F1 with Balilla). A total of twelve loci were identified, including four major-effect QTL: qBS2, qBS3.1, qBS3.2 and qBS3.3, and the genetic network of these twelve loci was established. The dome bud lost the potential to develop into rhizome with the increase in backcross generations under Balilla background. Considering the rapid loss of rhizome under Balilla background, the near-isogenic lines under O. longistaminata background were used to identify the effect of major-effect loci. According to the BC3F2, BC4F2 and BC5F2 under O. longistaminata background, there was some functional redundancy among qBS3.1, qBS3.2 and qBS3.3. Our results provided a new perspective for analyzing the genetic basis of perenniality and laid the foundation for fine mapping and verification of related genes.

关键信息:Oryza longistaminata根茎的形成取决于芽的形状。控制根状茎形成的位点qBS3.1、qBS3.2和qBS3.3在Oryza longistaminata背景下存在功能冗余。根状茎是一种根状地下茎,是禾本科植物实现多年生生长的关键器官。Oryza longistaminata是唯一与栽培稻具有相同AA基因组的根瘤野生稻种,是开发多年生水稻的重要种质。我们的研究发现,O. longistaminata的根状茎形成与芽的形状有关:圆顶状的腋芽(圆顶芽)通常穿透叶鞘,发育成根状茎(叶外分枝),而被叶鞘包裹的扁平腋芽(扁芽)只发育成分蘖(叶内分枝)。通过全群体基因分型法(O. longistaminata与Balilla(Oryza sativa)杂交的F2群体)和选择性基因分型法(F1与Balilla回交的BC1F2群体)绘制了控制芽形(BS)的遗传位点(QTL)。共鉴定出 12 个位点,包括 4 个主要效应 QTL:qBS2、qBS3.1、qBS3.2 和 qBS3.3,并建立了这 12 个位点的遗传网络。在巴利拉背景下,随着回交代数的增加,圆顶芽失去了发育成根茎的潜力。考虑到在巴利拉背景下根茎的迅速丧失,研究人员利用O. longistaminata背景下的近等基因系来鉴定主要效应位点的影响。结果表明,O.longistaminata背景下的BC3F2、BC4F2和BC5F2中,qBS3.1、qBS3.2和qBS3.3之间存在一定的功能冗余。我们的研究结果为分析多年生植物的遗传基础提供了一个新的视角,并为相关基因的精细图谱绘制和验证奠定了基础。
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引用次数: 0
Association mapping of tan spot and septoria nodorum blotch resistance in cultivated emmer wheat. 栽培小麦黑斑病和败酱病抗性的关联图谱。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-29 DOI: 10.1007/s00122-024-04700-2
Dhondup Lhamo, Qun Sun, Timothy L Friesen, Anil Karmacharya, Xuehui Li, Jason D Fiedler, Justin D Faris, Guangmin Xia, Mingcheng Luo, Yong-Qiang Gu, Zhaohui Liu, Steven S Xu

Key message: A total of 65 SNPs associated with resistance to tan spot and septoria nodorum blotch were identified in a panel of 180 cultivated emmer accessions through association mapping Tan spot and septoria nodorum blotch (SNB) are foliar diseases caused by the respective fungal pathogens Pyrenophora tritici-repentis and Parastagonospora nodorum that affect global wheat production. To find new sources of resistance, we evaluated a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for reactions to four P. tritici-repentis isolates Pti2, 86-124, 331-9 and DW5, two P. nodorum isolate, Sn4 and Sn2000, and four necrotrophic effectors (NEs) produced by the pathogens. About 8-36% of the accessions exhibited resistance to the four P. tritici-repentis isolates, with five accessions demonstrating resistance to all isolates. For SNB, 64% accessions showed resistance to Sn4, 43% to Sn2000 and 36% to both isolates, with Spain (11% accessions) as the most common origin of resistance. To understand the genetic basis of resistance, association mapping was performed using SNP (single nucleotide polymorphism) markers generated by genotype-by-sequencing and the 9 K SNP Infinium array. A total of 46 SNPs were significantly associated with tan spot and 19 SNPs with SNB resistance or susceptibility. Six trait loci on chromosome arms 1BL, 3BL, 4AL (2), 6BL and 7AL conferred resistance to two or more isolates. Known NE sensitivity genes for disease development were undetected except Snn5 for Sn2000, suggesting novel genetic factors are controlling host-pathogen interaction in cultivated emmer. The emmer accessions with the highest levels of resistance to the six pathogen isolates (e.g., CItr 14133-1, PI 94634-1 and PI 377672) could serve as donors for tan spot and SNB resistance in wheat breeding programs.

关键信息:通过关联图谱,在 180 个栽培小麦品种中发现了 65 个与抗赤霉病和节节孢霉斑病有关的 SNPs 赤霉病和节节孢霉斑病(SNB)是由影响全球小麦生产的真菌病原体三尖镰孢属(Pyrenophora tritici-repentis)和节节孢霉属(Parastagonospora nodorum)引起的叶面病害。为了寻找新的抗性来源,我们评估了 180 个栽培小麦(Triticum turgidum ssp. dicoccum)品种对四种 P. tritici-repentis 分离物 Pti2、86-124、331-9 和 DW5、两种 P. nodorum 分离物 Sn4 和 Sn2000 以及病原体产生的四种坏死性效应物(NEs)的反应。约有 8%-36% 的品种对四种 P. tritici-repentis 分离物表现出抗性,其中有五个品种对所有分离物均表现出抗性。在 SNB 方面,64% 的品种对 Sn4 表现出抗性,43% 的品种对 Sn2000 表现出抗性,36% 的品种对两种分离物都表现出抗性,西班牙(11% 的品种)是最常见的抗性来源地。为了解抗性的遗传基础,利用基因型测序和 9 K SNP Infinium 阵列产生的 SNP(单核苷酸多态性)标记进行了关联图谱绘制。共有 46 个 SNP 与褐斑病显著相关,19 个 SNP 与 SNB 抗性或易感性显著相关。染色体臂 1BL、3BL、4AL (2)、6BL 和 7AL 上的六个性状位点赋予两个或更多分离株抗性。除 Sn2000 的 Snn5 外,未检测到已知的 NE 对疾病发生敏感的基因,这表明新的遗传因素正在控制栽培蚕豆中宿主与病原体之间的相互作用。对六种病原菌分离物具有最高抗性水平的红豆品种(如 CItr 14133-1、PI 94634-1 和 PI 377672)可作为小麦育种计划中抗黑斑病和 SNB 的供体。
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引用次数: 0
Breeding and management of major resistance genes to stem canker/blackleg in Brassica crops. 甘蓝作物茎腐病/黑胫病主要抗性基因的培育与管理。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-07-25 DOI: 10.1007/s00122-024-04641-w
Paula Vasquez-Teuber, Thierry Rouxel, Annaliese S Mason, Jessica L Soyer

Blackleg (also known as Phoma or stem canker) is a major, worldwide disease of Brassica crop species, notably B. napus (rapeseed, canola), caused by the ascomycete fungus Leptosphaeria maculans. The outbreak and severity of this disease depend on environmental conditions and management practices, as well as a complex interaction between the pathogen and its hosts. Genetic resistance is a major method to control the disease (and the only control method in some parts of the world, such as continental Europe), but efficient use of genetic resistance is faced with many difficulties: (i) the scarcity of germplasm/genetic resources available, (ii) the different history of use of resistance genes in different parts of the world and the different populations of the fungus the resistance genes are exposed to, (iii) the complexity of the interactions between the plant and the pathogen that expand beyond typical gene-for-gene interactions, (iv) the incredible evolutionary potential of the pathogen and the importance of knowing the molecular processes set up by the fungus to "breakdown' resistances, so that we may design high-throughput diagnostic tools for population surveys, and (v) the different strategies and options to build up the best resistances and to manage them so that they are durable. In this paper, we aim to provide a comprehensive overview of these different points, stressing the differences between the different continents and the current prospects to generate new and durable resistances to blackleg disease.

黑胫病(也称茎腐病或茎腐病)是世界范围内芸薹属作物,特别是油菜(菜籽、油菜)的一种主要病害,由子囊真菌 Leptosphaeria maculans 引起。这种疾病的爆发和严重程度取决于环境条件和管理方法,以及病原体与其寄主之间复杂的相互作用。遗传抗性是控制该病害的主要方法(也是世界某些地区(如欧洲大陆)唯一的控制方法),但有效利用遗传抗性面临许多困难:(i) 可用的种质/遗传资源稀缺,(ii) 世界各地使用抗性基因的历史不同,抗性基因所接触的真菌种群也不同,(iii) 植物与病原体之间的相互作用非常复杂,超出了典型的基因与基因之间的相互作用、(iv) 病原体令人难以置信的进化潜力,以及了解真菌 "分解 "抗性的分子过程的重要性,这样我们才能设计出用于种群调查的高通量诊断工具,以及 (v) 建立最佳抗性并对其进行管理以使其持久的不同策略和方案。在本文中,我们旨在对这些不同点进行全面概述,强调各大洲之间的差异以及当前产生新的持久抗黑胫病能力的前景。
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Theoretical and Applied Genetics
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