Pub Date : 2024-08-11DOI: 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
{"title":"Genetic diversity and genome-wide association study of partial resistance to Sclerotinia stem rot in a Canadian soybean germplasm panel.","authors":"Deus Mugabe, Mohsen Yoosefzadeh-Najafabadi, Istvan Rajcan","doi":"10.1007/s00122-024-04708-8","DOIUrl":"10.1007/s00122-024-04708-8","url":null,"abstract":"<p><strong>Key message: </strong>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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Agrobacterium-mediated transformation of B. juncea reveals that BjuLKP2 functions in plant yellowing.","authors":"Jing Zeng, Liang Zhao, Yuanqing Lu, Tonghong Zuo, Baowen Huang, Diandong Wang, Yawen Zhou, Zhongxin Lei, Yanling Mo, Yihua Liu, Jian Gao","doi":"10.1007/s00122-024-04707-9","DOIUrl":"10.1007/s00122-024-04707-9","url":null,"abstract":"<p><strong>Key message: </strong>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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 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.
{"title":"Identification of stripe rust resistance gene YrBDT in Chinese landrace wheat Baidatou using BSE-seq and BSR-seq.","authors":"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","doi":"10.1007/s00122-024-04704-y","DOIUrl":"10.1007/s00122-024-04704-y","url":null,"abstract":"<p><strong>Key message: </strong>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 F<sub>1</sub>, F<sub>2</sub> plants and F<sub>2:3</sub> 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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 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。
{"title":"Mapping of a novel locus Ra conferring extreme resistance against potato virus A in cultivated potato (Solanum tuberosum L.).","authors":"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","doi":"10.1007/s00122-024-04705-x","DOIUrl":"10.1007/s00122-024-04705-x","url":null,"abstract":"<p><strong>Key message: </strong>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 Ry<sub>sto</sub> (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 BC<sub>1</sub> 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 Ry<sub>sto</sub>-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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 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。
{"title":"A framework for simulating genotype-by-environment interaction using multiplicative models.","authors":"J Bančič, G Gorjanc, D J Tolhurst","doi":"10.1007/s00122-024-04644-7","DOIUrl":"10.1007/s00122-024-04644-7","url":null,"abstract":"<p><strong>Key message: </strong>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 <math><mo>∼</mo></math> 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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11303478/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 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.
{"title":"Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models.","authors":"Owen Hudson, Marcio F R Resende, Charlie Messina, James Holland, Jeremy Brawner","doi":"10.1007/s00122-024-04698-7","DOIUrl":"10.1007/s00122-024-04698-7","url":null,"abstract":"<p><strong>Key message: </strong>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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11303470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Advances in functional studies of plant MYC transcription factors.","authors":"Zewei Li, Yunshuai Huang, Zhiwei Shen, Meifang Wu, Mujun Huang, Seung-Beom Hong, Liai Xu, Yunxiang Zang","doi":"10.1007/s00122-024-04697-8","DOIUrl":"10.1007/s00122-024-04697-8","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-30DOI: 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.
{"title":"Bud shapes dictate tiller-rhizome transition in African perennial rice (Oryza longistaminata).","authors":"Kai Wang, Yufei Lu, Suwen Jing, Ru Yang, Xianjie Xu, Yourong Fan, Jiangyi Yang","doi":"10.1007/s00122-024-04699-6","DOIUrl":"10.1007/s00122-024-04699-6","url":null,"abstract":"<p><strong>Key message: </strong>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 (F<sub>2</sub> population from crossing O. longistaminata with Balilla (Oryza sativa) and selective genotyping mapping method (BC<sub>1</sub>F<sub>2</sub> population from backcrossing F<sub>1</sub> 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 BC<sub>3</sub>F<sub>2</sub>, BC<sub>4</sub>F<sub>2</sub> and BC<sub>5</sub>F<sub>2</sub> 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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-29DOI: 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。
{"title":"Association mapping of tan spot and septoria nodorum blotch resistance in cultivated emmer wheat.","authors":"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","doi":"10.1007/s00122-024-04700-2","DOIUrl":"10.1007/s00122-024-04700-2","url":null,"abstract":"<p><strong>Key message: </strong>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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141789106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-25DOI: 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.
{"title":"Breeding and management of major resistance genes to stem canker/blackleg in Brassica crops.","authors":"Paula Vasquez-Teuber, Thierry Rouxel, Annaliese S Mason, Jessica L Soyer","doi":"10.1007/s00122-024-04641-w","DOIUrl":"10.1007/s00122-024-04641-w","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11272824/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141761050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}