Pub Date : 2024-09-13DOI: 10.1007/s00122-024-04735-5
Lei Wang, Xiaosong Ma, Yi Liu, Guolan Liu, Haibin Wei, Zhi Luo, Hongyan Liu, Ming Yan, Anning Zhang, Xinqiao Yu, Hui Xia, Lijun Luo
Key Message
The hybrid rice variety (Hanyou73) exhibits the maternal-like (HH7A) gene expression in roots and parental-like (HH3) gene expression in leaves to obtain both advantages of drought avoidance and drought tolerance from its two parents.
Background
Rice is one of the most important crops in the world. Rice production consumes lots of water and significantly suffers from the water deficiency and drought stress. The water-saving and drought-resistance rice (WDR) confers good drought resistance and performs well in the water-saving cultivation.
Main findings
A hybrid WDR variety Hanyou73 (HY73) exhibited superior drought resistance compared with its parents Hanhui3 (HH3) and Huhan7A (HH7A). Studies on drought resistance related traits revealed that HY73 performed like HH3 and HH7A on drought tolerance and drought avoidance, respectively. Transcriptomes were analyzed for samples with various phytohormone treatments and abiotic stresses, in which HY73 was closer to HH3 in leaf samples while HH7A in root samples. HY73 and its parents differed largely in DEGs and GO analysis for DEGs suggested the different pathways of drought response in HH3 and HH7A. Parent-like expression analysis revealed that the higher-parent-like expression pattern was prevailing in HY73. In addition, patterns of the parent-like expression significantly transformed between abiotic-stressed/phytohormone-treated and control samples, which might help HY73 to adapt to different environments. WGCNA analysis for those parent-like expression genes revealed some drought resistant genes that should contribute to the superior drought resistance of HY73. Genetic variation on the promotor sequence was confirmed as the reason for the flexible parent-like gene expression in HY73.
Conclusion
Our study uncovered the important roles of complementation of beneficial traits from parents and flexible gene expressions in drought resistance of HY73, which could facilitate the development of new WDR varieties.
{"title":"Flexibility of parental-like or maternal-like gene expression under diverse environments contributes to combined drought avoidance and drought tolerance in a water-saving and drought-resistance rice hybrid","authors":"Lei Wang, Xiaosong Ma, Yi Liu, Guolan Liu, Haibin Wei, Zhi Luo, Hongyan Liu, Ming Yan, Anning Zhang, Xinqiao Yu, Hui Xia, Lijun Luo","doi":"10.1007/s00122-024-04735-5","DOIUrl":"https://doi.org/10.1007/s00122-024-04735-5","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key Message</h3><p>The hybrid rice variety (Hanyou73) exhibits the maternal-like (HH7A) gene expression in roots and parental-like (HH3) gene expression in leaves to obtain both advantages of drought avoidance and drought tolerance from its two parents.</p><h3 data-test=\"abstract-sub-heading\">Background</h3><p>Rice is one of the most important crops in the world. Rice production consumes lots of water and significantly suffers from the water deficiency and drought stress. The water-saving and drought-resistance rice (WDR) confers good drought resistance and performs well in the water-saving cultivation.</p><h3 data-test=\"abstract-sub-heading\">Main findings</h3><p>A hybrid WDR variety Hanyou73 (HY73) exhibited superior drought resistance compared with its parents Hanhui3 (HH3) and Huhan7A (HH7A). Studies on drought resistance related traits revealed that HY73 performed like HH3 and HH7A on drought tolerance and drought avoidance, respectively. Transcriptomes were analyzed for samples with various phytohormone treatments and abiotic stresses, in which HY73 was closer to HH3 in leaf samples while HH7A in root samples. HY73 and its parents differed largely in DEGs and GO analysis for DEGs suggested the different pathways of drought response in HH3 and HH7A. Parent-like expression analysis revealed that the higher-parent-like expression pattern was prevailing in HY73. In addition, patterns of the parent-like expression significantly transformed between abiotic-stressed/phytohormone-treated and control samples, which might help HY73 to adapt to different environments. WGCNA analysis for those parent-like expression genes revealed some drought resistant genes that should contribute to the superior drought resistance of HY73. Genetic variation on the promotor sequence was confirmed as the reason for the flexible parent-like gene expression in HY73.</p><h3 data-test=\"abstract-sub-heading\">Conclusion</h3><p>Our study uncovered the important roles of complementation of beneficial traits from parents and flexible gene expressions in drought resistance of HY73, which could facilitate the development of new WDR varieties.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264439","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 : 2024-09-11DOI: 10.1007/s00122-024-04728-4
Erick O. Mikwa, Benjamin Wittkop, Steffen M. Windpassinger, Sven E. Weber, Dorit Ehrhardt, Rod J. Snowdon
Key message
We identified novel physiological and genetic responses to phosphorus starvation in sorghum diversity lines that augment current knowledge of breeding for climate-smart crops in Europe.
Abstract
Phosphorus (P) deficiency and finite P reserves for fertilizer production pose a threat to future global crop production. Understanding root system architecture (RSA) plasticity is central to breeding for P-efficient crops. Sorghum is regarded as a P-efficient and climate-smart crop with strong adaptability to different climatic regions of the world. Here we investigated early genetic responses of sorghum RSA to P deficiency in order to identified genotypes with interesting root phenotypes and responses under low P. A diverse set of sorghum lines (n = 285) was genotyped using DarTSeq generating 12,472 quality genome wide single-nucleotide polymorphisms. Root phenotyping was conducted in a paper-based hydroponic rhizotron system under controlled greenhouse conditions with low and optimal P nutrition, using 16 RSA traits to describe genetic and phenotypic variability at two time points. Genotypic and phenotypic P-response variations were observed for multiple root traits at 21 and 42 days after germination with high broad sense heritability (0.38–0.76). The classification of traits revealed four distinct sorghum RSA types, with genotypes clustering separately under both low and optimal P conditions, suggesting genetic control of root responses to P availability. Association studies identified quantitative trait loci in chromosomes Sb02, Sb03, Sb04, Sb06 and Sb09 linked with genes potentially involved in P transport and stress responses. The genetic dissection of key factors underlying RSA responses to P deficiency could enable early identification of P-efficient sorghum genotypes. Genotypes with interesting RSA traits for low P environments will be incorporated into current sorghum breeding programs for later growth stages and field-based evaluations.
关键信息 我们发现了高粱多样性品系对磷饥饿的新型生理和遗传反应,这些反应增强了欧洲气候智能型作物育种的现有知识。 摘要 磷(P)缺乏和用于化肥生产的磷储备有限对未来全球作物生产构成威胁。了解根系结构(RSA)的可塑性是培育高效节磷作物的核心。高粱被认为是一种钾高效、气候智能型作物,对世界不同气候地区具有很强的适应性。在此,我们研究了高粱 RSA 对缺钾的早期遗传反应,以确定在低钾条件下具有有趣的根表型和反应的基因型。根系表型分析是在纸质水培根瘤系统中进行的,该系统是在温室受控条件下,在低磷营养和最佳磷营养条件下进行的,利用 16 个 RSA 性状来描述两个时间点的遗传和表型变异性。在发芽后 21 天和 42 天观察到多个根系性状的基因型和表型对 P 的响应变化,广义遗传率较高(0.38-0.76)。性状分类揭示了四种不同的高粱 RSA 类型,基因型在低 P 和最佳 P 条件下分别聚类,表明根系对 P 供应的反应受遗传控制。关联研究发现了染色体 Sb02、Sb03、Sb04、Sb06 和 Sb09 中的数量性状位点,这些位点与可能参与钾转运和胁迫反应的基因有关。通过基因分析 RSA 对缺钾反应的关键因素,可以及早鉴定出高钾效的高粱基因型。针对低磷环境具有有趣的 RSA 性状的基因型将被纳入当前的高粱育种计划,用于后期生长阶段和田间评估。
{"title":"Early exposure to phosphorus starvation induces genetically determined responses in Sorghum bicolor roots","authors":"Erick O. Mikwa, Benjamin Wittkop, Steffen M. Windpassinger, Sven E. Weber, Dorit Ehrhardt, Rod J. Snowdon","doi":"10.1007/s00122-024-04728-4","DOIUrl":"https://doi.org/10.1007/s00122-024-04728-4","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key message</h3><p> We identified novel physiological and genetic responses to phosphorus starvation in sorghum diversity lines that augment current knowledge of breeding for climate-smart crops in Europe.</p><h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Phosphorus (P) deficiency and finite P reserves for fertilizer production pose a threat to future global crop production. Understanding root system architecture (RSA) plasticity is central to breeding for P-efficient crops. Sorghum is regarded as a P-efficient and climate-smart crop with strong adaptability to different climatic regions of the world. Here we investigated early genetic responses of sorghum RSA to P deficiency in order to identified genotypes with interesting root phenotypes and responses under low P. A diverse set of sorghum lines (<i>n</i> = 285) was genotyped using DarTSeq generating 12,472 quality genome wide single-nucleotide polymorphisms. Root phenotyping was conducted in a paper-based hydroponic rhizotron system under controlled greenhouse conditions with low and optimal P nutrition, using 16 RSA traits to describe genetic and phenotypic variability at two time points. Genotypic and phenotypic P-response variations were observed for multiple root traits at 21 and 42 days after germination with high broad sense heritability (0.38–0.76). The classification of traits revealed four distinct sorghum RSA types, with genotypes clustering separately under both low and optimal P conditions, suggesting genetic control of root responses to P availability. Association studies identified quantitative trait loci in chromosomes Sb02, Sb03, Sb04, Sb06 and Sb09 linked with genes potentially involved in P transport and stress responses. The genetic dissection of key factors underlying RSA responses to P deficiency could enable early identification of P-efficient sorghum genotypes. Genotypes with interesting RSA traits for low P environments will be incorporated into current sorghum breeding programs for later growth stages and field-based evaluations.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142188624","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 : 2024-09-10DOI: 10.1007/s00122-024-04732-8
Jeonghwa Kim, Andrew Scaboo, Katy Martin Rainey, Felix B. Fritschi, Kristin Bilyeu
Key Message
Soybean seed oil and meal composition traits can be combined without interference to provide additional value to the crop.
Abstract
Soybean [Glycine max (L.) Merr.] is an important crop worldwide; its overall value comes from seed oil and high protein meal. The development of soybean varieties with allele combinations for improved oil and meal quality is expected to provide a compositional value bundle for soybean. The high oleic and low linolenic acid seed oil trait (HOLL; > 70% oleic and < 3% linolenic acid) is targeted to optimize the health and functional properties of soybean oil. For soybean meal, metabolizable energy is improved by altering the carbohydrate profile with increased sucrose and decreased anti-nutritional factors, raffinose family of oligosaccharides (RFOs). Previous research identified four variant alleles of fatty acid desaturase (FAD) genes and two raffinose synthase (RS) genes necessary for the HOLL trait in soybean oil and Low or Ultra-Low (UL) RFO traits in soybean meal, respectively. We employed a molecular marker-assisted breeding approach to combine six alleles conferring the desired soybean oil and meal value traits. Eight environment field trials were conducted with twenty-four soybean lines to evaluate phenotypic interactions among the variant alleles of FAD and RS genes. The results indicated that the four FAD gene alleles conditioned the HOLL fatty acid profile of the seed oil regardless of the allele status of the RS genes. Independent of the allele combination of the FAD genes, soybean with two variant alleles of the RS genes had the desired RFO trait in the seeds. The results confirm the feasibility of soybean variety development with this unique combination of oil and meal traits.
{"title":"Redesigning soybean with improved oil and meal traits","authors":"Jeonghwa Kim, Andrew Scaboo, Katy Martin Rainey, Felix B. Fritschi, Kristin Bilyeu","doi":"10.1007/s00122-024-04732-8","DOIUrl":"https://doi.org/10.1007/s00122-024-04732-8","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key Message</h3><p>Soybean seed oil and meal composition traits can be combined without interference to provide additional value to the crop.</p><h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Soybean [<i>Glycine max</i> (L.) Merr.] is an important crop worldwide; its overall value comes from seed oil and high protein meal. The development of soybean varieties with allele combinations for improved oil and meal quality is expected to provide a compositional value bundle for soybean. The high oleic and low linolenic acid seed oil trait (HOLL; > 70% oleic and < 3% linolenic acid) is targeted to optimize the health and functional properties of soybean oil. For soybean meal, metabolizable energy is improved by altering the carbohydrate profile with increased sucrose and decreased anti-nutritional factors, raffinose family of oligosaccharides (RFOs). Previous research identified four variant alleles of fatty acid desaturase (<i>FAD</i>) genes and two raffinose synthase (<i>RS</i>) genes necessary for the HOLL trait in soybean oil and Low or Ultra-Low (UL) RFO traits in soybean meal, respectively. We employed a molecular marker-assisted breeding approach to combine six alleles conferring the desired soybean oil and meal value traits. Eight environment field trials were conducted with twenty-four soybean lines to evaluate phenotypic interactions among the variant alleles of <i>FAD</i> and <i>RS</i> genes. The results indicated that the four <i>FAD</i> gene alleles conditioned the HOLL fatty acid profile of the seed oil regardless of the allele status of the <i>RS</i> genes. Independent of the allele combination of the <i>FAD</i> genes, soybean with two variant alleles of the <i>RS</i> genes had the desired RFO trait in the seeds. The results confirm the feasibility of soybean variety development with this unique combination of oil and meal traits.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142188625","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 : 2024-09-10DOI: 10.1007/s00122-024-04729-3
Xiaoyan Cheng, Guohua Zhou, Wei Chen, Lin Tan, Qishi Long, Fusheng Cui, Lei Tan, Guoxing Zou, Yong Tan
In the past century, there have been great achievements in identifying resistance (R) genes and quantitative trait loci (QTLs) as well as revealing the corresponding molecular mechanisms for resistance in rice to major diseases and insect pests. The introgression of R genes to develop resistant rice cultivars has become the most effective and eco-friendly method to control pathogens/insects at present. However, little attention has been paid to durable and broad-spectrum resistance, which determines the real applicability of R genes. Here, we summarize all the R genes and QTLs conferring durable and broad-spectrum resistance in rice to fungal blast, bacterial leaf blight (BLB), and the brown planthopper (BPH) in molecular breeding. We discuss the molecular mechanisms and feasible methods of improving durable and broad-spectrum resistance to blast, BLB, and BPH. We will particularly focus on pyramiding multiple R genes or QTLs as the most useful method to improve durability and broaden the disease/insect spectrum in practical breeding regardless of its uncertainty. We believe that this review provides useful information for scientists and breeders in rice breeding for multiple stress resistance in the future.
上个世纪,在鉴定水稻主要病虫害的抗性(R)基因和数量性状位点(QTLs)以及揭示相应的分子机制方面取得了巨大成就。引入 R 基因培育抗性水稻栽培品种已成为目前控制病原体/虫害最有效、最环保的方法。然而,人们很少关注持久和广谱的抗性,这决定了 R 基因的真正适用性。在此,我们总结了分子育种中赋予水稻对真菌稻瘟病、细菌性叶枯病(BLB)和褐斑病(BPH)持久和广谱抗性的所有 R 基因和 QTL。我们将讨论提高对稻瘟病、细菌性叶枯病和褐飞虱的持久和广谱抗性的分子机制和可行方法。我们将特别关注将多个 R 基因或 QTLs 排列成金字塔,作为在实际育种中提高耐久性和扩大病/虫谱的最有用的方法,而不考虑其不确定性。我们相信,本综述将为科学家和育种家今后进行水稻抗多种胁迫育种提供有用的信息。
{"title":"Current status of molecular rice breeding for durable and broad-spectrum resistance to major diseases and insect pests","authors":"Xiaoyan Cheng, Guohua Zhou, Wei Chen, Lin Tan, Qishi Long, Fusheng Cui, Lei Tan, Guoxing Zou, Yong Tan","doi":"10.1007/s00122-024-04729-3","DOIUrl":"https://doi.org/10.1007/s00122-024-04729-3","url":null,"abstract":"<p>In the past century, there have been great achievements in identifying resistance (<i>R</i>) genes and quantitative trait loci (QTLs) as well as revealing the corresponding molecular mechanisms for resistance in rice to major diseases and insect pests. The introgression of <i>R</i> genes to develop resistant rice cultivars has become the most effective and eco-friendly method to control pathogens/insects at present. However, little attention has been paid to durable and broad-spectrum resistance, which determines the real applicability of <i>R</i> genes. Here, we summarize all the <i>R</i> genes and QTLs conferring durable and broad-spectrum resistance in rice to fungal blast, bacterial leaf blight (BLB), and the brown planthopper (BPH) in molecular breeding. We discuss the molecular mechanisms and feasible methods of improving durable and broad-spectrum resistance to blast, BLB, and BPH. We will particularly focus on pyramiding multiple <i>R</i> genes or QTLs as the most useful method to improve durability and broaden the disease/insect spectrum in practical breeding regardless of its uncertainty. We believe that this review provides useful information for scientists and breeders in rice breeding for multiple stress resistance in the future.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142188626","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: GhSOT (GH_D05G3950) plays a negative role in regulating plant height development by modulating the GA signaling. Plant height is an important indicator affecting mechanical harvesting for cotton. Therefore, understanding the genes associated with the plant height is crucial for cotton breeding and production. In this study, we used bulk segregant analysis sequencing to identify a new quantitative trait locu (QTL) called qPH5.1, which is linked to plant height. Local QTL mapping using seven kompetitive allele-specific PCR (KASP) markers and linkage analysis successfully narrowed down qPH5.1 to ~ 0.34 Mb region harbored five candidate genes. Subsequently, RNA sequencing (RNA-seq) analysis and examination of expression patterns revealed that GhSOT exhibited the highest likelihood of being the candidate gene responsible for the plant height at this locus. Seven SNP site variations were identified in the GhSOT promoter between the two parents, and Luciferase experiments confirmed that the promoter of GhSOT from cz3 enhances downstream gene expression more effectively. Additionally, suppression of GhSOT in cz3 resulted in the restoration of plant height, further emphasizing the functional significance of this gene. Application of exogenous gibberellin acid (GA) significantly restored plant height in cz3, as demonstrated by RNA-seq analysis and exogenous hormone treatment, which revealed alterations in genes associated with GA signaling pathways. These results reveal GhSOT is a key gene controlling plant height, which may affect plant height by regulating GA signaling.
{"title":"Fine-mapping of a major QTL controlling plant height by BSA-seq and transcriptome sequencing in cotton.","authors":"Chao Li, Longyu Huang, Yiwen Huang, Meng Kuang, Yuzhen Wu, Zhiying Ma, Xiaoqiong Fu","doi":"10.1007/s00122-024-04714-w","DOIUrl":"10.1007/s00122-024-04714-w","url":null,"abstract":"<p><strong>Key message: </strong>GhSOT (GH_D05G3950) plays a negative role in regulating plant height development by modulating the GA signaling. Plant height is an important indicator affecting mechanical harvesting for cotton. Therefore, understanding the genes associated with the plant height is crucial for cotton breeding and production. In this study, we used bulk segregant analysis sequencing to identify a new quantitative trait locu (QTL) called qPH5.1, which is linked to plant height. Local QTL mapping using seven kompetitive allele-specific PCR (KASP) markers and linkage analysis successfully narrowed down qPH5.1 to ~ 0.34 Mb region harbored five candidate genes. Subsequently, RNA sequencing (RNA-seq) analysis and examination of expression patterns revealed that GhSOT exhibited the highest likelihood of being the candidate gene responsible for the plant height at this locus. Seven SNP site variations were identified in the GhSOT promoter between the two parents, and Luciferase experiments confirmed that the promoter of GhSOT from cz3 enhances downstream gene expression more effectively. Additionally, suppression of GhSOT in cz3 resulted in the restoration of plant height, further emphasizing the functional significance of this gene. Application of exogenous gibberellin acid (GA) significantly restored plant height in cz3, as demonstrated by RNA-seq analysis and exogenous hormone treatment, which revealed alterations in genes associated with GA signaling pathways. These results reveal GhSOT is a key gene controlling plant height, which may affect plant height by regulating GA signaling.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154981","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 critical gene for leaf prickle development (LPD) in eggplant was mapped on chromosome E06 and was confirmed to be SmARF10B through RNA interference using a new genetic transformation technique called SACI developed in this study Prickles on eggplant pose challenges for agriculture and are undesirable in cultivated varieties. This study aimed to uncover the genetic mechanisms behind prickle formation in eggplant. Using the F2 and F2:3 populations derived from a cross between the prickly wild eggplant, YQ, and the prickle-free cultivated variety, YZQ, we identified a key genetic locus (LPD, leaf prickle development) on chromosome E06 associated with leaf prickle development through BSA-seq and QTL mapping. An auxin response factor gene, SmARF10B, was predicted as the candidate gene as it exhibited high expression in YQ's mature leaves, while being significantly low in YZQ. Downregulating SmARF10B in YQ through RNAi using a simple and efficient Agrobacterium-mediated genetic transformation method named Seedling Apical Cut Infection (SACI) developed in this study substantially reduced the size and density of leaf prickles, confirming the role of this gene in prickle development. Besides, an effective SNP was identified in SmARF10B, resulting in an amino acid change between YQ and YZQ. However, this SNP did not consistently correlate with prickle formation in eight other eggplant materials examined. This study sheds light on the pivotal role of SmARF10B in eggplant prickle development and introduces a new genetic transformation method for eggplant, paving the way for future research in this field.
{"title":"Map-based cloning of LPD, a major gene positively regulates leaf prickle development in eggplant.","authors":"Changjiao Ke, Wenxiang Guan, Jialong Jiang, Likun Huang, Hui Li, Wenjing Li, Yanyu Lin, Lihui Lin, Xiaofang Xie, Weiren Wu, Wenxia Gao, Yan Zheng","doi":"10.1007/s00122-024-04726-6","DOIUrl":"10.1007/s00122-024-04726-6","url":null,"abstract":"<p><strong>Key message: </strong>A critical gene for leaf prickle development (LPD) in eggplant was mapped on chromosome E06 and was confirmed to be SmARF10B through RNA interference using a new genetic transformation technique called SACI developed in this study Prickles on eggplant pose challenges for agriculture and are undesirable in cultivated varieties. This study aimed to uncover the genetic mechanisms behind prickle formation in eggplant. Using the F<sub>2</sub> and F<sub>2:3</sub> populations derived from a cross between the prickly wild eggplant, YQ, and the prickle-free cultivated variety, YZQ, we identified a key genetic locus (LPD, leaf prickle development) on chromosome E06 associated with leaf prickle development through BSA-seq and QTL mapping. An auxin response factor gene, SmARF10B, was predicted as the candidate gene as it exhibited high expression in YQ's mature leaves, while being significantly low in YZQ. Downregulating SmARF10B in YQ through RNAi using a simple and efficient Agrobacterium-mediated genetic transformation method named Seedling Apical Cut Infection (SACI) developed in this study substantially reduced the size and density of leaf prickles, confirming the role of this gene in prickle development. Besides, an effective SNP was identified in SmARF10B, resulting in an amino acid change between YQ and YZQ. However, this SNP did not consistently correlate with prickle formation in eight other eggplant materials examined. This study sheds light on the pivotal role of SmARF10B in eggplant prickle development and introduces a new genetic transformation method for eggplant, paving the way for future research in this field.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154982","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 : 2024-09-05DOI: 10.1007/s00122-024-04731-9
Thomas Miedaner, Wera Eckhoff, Kerstin Flath, Anne-Kristin Schmitt, Philipp Schulz, Johannes Schacht, Philipp Boeven, Wessam Akel, Hubert Kempf, Paul Gruner
Key message: Stem rust resistance was mainly based on a few, already known resistance genes; for yellow rust resistance there was a combination of designated genes and minor QTLs. Yellow rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) and stem rust (SR) caused by Puccinia graminis f. sp. tritici (Pgt) are among the most damaging wheat diseases. Although, yellow rust has occurred regularly in Europe since the advent of the Warrior race in 2011, damaging stem rust epidemics are still unusual. We analyzed the resistance of seven segregating populations at the adult growth stage with the parents being selected for YR and SR resistances across three to six environments (location-year combinations) following inoculation with defined Pst and Pgt races. In total, 600 progenies were phenotyped and 563 were genotyped with a 25k SNP array. For SR resistance, three major resistance genes (Sr24, Sr31, Sr38/Yr17) were detected in different combinations. Additional QTLs provided much smaller effects except for a gene on chromosome 4B that explained much of the genetic variance. For YR resistance, ten loci with highly varying percentages of explained genetic variance (pG, 6-99%) were mapped. Our results imply that introgression of new SR resistances will be necessary for breeding future rust resistant cultivars, whereas YR resistance can be achieved by genomic selection of many of the detected QTLs.
关键信息:茎锈病的抗性主要基于几个已知的抗性基因;黄锈病的抗性则是指定基因和次要 QTLs 的组合。由条锈病菌(Puccinia striiformis f. sp. tritici,Pst)引起的黄锈病(YR)和由禾谷镰孢菌(Puccinia graminis f. sp. tritici,Pgt)引起的茎锈病(SR)是危害最大的小麦病害之一。虽然自 2011 年 Warrior 种族出现以来,黄锈病在欧洲经常发生,但破坏性的茎锈病流行仍不常见。我们分析了七个分离群体在成株生长阶段的抗性,其亲本在接种确定的 Pst 和 Pgt 株系后,在三至六个环境(地点-年份组合)中进行了 YR 和 SR 抗性筛选。总共对 600 个后代进行了表型分析,并用 25k SNP 阵列对 563 个后代进行了基因分型。在 SR 抗性方面,以不同组合检测到三个主要抗性基因(Sr24、Sr31、Sr38/Yr17)。除了 4B 染色体上的一个基因能解释大部分遗传变异外,其他 QTL 的影响要小得多。在抗 YR 方面,绘制了 10 个基因座,其解释的遗传变异百分比(pG,6-99%)差异很大。我们的研究结果表明,要培育未来的抗锈病栽培品种,必须引入新的SR抗性,而YR抗性则可以通过对许多检测到的QTL进行基因组选择来实现。
{"title":"Mapping rust resistance in European winter wheat: many QTLs for yellow rust resistance, but only a few well characterized genes for stem rust resistance.","authors":"Thomas Miedaner, Wera Eckhoff, Kerstin Flath, Anne-Kristin Schmitt, Philipp Schulz, Johannes Schacht, Philipp Boeven, Wessam Akel, Hubert Kempf, Paul Gruner","doi":"10.1007/s00122-024-04731-9","DOIUrl":"10.1007/s00122-024-04731-9","url":null,"abstract":"<p><strong>Key message: </strong>Stem rust resistance was mainly based on a few, already known resistance genes; for yellow rust resistance there was a combination of designated genes and minor QTLs. Yellow rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) and stem rust (SR) caused by Puccinia graminis f. sp. tritici (Pgt) are among the most damaging wheat diseases. Although, yellow rust has occurred regularly in Europe since the advent of the Warrior race in 2011, damaging stem rust epidemics are still unusual. We analyzed the resistance of seven segregating populations at the adult growth stage with the parents being selected for YR and SR resistances across three to six environments (location-year combinations) following inoculation with defined Pst and Pgt races. In total, 600 progenies were phenotyped and 563 were genotyped with a 25k SNP array. For SR resistance, three major resistance genes (Sr24, Sr31, Sr38/Yr17) were detected in different combinations. Additional QTLs provided much smaller effects except for a gene on chromosome 4B that explained much of the genetic variance. For YR resistance, ten loci with highly varying percentages of explained genetic variance (pG, 6-99%) were mapped. Our results imply that introgression of new SR resistances will be necessary for breeding future rust resistant cultivars, whereas YR resistance can be achieved by genomic selection of many of the detected QTLs.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11377555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133830","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 : 2024-09-03DOI: 10.1007/s00122-024-04717-7
S Anjan Gowda, Hui Fang, Priyanka Tyagi, Fred Bourland, Jane Dever, Benjamin Todd Campbell, Jinfa Zhang, Abdelraheem Abdelraheem, Shilpa Sood, Don C Jones, Vasu Kuraparthy
Key message: A GWAS in an elite diversity panel, evaluated across 10 environments, identified genomic regions regulating six fiber quality traits, facilitating genomics-assisted breeding and gene discovery in upland cotton. In this study, an elite diversity panel of 348 upland cotton accessions was evaluated in 10 environments across the US Cotton Belt and genotyped with the cottonSNP63K array, for a genome-wide association study of six fiber quality traits. All fiber quality traits, upper half mean length (UHML: mm), fiber strength (FS: g tex-1), fiber uniformity (FU: %), fiber elongation (FE: %), micronaire (MIC) and short fiber content (SFC: %), showed high broad-sense heritability (> 60%). All traits except FE showed high genomic heritability. UHML, FS and FU were all positively correlated with each other and negatively correlated with FE, MIC and SFC. GWAS of these six traits identified 380 significant marker-trait associations (MTAs) including 143 MTAs on 30 genomic regions. These 30 genomic regions included MTAs identified in at least three environments, and 23 of them were novel associations. Phenotypic variation explained for the MTAs in these 30 genomic regions ranged from 6.68 to 11.42%. Most of the fiber quality-associated genomic regions were mapped in the D-subgenome. Further, this study confirmed the pleiotropic region on chromosome D11 (UHML, FS and FU) and identified novel co-localized regions on D04 (FU, SFC), D05 (UHML, FU, and D06 UHML, FU). Marker haplotype analysis identified superior combinations of fiber quality-associated genomic regions with high trait values (UHML = 32.34 mm; FS = 32.73 g tex-1; FE = 6.75%). Genomic analyses of traits, haplotype combinations and candidate gene information described in the current study could help leverage genetic diversity for targeted genetic improvement and gene discovery for fiber quality traits in cotton.
{"title":"Genome-wide association study of fiber quality traits in US upland cotton (Gossypium hirsutum L.).","authors":"S Anjan Gowda, Hui Fang, Priyanka Tyagi, Fred Bourland, Jane Dever, Benjamin Todd Campbell, Jinfa Zhang, Abdelraheem Abdelraheem, Shilpa Sood, Don C Jones, Vasu Kuraparthy","doi":"10.1007/s00122-024-04717-7","DOIUrl":"10.1007/s00122-024-04717-7","url":null,"abstract":"<p><strong>Key message: </strong>A GWAS in an elite diversity panel, evaluated across 10 environments, identified genomic regions regulating six fiber quality traits, facilitating genomics-assisted breeding and gene discovery in upland cotton. In this study, an elite diversity panel of 348 upland cotton accessions was evaluated in 10 environments across the US Cotton Belt and genotyped with the cottonSNP63K array, for a genome-wide association study of six fiber quality traits. All fiber quality traits, upper half mean length (UHML: mm), fiber strength (FS: g tex<sup>-1</sup>), fiber uniformity (FU: %), fiber elongation (FE: %), micronaire (MIC) and short fiber content (SFC: %), showed high broad-sense heritability (> 60%). All traits except FE showed high genomic heritability. UHML, FS and FU were all positively correlated with each other and negatively correlated with FE, MIC and SFC. GWAS of these six traits identified 380 significant marker-trait associations (MTAs) including 143 MTAs on 30 genomic regions. These 30 genomic regions included MTAs identified in at least three environments, and 23 of them were novel associations. Phenotypic variation explained for the MTAs in these 30 genomic regions ranged from 6.68 to 11.42%. Most of the fiber quality-associated genomic regions were mapped in the D-subgenome. Further, this study confirmed the pleiotropic region on chromosome D11 (UHML, FS and FU) and identified novel co-localized regions on D04 (FU, SFC), D05 (UHML, FU, and D06 UHML, FU). Marker haplotype analysis identified superior combinations of fiber quality-associated genomic regions with high trait values (UHML = 32.34 mm; FS = 32.73 g tex<sup>-1</sup>; FE = 6.75%). Genomic analyses of traits, haplotype combinations and candidate gene information described in the current study could help leverage genetic diversity for targeted genetic improvement and gene discovery for fiber quality traits in cotton.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142120669","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 : 2024-09-02DOI: 10.1007/s00122-024-04709-7
Martina Bruschi, Matteo Bozzoli, Claudio Ratti, Giuseppe Sciara, Ellen Goudemand, Pierre Devaux, Danara Ormanbekova, Cristian Forestan, Simona Corneti, Sandra Stefanelli, Sara Castelletti, Elena Fusari, Jad B Novi, Elisabetta Frascaroli, Silvio Salvi, Dragan Perovic, Agata Gadaleta, Concepcion Rubies-Autonell, Maria Corinna Sanguineti, Roberto Tuberosa, Marco Maccaferri
Soil-borne cereal mosaic virus (SBCMV), the causative agent of wheat mosaic, is a Furovirus challenging wheat production all over Europe. Differently from bread wheat, durum wheat shows greater susceptibility and stronger yield penalties, so identification and genetic characterization of resistance sources are major targets for durum genetics and breeding. The Sbm1 locus providing high level of resistance to SBCMV was mapped in bread wheat to the 5DL chromosome arm (Bass in Genome 49:1140-1148, 2006). This excluded the direct use of Sbm1 for durum wheat improvement. Only one major QTL has been mapped in durum wheat, namely QSbm.ubo-2B, on the 2BS chromosome region coincident with Sbm2, already known in bread wheat as reported (Bayles in HGCA Project Report, 2007). Therefore, QSbm.ubo-2B = Sbm2 is considered a pillar for growing durum in SBCMV-affected areas. Herein, we report the fine mapping of Sbm2 based on bi-parental mapping and GWAS, using the Infinium 90 K SNP array and high-throughput KASP®. Fine mapping pointed out a critical haploblock of 3.2 Mb defined by concatenated SNPs successfully converted to high-throughput KASP® markers coded as KUBO. The combination of KUBO-27, wPt-2106-ASO/HRM, KUBO-29, and KUBO-1 allows unequivocal tracing of the Sbm2-resistant haplotype. The interval harbors 52 high- and 41 low-confidence genes, encoding 17 cytochrome p450, three receptor kinases, two defensins, and three NBS-LRR genes. These results pave the way for Sbm2 positional cloning. Importantly, the development of Sbm2 haplotype tagging KASP® provides a valuable case study for improving efficacy of the European variety testing system and, ultimately, the decision-making process related to varietal characterization and choice.
{"title":"Dissecting the genetic basis of resistance to Soil-borne cereal mosaic virus (SBCMV) in durum wheat by bi-parental mapping and GWAS.","authors":"Martina Bruschi, Matteo Bozzoli, Claudio Ratti, Giuseppe Sciara, Ellen Goudemand, Pierre Devaux, Danara Ormanbekova, Cristian Forestan, Simona Corneti, Sandra Stefanelli, Sara Castelletti, Elena Fusari, Jad B Novi, Elisabetta Frascaroli, Silvio Salvi, Dragan Perovic, Agata Gadaleta, Concepcion Rubies-Autonell, Maria Corinna Sanguineti, Roberto Tuberosa, Marco Maccaferri","doi":"10.1007/s00122-024-04709-7","DOIUrl":"10.1007/s00122-024-04709-7","url":null,"abstract":"<p><p>Soil-borne cereal mosaic virus (SBCMV), the causative agent of wheat mosaic, is a Furovirus challenging wheat production all over Europe. Differently from bread wheat, durum wheat shows greater susceptibility and stronger yield penalties, so identification and genetic characterization of resistance sources are major targets for durum genetics and breeding. The Sbm1 locus providing high level of resistance to SBCMV was mapped in bread wheat to the 5DL chromosome arm (Bass in Genome 49:1140-1148, 2006). This excluded the direct use of Sbm1 for durum wheat improvement. Only one major QTL has been mapped in durum wheat, namely QSbm.ubo-2B, on the 2BS chromosome region coincident with Sbm2, already known in bread wheat as reported (Bayles in HGCA Project Report, 2007). Therefore, QSbm.ubo-2B = Sbm2 is considered a pillar for growing durum in SBCMV-affected areas. Herein, we report the fine mapping of Sbm2 based on bi-parental mapping and GWAS, using the Infinium 90 K SNP array and high-throughput KASP®. Fine mapping pointed out a critical haploblock of 3.2 Mb defined by concatenated SNPs successfully converted to high-throughput KASP® markers coded as KUBO. The combination of KUBO-27, wPt-2106-ASO/HRM, KUBO-29, and KUBO-1 allows unequivocal tracing of the Sbm2-resistant haplotype. The interval harbors 52 high- and 41 low-confidence genes, encoding 17 cytochrome p450, three receptor kinases, two defensins, and three NBS-LRR genes. These results pave the way for Sbm2 positional cloning. Importantly, the development of Sbm2 haplotype tagging KASP® provides a valuable case study for improving efficacy of the European variety testing system and, ultimately, the decision-making process related to varietal characterization and choice.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369050/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142112311","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 : 2024-08-31DOI: 10.1007/s00122-024-04725-7
Ryo Matsushima, Hiroshi Hisano, June-Sik Kim, Rose McNelly, Naoko F Oitome, David Seung, Naoko Fujita, Kazuhiro Sato
Key message: The hvbe2a mutations restore the starch-deficient phenotype caused by the hvisa1 and hvflo6 mutations in barley endosperm. The genetic interactions among starch biosynthesis genes can be exploited to alter starch properties, but they remain poorly understood due to the various combinations of mutations to be tested. Here, we isolated two novel barley mutants defective in starch BRANCHING ENZYME 2a (hvbe2a-1 and hvbe2a-2) based on the starch granule (SG) morphology. Both hvbe2a mutants showed elongated SGs in the endosperm and increased resistant starch content. hvbe2a-1 had a base change in HvBE2a gene, substituting the amino acid essential for its enzyme activity, while hvbe2a-2 is completely missing HvBE2a due to a chromosomal deletion. Further genetic crosses with barley isoamylase1 mutants (hvisa1) revealed that both hvbe2a mutations could suppress defects in endosperm caused by hvisa1, such as reduction in starch, increase in phytoglycogen, and changes in the glucan chain length distribution. Remarkably, hvbe2a mutations also transformed the endosperm SG morphology from the compound SG caused by hvisa1 to bimodal simple SGs, resembling that of wild-type barley. The suppressive impact was in competition with floury endosperm 6 mutation (hvflo6), which could enhance the phenotype of hvisa1 in the endosperm. In contrast, the compound SG formation induced by the hvflo6 hvisa1 mutation in pollen was not suppressed by hvbe2a mutations. Our findings provide new insights into genetic interactions in the starch biosynthetic pathway, demonstrating how specific genetic alterations can influence starch properties and SG morphology, with potential applications in cereal breeding for desired starch properties.
{"title":"Mutations in starch BRANCHING ENZYME 2a suppress the traits caused by the loss of ISOAMYLASE1 in barley.","authors":"Ryo Matsushima, Hiroshi Hisano, June-Sik Kim, Rose McNelly, Naoko F Oitome, David Seung, Naoko Fujita, Kazuhiro Sato","doi":"10.1007/s00122-024-04725-7","DOIUrl":"10.1007/s00122-024-04725-7","url":null,"abstract":"<p><strong>Key message: </strong>The hvbe2a mutations restore the starch-deficient phenotype caused by the hvisa1 and hvflo6 mutations in barley endosperm. The genetic interactions among starch biosynthesis genes can be exploited to alter starch properties, but they remain poorly understood due to the various combinations of mutations to be tested. Here, we isolated two novel barley mutants defective in starch BRANCHING ENZYME 2a (hvbe2a-1 and hvbe2a-2) based on the starch granule (SG) morphology. Both hvbe2a mutants showed elongated SGs in the endosperm and increased resistant starch content. hvbe2a-1 had a base change in HvBE2a gene, substituting the amino acid essential for its enzyme activity, while hvbe2a-2 is completely missing HvBE2a due to a chromosomal deletion. Further genetic crosses with barley isoamylase1 mutants (hvisa1) revealed that both hvbe2a mutations could suppress defects in endosperm caused by hvisa1, such as reduction in starch, increase in phytoglycogen, and changes in the glucan chain length distribution. Remarkably, hvbe2a mutations also transformed the endosperm SG morphology from the compound SG caused by hvisa1 to bimodal simple SGs, resembling that of wild-type barley. The suppressive impact was in competition with floury endosperm 6 mutation (hvflo6), which could enhance the phenotype of hvisa1 in the endosperm. In contrast, the compound SG formation induced by the hvflo6 hvisa1 mutation in pollen was not suppressed by hvbe2a mutations. Our findings provide new insights into genetic interactions in the starch biosynthetic pathway, demonstrating how specific genetic alterations can influence starch properties and SG morphology, with potential applications in cereal breeding for desired starch properties.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11365852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142112313","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}