首页 > 最新文献

Theoretical and Applied Genetics最新文献

英文 中文
SlJMJ14, identified via QTL‑seq and fine mapping, controls flowering time in tomatoes. 通过 QTL-seq 和精细作图确定的 SlJMJ14 控制着番茄的开花时间。
IF 4.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-20 DOI: 10.1007/s00122-024-04737-3
Tairu Wu, Baohang Su, He Zhang, Dalong Li, Hanqiao Zhang, Guanglong Xiao, Ao Sun, Tingting Zhao, Xiangyang Xu

Key message: A major QTL, qLF2.1, for flowering time in tomatoes, was fine mapped to chromosome 2 within a 51.37-kb interval, and the SlJMJ14 gene was verified as the causal gene by knockout. Tomato flowering time is an important agronomic trait that affects yield, fruit quality, and environmental adaptation. In this study, the high-generation inbred line 19108 with a late-flowering phenotype was selected for the mapping of the gene that causes late flowering. In the F2 population derived from 19108 (late flowering) × MM (early flowering), we identified a major late-flowering time quantitative trait locus (QTL) using QTL-seq, designated qLF2.1. This QTL was fine mapped to a 51.37-kb genomic interval using recombinant analysis. Through functional analysis of homologous genes, Solyc02g082400 (SlJMJ14), encoding a histone demethylase, was determined to be the most promising candidate gene. Knocking out SlJMJ14 in MM resulted in a flowering time approximately 5-6 days later than that in the wild-type plants. These results suggest that mutational SlJMJ14 is the major QTL for the late-flowering phenotype of the 19108 parental line.

关键信息:番茄花期的一个主要QTL qLF2.1被精细地映射到2号染色体上的51.37kb间隔内,通过基因敲除验证了SlJMJ14基因是致病基因。番茄花期是影响产量、果实品质和环境适应性的重要农艺性状。本研究选择了具有晚花表型的高代近交系 19108 来绘制导致晚花的基因图谱。在 19108(晚花)×MM(早花)的 F2 群体中,我们利用 QTL-seq 鉴定出了一个主要的晚花时间数量性状位点(QTL),命名为 qLF2.1。通过重组分析,该 QTL 被精细映射到一个 51.37-kb 的基因组区间。通过对同源基因的功能分析,编码组蛋白去甲基化酶的Solyc02g082400(SlJMJ14)被确定为最有希望的候选基因。在 MM 中敲除 SlJMJ14 会导致开花时间比野生型植株晚约 5-6 天。这些结果表明,突变的 SlJMJ14 是 19108 亲本品系晚开花表型的主要 QTL。
{"title":"SlJMJ14, identified via QTL‑seq and fine mapping, controls flowering time in tomatoes.","authors":"Tairu Wu, Baohang Su, He Zhang, Dalong Li, Hanqiao Zhang, Guanglong Xiao, Ao Sun, Tingting Zhao, Xiangyang Xu","doi":"10.1007/s00122-024-04737-3","DOIUrl":"10.1007/s00122-024-04737-3","url":null,"abstract":"<p><strong>Key message: </strong>A major QTL, qLF2.1, for flowering time in tomatoes, was fine mapped to chromosome 2 within a 51.37-kb interval, and the SlJMJ14 gene was verified as the causal gene by knockout. Tomato flowering time is an important agronomic trait that affects yield, fruit quality, and environmental adaptation. In this study, the high-generation inbred line 19108 with a late-flowering phenotype was selected for the mapping of the gene that causes late flowering. In the F<sub>2</sub> population derived from 19108 (late flowering) × MM (early flowering), we identified a major late-flowering time quantitative trait locus (QTL) using QTL-seq, designated qLF2.1. This QTL was fine mapped to a 51.37-kb genomic interval using recombinant analysis. Through functional analysis of homologous genes, Solyc02g082400 (SlJMJ14), encoding a histone demethylase, was determined to be the most promising candidate gene. Knocking out SlJMJ14 in MM resulted in a flowering time approximately 5-6 days later than that in the wild-type plants. These results suggest that mutational SlJMJ14 is the major QTL for the late-flowering phenotype of the 19108 parental line.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"137 10","pages":"228"},"PeriodicalIF":4.4,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142296095","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}
引用次数: 0
Validation of cross-progeny variance genomic prediction using simulations and experimental data in winter elite bread wheat 利用模拟和实验数据验证冬季精英面包小麦的杂交后代方差基因组预测
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-18 DOI: 10.1007/s00122-024-04718-6
Claire Oget-Ebrad, Emmanuel Heumez, Laure Duchalais, Ellen Goudemand-Dugué, François-Xavier Oury, Jean-Michel Elsen, Sophie Bouchet

Key message

From simulations and experimental data, the quality of cross progeny variance genomic predictions may be high, but depends on trait architecture and necessitates sufficient number of progenies.

Abstract

Genomic predictions are used to select genitors and crosses in plant breeding. The usefulness criterion (UC) is a cross-selection criterion that necessitates the estimation of parental mean (PM) and progeny standard deviation (SD). This study evaluates the parameters that affect the predictive ability of UC and its two components using simulations. Predictive ability increased with heritability and progeny size and decreased with QTL number, most notably for SD. Comparing scenarios where marker effects were known or estimated using prediction models, SD was strongly impacted by the quality of marker effect estimates. We proposed a new algebraic formula for SD estimation that takes into account the uncertainty of the estimation of marker effects. It improved predictions when the number of QTL was superior to 300, especially when heritability was low. We also compared estimated and observed UC using experimental data for heading date, plant height, grain protein content and yield. PM and UC estimates were significantly correlated for all traits (PM: 0.38, 0.63, 0.51 and 0.91; UC: 0.45, 0.52, 0.54 and 0.74; for yield, grain protein content, plant height and heading date, respectively), while SD was correlated only for heading date and plant height (0.64 and 0.49, respectively). According to simulations, SD estimations in the field would necessitate large progenies. This pioneering study experimentally validates genomic prediction of UC but the predictive ability depends on trait architecture and precision of marker effect estimates. We advise the breeders to adjust progeny size to realize the SD potential of a cross.

关键信息从模拟和实验数据来看,杂交后代方差基因组预测的质量可能很高,但这取决于性状结构,而且需要足够数量的后代。有用性标准(UC)是一种杂交选择标准,需要估计亲本平均值(PM)和后代标准偏差(SD)。本研究通过模拟评估了影响有用性标准预测能力的参数及其两个组成部分。预测能力随遗传率和后代大小的增加而提高,随 QTL 数量的增加而降低,尤其是 SD。在已知标记效应或使用预测模型估计标记效应的情况下,SD 受标记效应估计质量的影响很大。我们提出了一种新的 SD 估算代数公式,该公式考虑了标记效应估算的不确定性。当 QTL 数量多于 300 时,尤其是遗传率较低时,它能改善预测结果。我们还利用打顶日期、株高、谷物蛋白质含量和产量的实验数据,比较了估计的 UC 和观察到的 UC。在所有性状中,PM 和 UC 估计值都有明显的相关性(PM:0.38、0.63、0.51 和 0.91;UC:UC:0.45、0.52、0.54 和 0.74;分别针对产量、谷物蛋白质含量、株高和打顶日期),而 SD 仅针对打顶日期和株高具有相关性(分别为 0.64 和 0.49)。模拟结果表明,在田间进行自交系测定需要大量后代。这项开创性的研究通过实验验证了 UC 的基因组预测,但预测能力取决于性状结构和标记效应估计的精确度。我们建议育种者调整后代大小,以发挥杂交种的自交系潜力。
{"title":"Validation of cross-progeny variance genomic prediction using simulations and experimental data in winter elite bread wheat","authors":"Claire Oget-Ebrad, Emmanuel Heumez, Laure Duchalais, Ellen Goudemand-Dugué, François-Xavier Oury, Jean-Michel Elsen, Sophie Bouchet","doi":"10.1007/s00122-024-04718-6","DOIUrl":"https://doi.org/10.1007/s00122-024-04718-6","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key message</h3><p><b>From simulations and experimental data, the quality of cross progeny variance genomic predictions may be high, but depends on trait architecture and necessitates sufficient number of progenies.</b></p><h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Genomic predictions are used to select genitors and crosses in plant breeding. The usefulness criterion (UC) is a cross-selection criterion that necessitates the estimation of parental mean (PM) and progeny standard deviation (SD). This study evaluates the parameters that affect the predictive ability of UC and its two components using simulations. Predictive ability increased with heritability and progeny size and decreased with QTL number, most notably for SD. Comparing scenarios where marker effects were known or estimated using prediction models, SD was strongly impacted by the quality of marker effect estimates. We proposed a new algebraic formula for SD estimation that takes into account the uncertainty of the estimation of marker effects. It improved predictions when the number of QTL was superior to 300, especially when heritability was low. We also compared estimated and observed UC using experimental data for heading date, plant height, grain protein content and yield. PM and UC estimates were significantly correlated for all traits (PM: 0.38, 0.63, 0.51 and 0.91; UC: 0.45, 0.52, 0.54 and 0.74; for yield, grain protein content, plant height and heading date, respectively), while SD was correlated only for heading date and plant height (0.64 and 0.49, respectively). According to simulations, SD estimations in the field would necessitate large progenies. This pioneering study experimentally validates genomic prediction of UC but the predictive ability depends on trait architecture and precision of marker effect estimates. We advise the breeders to adjust progeny size to realize the SD potential of a cross.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"21 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264443","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}
引用次数: 0
Mapping and transcriptomic profiling reveal that the KNAT6 gene is involved in the dark green peel colour of mature pumpkin fruit (Cucurbita maxima L.) 图谱和转录组分析表明,KNAT6 基因与成熟南瓜果实(Cucurbita maxima L.)深绿色果皮的颜色有关
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-17 DOI: 10.1007/s00122-024-04741-7
ChaoJie Wang, Wenqi Ding, Fangyuan Chen, Ke Zhang, Yuetong Hou, Guichao Wang, Wenlong Xu, Yunli Wang, Shuping Qu

Key message

We identified a 580 bp deletion of CmaKNAT6 coding region influences peel colour of mature Cucurbita maxima fruit.

Abstract

Peel colour is an important agronomic characteristic affecting commodity quality in Cucurbit plants. Genetic mapping of fruit peel colour promotes molecular breeding and provides an important basis for understanding the regulatory mechanism in Cucurbit plants. In the present study, the Cucurbita maxima inbred line ‘9-6’ which has a grey peel colour and ‘U3-3-44’ which has a dark green peel colour in the mature fruit stage, were used as plant materials. At 5–40 days after pollination (DAP), the contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids in the ‘U3-3-44’ peels were significantly greater than those in the ‘9-6’ peels. In the epicarp of the ‘9-6’ mature fruit, the presence of nonpigmented cell layers and few chloroplasts in each cell in the pigmented layers were observed. Six generations derived by crossing ‘9-6’ and ‘U3-3-44’ were constructed, and the dark green peel was found to be controlled by a single dominant locus, which was named CmaMg (mature green peel). Through bulked-segregant analysis sequencing (BSA-seq) and insertion-deletion (InDel) markers, CmaMg was mapped to a region of approximately 449.51 kb on chromosome 11 using 177 F2 individuals. Additionally, 1703 F2 plants were used for fine mapping to compress the candidate interval to a region of 32.34 kb. Five coding genes were in this region, and CmaCh11G000900 was identified as a promising candidate gene according to the reported function, sequence alignment, and expression analyses. CmaCh11G000900 (CmaKNAT6) encodes the homeobox protein knotted-1-like 6 and contains 4 conserved domains. CmaKNAT6 of ‘9-6’ had a 580 bp deletion, leading to premature transcriptional termination. The expression of CmaKNAT6 tended to increase sharply during the early fruit development stage but decrease gradually during the late period of fruit development. Allelic diversity analysis of pumpkin germplasm resources indicated that the 580 bp deletion in the of CmaKNAT6 coding region was associated with peel colour. Subcellular localization analysis indicated that CmaKNAT6 is a nuclear protein. Transcriptomic analysis of the inbred lines ‘9-6’ and ‘U3-3-44’ indicated that genes involved in chlorophyll biosynthesis were more enriched in ‘U3-3-44’ than in ‘9-6’. Additionally, the expression of transcription factor genes that positively regulate chlorophyll synthesis and light signal transduction pathways was upregulated in ‘U3-3-44’. These results lay a foundation for further studies on the genetic mechanism underlying peel colour and for optimizing peel colour-based breeding strategies for C. maxima.

摘要果皮颜色是影响葫芦科植物商品质量的重要农艺性状。果皮颜色的遗传图谱促进了分子育种,并为了解葫芦科植物的调控机制提供了重要依据。本研究以果皮颜色为灰色的 Cucurbita maxima 近交系'9-6'和成熟果实阶段果皮颜色为深绿色的'U3-3-44'为植物材料。授粉后 5-40 天,'U3-3-44'果皮中叶绿素 a、叶绿素 b、总叶绿素和类胡萝卜素的含量明显高于'9-6'果皮。在'9-6'成熟果实的外果皮中,观察到存在非色素细胞层,色素层中每个细胞中的叶绿体数量很少。通过构建'9-6'和'U3-3-44'杂交产生的六代,发现深绿色果皮由一个显性基因座控制,该基因座被命名为 CmaMg(成熟绿色果皮)。通过大量分离分析测序(BSA-seg)和插入-缺失(InDel)标记,利用177个F2个体将CmaMg映射到11号染色体上约449.51 kb的区域。此外,还利用 1703 株 F2 进行了精细图谱绘制,将候选区间压缩到 32.34 kb 的区域。该区域有五个编码基因,根据报告的功能、序列比对和表达分析,CmaCh11G000900 被确定为有希望的候选基因。CmaCh11G000900 (CmaKNAT6)编码同源框蛋白结-1-样 6,包含 4 个保守结构域。9-6'的 CmaKNAT6 有 580 bp 的缺失,导致转录过早终止。CmaKNAT6 的表达量在果实发育早期急剧增加,但在果实发育后期逐渐减少。南瓜种质资源的等位基因多样性分析表明,CmaKNAT6编码区的580 bp缺失与果皮颜色有关。亚细胞定位分析表明,CmaKNAT6 是一种核蛋白。对近交系 "9-6 "和 "U3-3-44 "的转录组分析表明,与 "9-6 "相比,"U3-3-44 "中参与叶绿素生物合成的基因更为丰富。此外,'U3-3-44'中对叶绿素合成和光信号转导途径有正向调节作用的转录因子基因的表达上调。这些结果为进一步研究果皮颜色的遗传机制和优化基于果皮颜色的 C. maxima 育种策略奠定了基础。
{"title":"Mapping and transcriptomic profiling reveal that the KNAT6 gene is involved in the dark green peel colour of mature pumpkin fruit (Cucurbita maxima L.)","authors":"ChaoJie Wang, Wenqi Ding, Fangyuan Chen, Ke Zhang, Yuetong Hou, Guichao Wang, Wenlong Xu, Yunli Wang, Shuping Qu","doi":"10.1007/s00122-024-04741-7","DOIUrl":"https://doi.org/10.1007/s00122-024-04741-7","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key message</h3><p>We identified a 580 bp deletion of <i>CmaKNAT6</i> coding region influences peel colour of mature <i>Cucurbita maxima</i> fruit.</p><h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Peel colour is an important agronomic characteristic affecting commodity quality in <i>Cucurbit</i> plants. Genetic mapping of fruit peel colour promotes molecular breeding and provides an important basis for understanding the regulatory mechanism in <i>Cucurbit</i> plants. In the present study, the <i>Cucurbita maxima</i> inbred line ‘9-6’ which has a grey peel colour and ‘U3-3-44’ which has a dark green peel colour in the mature fruit stage, were used as plant materials. At 5–40 days after pollination (DAP), the contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoids in the ‘U3-3-44’ peels were significantly greater than those in the ‘9-6’ peels. In the epicarp of the ‘9-6’ mature fruit, the presence of nonpigmented cell layers and few chloroplasts in each cell in the pigmented layers were observed. Six generations derived by crossing ‘9-6’ and ‘U3-3-44’ were constructed, and the dark green peel was found to be controlled by a single dominant locus, which was named <i>CmaMg</i> (<i>mature green peel</i>). Through bulked-segregant analysis sequencing (BSA-seq) and insertion-deletion (InDel) markers, <i>CmaMg</i> was mapped to a region of approximately 449.51 kb on chromosome 11 using 177 F<sub>2</sub> individuals. Additionally, 1703 F<sub>2</sub> plants were used for fine mapping to compress the candidate interval to a region of 32.34 kb. Five coding genes were in this region, and <i>CmaCh11G000900</i> was identified as a promising candidate gene according to the reported function, sequence alignment, and expression analyses. <i>CmaCh11G000900</i> (<i>CmaKNAT6</i>) encodes the homeobox protein knotted-1-like 6 and contains 4 conserved domains. <i>CmaKNAT6</i> of ‘9-6’ had a 580 bp deletion, leading to premature transcriptional termination. The expression of <i>CmaKNAT6</i> tended to increase sharply during the early fruit development stage but decrease gradually during the late period of fruit development. Allelic diversity analysis of pumpkin germplasm resources indicated that the 580 bp deletion in the of <i>CmaKNAT6</i> coding region was associated with peel colour. Subcellular localization analysis indicated that CmaKNAT6 is a nuclear protein. Transcriptomic analysis of the inbred lines ‘9-6’ and ‘U3-3-44’ indicated that genes involved in chlorophyll biosynthesis were more enriched in ‘U3-3-44’ than in ‘9-6’. Additionally, the expression of transcription factor genes that positively regulate chlorophyll synthesis and light signal transduction pathways was upregulated in ‘U3-3-44’. These results lay a foundation for further studies on the genetic mechanism underlying peel colour and for optimizing peel colour-based breeding strategies for <i>C. maxima</i>.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"22 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264436","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}
引用次数: 0
Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance 通过单核苷酸多态性 (SNP) 检测和基因分型技术的进步改良小麦,特别强调锈病抗性
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-16 DOI: 10.1007/s00122-024-04730-w
Subramaniam Geethanjali, Palchamy Kadirvel, Sambasivam Periyannan

Key message

Single nucleotide polymorphism (SNP) markers in wheat and their prospects in breeding with special reference to rust resistance.

Abstract

Single nucleotide polymorphism (SNP)-based markers are increasingly gaining momentum for screening and utilizing vital agronomic traits in wheat. To date, more than 260 million SNPs have been detected in modern cultivars and landraces of wheat. This rapid SNP discovery was made possible through the release of near-complete reference and pan-genome assemblies of wheat and its wild relatives, coupled with whole genome sequencing (WGS) of thousands of wheat accessions. Further, genotyping customized SNP sites were facilitated by a series of arrays (9 to 820Ks), a cost effective substitute WGS. Lately, germplasm-specific SNP arrays have been introduced to characterize novel traits and detect closely linked SNPs for marker-assisted breeding. Subsequently, the kompetitive allele-specific PCR (KASP) assay was introduced for rapid and large-scale screening of specific SNP markers. Moreover, with the advances and reduction in sequencing costs, ample opportunities arise for generating SNPs artificially through mutations and in combination with next-generation sequencing and comparative genomic analyses. In this review, we provide historical developments and prospects of SNP markers in wheat breeding with special reference to rust resistance where over 50 genetic loci have been characterized through SNP markers. Rust resistance is one of the most essential traits for wheat breeding as new strains of the Puccinia fungus, responsible for rust diseases, evolve frequently and globally.

摘要以单核苷酸多态性(SNP)为基础的标记在筛选和利用小麦重要农艺性状方面的势头日益强劲。迄今为止,已在现代小麦栽培品种和陆地品系中检测到超过 2.6 亿个 SNP。小麦及其野生近缘种近乎完整的参考基因组和泛基因组组装的发布,加上对数千个小麦品种的全基因组测序(WGS),使得这种快速的 SNP 发现成为可能。此外,一系列阵列(9 至 820Ks)为定制 SNP 位点的基因分型提供了便利,这是一种具有成本效益的 WGS 替代品。最近,又引入了种质特异性 SNP 阵列,以表征新性状和检测密切相关的 SNP,用于标记辅助育种。随后,又引入了竞争性等位基因特异性 PCR(KASP)测定法,用于快速、大规模筛选特异性 SNP 标记。此外,随着测序技术的进步和测序成本的降低,通过突变以及结合新一代测序和比较基因组分析人工产生 SNP 的机会也越来越多。在本综述中,我们将介绍 SNP 标记在小麦育种中的历史发展和前景,特别是在抗锈病方面,已有 50 多个遗传位点通过 SNP 标记得到了表征。抗锈病性是小麦育种最基本的性状之一,因为导致锈病的普氏真菌的新菌株在全球范围内频繁进化。
{"title":"Wheat improvement through advances in single nucleotide polymorphism (SNP) detection and genotyping with a special emphasis on rust resistance","authors":"Subramaniam Geethanjali, Palchamy Kadirvel, Sambasivam Periyannan","doi":"10.1007/s00122-024-04730-w","DOIUrl":"https://doi.org/10.1007/s00122-024-04730-w","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key message</h3><p>Single nucleotide polymorphism (SNP) markers in wheat and their prospects in breeding with special reference to rust resistance.</p><h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Single nucleotide polymorphism (SNP)-based markers are increasingly gaining momentum for screening and utilizing vital agronomic traits in wheat. To date, more than 260 million SNPs have been detected in modern cultivars and landraces of wheat. This rapid SNP discovery was made possible through the release of near-complete reference and pan-genome assemblies of wheat and its wild relatives, coupled with whole genome sequencing (WGS) of thousands of wheat accessions. Further, genotyping customized SNP sites were facilitated by a series of arrays (9 to 820Ks), a cost effective substitute WGS. Lately, germplasm-specific SNP arrays have been introduced to characterize novel traits and detect closely linked SNPs for marker-assisted breeding. Subsequently, the kompetitive allele-specific PCR (KASP) assay was introduced for rapid and large-scale screening of specific SNP markers. Moreover, with the advances and reduction in sequencing costs, ample opportunities arise for generating SNPs artificially through mutations and in combination with next-generation sequencing and comparative genomic analyses. In this review, we provide historical developments and prospects of SNP markers in wheat breeding with special reference to rust resistance where over 50 genetic loci have been characterized through SNP markers. Rust resistance is one of the most essential traits for wheat breeding as new strains of the <i>Puccinia</i> fungus, responsible for rust diseases, evolve frequently and globally.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"8 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264438","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}
引用次数: 0
EMS-induced missense mutation in TaCHLI-7D affects leaf color and yield-related traits in wheat EMS 诱导的 TaCHLI-7D 错义突变会影响小麦的叶色和产量相关性状
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-15 DOI: 10.1007/s00122-024-04740-8
Zixu Wang, Huiyuan Xu, Faxiang Wang, Lingling Sun, Xiangrui Meng, Zhuochun Li, Chang Xie, Huijiao Jiang, Guangshuo Ding, Xinrong Hu, Yuhang Gao, Ran Qin, Chunhua Zhao, Han Sun, Fa Cui, Yongzhen Wu

Key message

Mutations in TaCHLI impact chlorophyll levels and yield-related traits in wheat.Natural variations in TaCHLI-7A/B influence plant productivity, offering potential for molecularbreeding.

Abstract

Chlorophyll is essential for plant growth and productivity. The CHLI subunit of the magnesium chelatase protein plays a key role inserting magnesium into protoporphyrin IX during chlorophyll biosynthesis. Here, we identify a novel wheat mutant chlorophyll (chl) that exhibits yellow-green leaves, reduced chlorophyll levels, and increased carotenoid content, leading to an overall decline in yield-related traits. Map-based cloning reveals that the chl phenotype is caused by a point mutation (Asp186Asn) in the TaCHLI-7D gene, which encodes subunit I of magnesium chelatase. Furthermore, the three TaCHLI mutants: chl-7b-1 (Pro82Ser), chl-7b-2 (Ala291Thr), and chl-7d-1 (Gly357Glu), also showed significant reductions in chlorophyll content and yield-related traits. However, TaCHLI-7D overexpression in rice significantly decreased thousand kernel weight, yield per plant, and germination. Additionally, natural variations in TaCHLI-7A/B are significantly associated with flag leaf, spike exsertion length, and yield per plant. Notably, the favorable haplotype, TaCHLI-7B-HapII, which displayed higher thousand kernel weight and yield per plant, is positively selected in wheat breeding. Our study provides insights on the regulatory molecular mechanisms underpinning leaf color and chlorophyll biosynthesis, and highlights TaCHLI functions, which provide useful molecular markers and genetic resources for wheat breeding.

关键信息TaCHLI的突变影响小麦的叶绿素水平和产量相关性状。TaCHLI-7A/B的自然变异影响植物的产量,为分子育种提供了潜力。 摘要叶绿素对植物的生长和产量至关重要。镁螯合酶蛋白的 CHLI 亚基在叶绿素的生物合成过程中起着将镁插入原卟啉 IX 的关键作用。在这里,我们发现了一种新的小麦叶绿素突变体(chl),该突变体叶片呈黄绿色,叶绿素含量降低,类胡萝卜素含量增加,导致产量相关性状整体下降。基于图谱的克隆发现,chl 表型是由编码镁螯合酶 I 亚基的 TaCHLI-7D 基因中的一个点突变(Asp186Asn)引起的。此外,三个 TaCHLI 突变体:chl-7b-1(Pro82Ser)、chl-7b-2(Ala291Thr)和 chl-7d-1(Gly357Glu)也显示出叶绿素含量和产量相关性状的显著降低。然而,TaCHLI-7D 在水稻中的过表达会显著降低千粒重、单株产量和发芽率。此外,TaCHLI-7A/B 的自然变异与旗叶、穗膨大长度和单株产量显著相关。值得注意的是,有利的单倍型 TaCHLI-7B-HapII 显示出更高的千粒重和单株产量,在小麦育种中被积极选择。我们的研究揭示了叶色和叶绿素生物合成的分子调控机制,突出了 TaCHLI 的功能,为小麦育种提供了有用的分子标记和遗传资源。
{"title":"EMS-induced missense mutation in TaCHLI-7D affects leaf color and yield-related traits in wheat","authors":"Zixu Wang, Huiyuan Xu, Faxiang Wang, Lingling Sun, Xiangrui Meng, Zhuochun Li, Chang Xie, Huijiao Jiang, Guangshuo Ding, Xinrong Hu, Yuhang Gao, Ran Qin, Chunhua Zhao, Han Sun, Fa Cui, Yongzhen Wu","doi":"10.1007/s00122-024-04740-8","DOIUrl":"https://doi.org/10.1007/s00122-024-04740-8","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key message</h3><p>Mutations in<i> TaCHLI</i> impact chlorophyll levels and yield-related traits in wheat.\u0000Natural variations in<i> TaCHLI-7A/B</i> influence plant productivity, offering potential for molecular\u0000breeding.</p><h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Chlorophyll is essential for plant growth and productivity. The CHLI subunit of the magnesium chelatase protein plays a key role inserting magnesium into protoporphyrin IX during chlorophyll biosynthesis. Here, we identify a novel wheat mutant <i>chlorophyll</i> (<i>chl</i>) that exhibits yellow-green leaves, reduced chlorophyll levels, and increased carotenoid content, leading to an overall decline in yield-related traits. Map-based cloning reveals that the <i>chl</i> phenotype is caused by a point mutation (Asp186Asn) in the <i>TaCHLI-7D</i> gene, which encodes subunit I of magnesium chelatase. Furthermore, the three <i>TaCHLI</i> mutants: <i>chl-7b-1</i> (Pro82Ser)<i>, chl-7b-2</i> (Ala291Thr), and <i>chl-7d-1</i> (Gly357Glu), also showed significant reductions in chlorophyll content and yield-related traits. However, <i>TaCHLI-7D</i> overexpression in rice significantly decreased thousand kernel weight, yield per plant, and germination. Additionally, natural variations in <i>TaCHLI-7A/B</i> are significantly associated with flag leaf, spike exsertion length, and yield per plant. Notably, the favorable haplotype, <i>TaCHLI-7B-HapII</i>, which displayed higher thousand kernel weight and yield per plant, is positively selected in wheat breeding. Our study provides insights on the regulatory molecular mechanisms underpinning leaf color and chlorophyll biosynthesis, and highlights <i>TaCHLI</i> functions, which provide useful molecular markers and genetic resources for wheat breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"31 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264437","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}
引用次数: 0
Genome-wide association study and molecular marker development for susceptibility to Gibberella ear rot in maize 玉米吉伯菌穗腐病易感性的全基因组关联研究和分子标记开发
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-14 DOI: 10.1007/s00122-024-04711-z
Guangfei Zhou, Liang Ma, Caihong Zhao, Fugui Xie, Yang Xu, Qing Wang, Derong Hao, Xiquan Gao

Key messages

Sixty-nine quantitative trait nucleotides conferring maize resistance to Gibberella ear rot were detected, including eighteen novel loci. Four candidate genes were predicted, and four kompetitive allele-specific PCR markers were developed.

Abstract

Maize Gibberella ear rot (GER), caused by Fusarium graminearum, is one of the most devastating diseases in maize-growing regions worldwide. Enhancing maize cultivar resistance to this disease requires a comprehensive understanding of the genetic basis of resistance to GER. In this study, 334 maize inbred lines were phenotyped for GER resistance in five environments and genotyped using the Affymetrix CGMB56K SNP Array, and a genome-wide association study of resistance to GER was performed using a 3V multi-locus random-SNP-effect mixed linear model. A total of 69 quantitative trait nucleotides (QTNs) conferring resistance to GER were detected, and all of them explained individually less than 10% of the phenotypic variation, suggesting that resistance to GER is controlled by multiple minor-effect genetic loci. A total of 348 genes located around the 200-kb genomic region of these 69 QTNs were identified, and four of them (Zm00001d029648, Zm00001d031449, Zm00001d006397, and Zm00001d053145) were considered candidate genes conferring susceptibility to GER based on gene expression patterns. Moreover, four kompetitive allele-specific PCR markers were developed based on the non-synonymous variation of these four candidate genes and validated in two genetic populations. This study provides useful genetic resources for improving resistance to GER in maize.

关键信息检测到69个数量性状核苷酸赋予玉米对吉伯菌穗腐病的抗性,其中包括18个新的位点。摘要由禾谷镰刀菌引起的玉米吉伯菌穗腐病(GER)是全球玉米种植区最具毁灭性的病害之一。要提高玉米品种对该病害的抗性,就必须全面了解玉米抗吉伯菌穗腐病的遗传基础。本研究利用 Affymetrix CGMB56K SNP 阵列对 334 个玉米近交系在 5 种环境中的 GER 抗性进行了表型分析和基因分型,并利用 3V 多焦点随机-SNP-效应混合线性模型对 GER 的抗性进行了全基因组关联研究。共检测到69个赋予GER抗性的数量性状核苷酸(QTNs),所有QTNs单独解释的表型变异均小于10%,表明GER抗性受多个次要效应遗传位点控制。在这69个QTN的200kb基因组区域周围共鉴定出348个基因,其中4个基因(Zm00001d029648、Zm00001d031449、Zm00001d006397和Zm00001d053145)根据基因表达模式被认为是GER易感性的候选基因。此外,还根据这四个候选基因的非同义变异开发了四个竞争性等位基因特异性 PCR 标记,并在两个遗传群体中进行了验证。这项研究为提高玉米对 GER 的抗性提供了有用的遗传资源。
{"title":"Genome-wide association study and molecular marker development for susceptibility to Gibberella ear rot in maize","authors":"Guangfei Zhou, Liang Ma, Caihong Zhao, Fugui Xie, Yang Xu, Qing Wang, Derong Hao, Xiquan Gao","doi":"10.1007/s00122-024-04711-z","DOIUrl":"https://doi.org/10.1007/s00122-024-04711-z","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Key messages</h3><p>Sixty-nine quantitative trait nucleotides conferring maize resistance to Gibberella ear rot were detected, including eighteen novel loci. Four candidate genes were predicted, and four kompetitive allele-specific PCR markers were developed.</p><h3 data-test=\"abstract-sub-heading\">\u0000<b>Abstract</b>\u0000</h3><p>Maize Gibberella ear rot (GER), caused by <i>Fusarium graminearum</i>, is one of the most devastating diseases in maize-growing regions worldwide. Enhancing maize cultivar resistance to this disease requires a comprehensive understanding of the genetic basis of resistance to GER. In this study, 334 maize inbred lines were phenotyped for GER resistance in five environments and genotyped using the Affymetrix CGMB56K SNP Array, and a genome-wide association study of resistance to GER was performed using a 3V multi-locus random-SNP-effect mixed linear model. A total of 69 quantitative trait nucleotides (QTNs) conferring resistance to GER were detected, and all of them explained individually less than 10% of the phenotypic variation, suggesting that resistance to GER is controlled by multiple minor-effect genetic loci. A total of 348 genes located around the 200-kb genomic region of these 69 QTNs were identified, and four of them (<i>Zm00001d029648</i>, <i>Zm00001d031449</i>, <i>Zm00001d006397</i>, and <i>Zm00001d053145</i>) were considered candidate genes conferring susceptibility to GER based on gene expression patterns. Moreover, four kompetitive allele-specific PCR markers were developed based on the non-synonymous variation of these four candidate genes and validated in two genetic populations. This study provides useful genetic resources for improving resistance to GER in maize.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"25 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264615","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}
引用次数: 0
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 不同环境下亲本或母本类基因表达的灵活性有助于节水抗旱杂交水稻避旱和耐旱的结合
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-13 DOI: 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.

背景水稻是世界上最重要的农作物之一。水稻是世界上最重要的农作物之一,水稻生产耗水量大,缺水和干旱胁迫严重。主要发现与亲本汉恢3号(HH3)和汉恢7A(HH7A)相比,杂交WDR品种汉优73(HY73)表现出更优越的抗旱性。对抗旱性相关性状的研究表明,HY73 在耐旱性和抗旱性方面的表现分别与 HH3 和 HH7A 相似。对不同植物激素处理和非生物胁迫下的样本进行了转录组分析,其中叶片样本中 HY73 与 HH3 比较接近,而根部样本中则与 HH7A 比较接近。HY73 与其亲本在 DEGs 上有很大差异,对 DEGs 的 GO 分析表明 HH3 和 HH7A 的干旱响应途径不同。类父本表达分析表明,HY73 的类父本表达模式较高。此外,亲本样表达模式在非生物胁迫/植物激素处理样本和对照样本之间发生了显著的转化,这可能有助于 HY73 适应不同的环境。对这些类父本表达基因进行的 WGCNA 分析发现了一些抗旱基因,这些基因应该是 HY73 抗旱性更强的原因。结论:我们的研究揭示了亲本有益性状互补和基因灵活表达在 HY73 抗旱性中的重要作用,这将促进 WDR 新品种的开发。
{"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":"13 1","pages":""},"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}
引用次数: 0
Early exposure to phosphorus starvation induces genetically determined responses in Sorghum bicolor roots 早期暴露于磷饥饿诱导高粱双色根的基因决定反应
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-11 DOI: 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":"34 1","pages":""},"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}
引用次数: 0
Redesigning soybean with improved oil and meal traits 重新设计大豆,改良油脂和粕的特性
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-10 DOI: 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.

摘要大豆[Glycine max (L.) Merr.]是世界上一种重要的农作物;其总体价值来自籽油和高蛋白粕。开发具有等位基因组合的大豆品种以提高油和粕的质量,有望为大豆提供一个成分价值束。高油酸和低亚麻酸籽油性状(HOLL; > 70% 油酸和 < 3% 亚麻酸)的目标是优化大豆油的健康和功能特性。就豆粕而言,通过改变碳水化合物结构,增加蔗糖,减少抗营养因子--棉子糖系列低聚糖(RFO),可提高代谢能。先前的研究发现,脂肪酸去饱和酶(FAD)基因的四个变异等位基因和棉子糖合成酶(RS)基因的两个变异等位基因分别是大豆油中 HOLL 性状和豆粕中低或超低(UL)RFO 性状所必需的。我们采用了分子标记辅助育种方法,将赋予所需大豆油和粕价值性状的六个等位基因组合在一起。我们用 24 个大豆品系进行了 8 个环境田间试验,以评估 FAD 和 RS 基因变异等位基因之间的表型相互作用。结果表明,无论 RS 基因的等位基因状况如何,四个 FAD 基因等位基因都会对籽油的 HOLL 脂肪酸谱产生影响。与 FAD 基因的等位基因组合无关,具有两个 RS 基因变异等位基因的大豆种子具有理想的 RFO 性状。这些结果证实了利用这种独特的油和粕性状组合开发大豆品种的可行性。
{"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; &gt; 70% oleic and &lt; 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":"28 1","pages":""},"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}
引用次数: 0
Current status of molecular rice breeding for durable and broad-spectrum resistance to major diseases and insect pests 针对主要病虫害的持久和广谱抗性的分子水稻育种现状
IF 5.4 1区 农林科学 Q1 AGRONOMY Pub Date : 2024-09-10 DOI: 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":"45 1","pages":""},"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}
引用次数: 0
期刊
Theoretical and Applied Genetics
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1