Plant Genome最新文献

Multi-trait/environment sparse genomic prediction using the SFSI R-package. 利用SFSI R-package进行多性状/环境稀疏基因组预测。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70050

Marco Lopez-Cruz, Gustavo de Los Campos

{"title":"Multi-trait/environment sparse genomic prediction using the SFSI R-package.","authors":"Marco Lopez-Cruz, Gustavo de Los Campos","doi":"10.1002/tpg2.70050","DOIUrl":"10.1002/tpg2.70050","url":null,"abstract":"Sparse selection indices (SSIs) can be used to predict the genetic merit of selection candidates using high-dimensional phenotypes (e.g., crop imaging) measured on each of the candidates of selection. Unlike traditional selection indices, SSIs can perform variable selection, thus enabling borrowing of information from a subset of the measured phenotypes. Likewise, sparse genomic prediction (SGP) can be used to predict genetic merit by borrowing information from a subset of the training dataset. In this study, we introduce a framework for multi-trait/environment SGP (MT-SGP) that combines the features of SSI and SGP into a single model. For candidates of selection, an MT-SGP produces prediction equations that use subsets of the training data, borrowing information from correlated traits expressed in training genotypes that are genetically close to the candidates of selection. Along with the methodology, we present an R-package (sparse family and selection index) that provides functions to solve SSIs, SGP, and MT-SGP problems. After presenting simplified examples that illustrate the use of the functions included in the package, we provide extensive benchmarks (using three data sets covering three crops and 30 traits/environments). Our results suggest that MT-SGP either outperforms (with up to 15% gains in prediction accuracy) or performs similarly to MT-genomic best linear unbiased prediction. The benchmarks provide insight regarding the conditions (sample size, genetic correlation among traits, and trait heritability) under which the use of MT-SGP can lead to gains in prediction accuracy.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 2","pages":"e70050"},"PeriodicalIF":3.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic selection: Essence, applications, and prospects. 基因组选择：本质、应用与前景。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70053

Diana M Escamilla, Dongdong Li, Karlene L Negus, Kiara L Kappelmann, Aaron Kusmec, Adam E Vanous, Patrick S Schnable, Xianran Li, Jianming Yu

{"title":"Genomic selection: Essence, applications, and prospects.","authors":"Diana M Escamilla, Dongdong Li, Karlene L Negus, Kiara L Kappelmann, Aaron Kusmec, Adam E Vanous, Patrick S Schnable, Xianran Li, Jianming Yu","doi":"10.1002/tpg2.70053","DOIUrl":"10.1002/tpg2.70053","url":null,"abstract":"Genomic selection (GS) emerged as a key part of the solution to ensure the food supply for the growing human population thanks to advances in genotyping and other enabling technologies and improved understanding of the genotype-phenotype relationship in quantitative genetics. GS is a breeding strategy to predict the genotypic values of individuals for selection using their genotypic data and a trained model. It includes four major steps: training population design, model building, prediction, and selection. GS revises the traditional breeding process by assigning phenotyping a new role of generating data for the building of prediction models. The increased capacity of GS to evaluate more individuals, in combination with shorter breeding cycle times, has led to wide adoption in plant breeding. Research studies have been conducted to implement GS with different emphases in crop- and trait-specific applications, prediction models, design of training populations, and identifying factors influencing prediction accuracy. GS plays different roles in plant breeding such as turbocharging of gene banks, parental selection, and candidate selection at different stages of the breeding cycle. It can be enhanced by additional data types such as phenomics, transcriptomics, metabolomics, and enviromics. In light of the rapid development of artificial intelligence, GS can be further improved by either upgrading the entire framework or individual components. Technological advances, research innovations, and emerging challenges in agriculture will continue to shape the role of GS in plant breeding.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 2","pages":"e70053"},"PeriodicalIF":3.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12127607/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of significant genome-wide associations and QTL underlying variation in seed protein composition in pea (Pisum sativum L.). 豌豆（Pisum sativum L.）种子蛋白质组成显著全基因组关联及QTL变异的鉴定

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70051

Ahmed O Warsame, Janneke Balk, Claire Domoney

{"title":"Identification of significant genome-wide associations and QTL underlying variation in seed protein composition in pea (Pisum sativum L.).","authors":"Ahmed O Warsame, Janneke Balk, Claire Domoney","doi":"10.1002/tpg2.70051","DOIUrl":"10.1002/tpg2.70051","url":null,"abstract":"Pulses are a valuable source of plant proteins for human and animal nutrition and have various industrial applications. Understanding the genetic basis for the relative abundance of different seed storage proteins is crucial for developing cultivars with improved protein quality and functional properties. In this study, we employed two complementary approaches, genome-wide association study (GWAS) and quantitative trait locus (QTL) mapping, to identify genetic loci underlying seed protein composition in pea (Pisum sativum L.). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was used to separate the seed proteins, and their relative abundance was quantified using densitometric analysis. For GWAS, we analyzed a diverse panel of 209 accessions genotyped with an 84,691 single-nucleotide polymorphism (SNP) array and identified genetic loci significantly associated with globulins, such as convicilin, vicilin, legumins, and non-globulins, including lipoxygenase, late embryogenesis abundant protein, and annexin-like protein. Additionally, using QTL mapping with 96 recombinant inbred lines, we mapped 11 QTL, including five that overlapped with regions identified by GWAS for the same proteins. Some of the significant SNPs were within or near the genes encoding seed proteins and other genes with predicted functions in protein biosynthesis, trafficking, and modification. This comprehensive genetic mapping study serves as a foundation for future breeding efforts to improve protein quality in pea and other legumes.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 2","pages":"e70051"},"PeriodicalIF":3.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12163866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144286851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alanine aminotransferase contributes to hypoxia sensitivity and dormancy in barley seeds. 谷丙转氨酶与大麦种子缺氧敏感性和休眠有关。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70063

Lochlen G H Farquharson, Bahram Samanfar, Raja Khanal, Elizabeth K Brauer

{"title":"Alanine aminotransferase contributes to hypoxia sensitivity and dormancy in barley seeds.","authors":"Lochlen G H Farquharson, Bahram Samanfar, Raja Khanal, Elizabeth K Brauer","doi":"10.1002/tpg2.70063","DOIUrl":"https://doi.org/10.1002/tpg2.70063","url":null,"abstract":"Seed dormancy is regulated by a combination of developmental and environmental cues to ensure seedling survival in a changing environment. In barley (Hordeum vulgare L.), the SD1 and SD2 (where SD is standard deviation) loci regulate dormancy and pre-harvest sprouting (PHS), though their role in physiological development remains unclear. Malting barley production in Eastern Canada is currently limited due to the high potential for PHS in the region. To understand what genetic loci might be influencing dormancy in Eastern Canadian barley, we evaluated the LegCi biparental population, which was derived from the Léger variety. A quantitative trait loci close to the SD1 on chromosome 5 locus was identified as regulating germination in LegCi, suggesting that the alanine aminotransferase gene (AlaAT1), which underlies dormancy regulation at SD1, influences dormancy in LegCi. Alanine aminotransferases influence energy production in the cell, particularly during nitrogen limitation or oxygen deprivation. LegCi genotypes segregating for dormancy at the SD1 allele showed no differences in abscisic acid or GA-dependent gene expression during grain fill but varied for hypoxia-induced gene expression. Hypoxia suppressed germination in all genotypes but had a significantly higher impact on genotypes with the dormant AlaAT1 relative to genotypes with the non-dormant AlaAT1. This trend was not dependent on the presence of the hull, suggesting that signaling or metabolism inside the germinating seed is influencing hypoxia sensitivity. This work suggests that the non-dormant allele of SD1 is associated with reduced hypoxia stress sensitivity to promote germination. Further work is needed to determine if this trend extends to other barley genotypes.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 2","pages":"e70063"},"PeriodicalIF":3.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to "Insights into the roles of long noncoding RNAs in the communication between plants and the environment". 对“深入了解长链非编码rna在植物与环境之间的交流中的作用”的更正。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70045

引用次数: 0

Discovery of major QTL and a massive haplotype associated with cannabinoid biosynthesis in drug-type Cannabis. 在药物型大麻中发现与大麻素生物合成相关的主要QTL和大量单倍型。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70031

Maxime de Ronne, Davoud Torkamaneh

{"title":"Discovery of major QTL and a massive haplotype associated with cannabinoid biosynthesis in drug-type Cannabis.","authors":"Maxime de Ronne, Davoud Torkamaneh","doi":"10.1002/tpg2.70031","DOIUrl":"10.1002/tpg2.70031","url":null,"abstract":"Cannabis (Cannabis sativa L.), once sidelined by decades of prohibition, has now gained recognition as a multifaceted and promising plant in both medical research and commercial applications following its recent legalization. This study leverages a genome-wide association study (GWAS) on 174 drug-type Cannabis accessions from the legal Canadian market, focusing on identifying quantitative trait loci (QTL) and candidate genes associated with eleven cannabinoid traits using 282K common single-nucleotide polymorphisms. This approach aims to transform our understanding of Cannabis genetics. We have pinpointed 33 significant markers that significantly influence cannabinoid production, promising to drive the development of Cannabis varieties with specific cannabinoid profiles. Among the notable findings is a massive haplotype of ∼60 Mb on chromosome 7 in Type I (i.e., tetrahydrocannabinol [THC]-dominant) accessions, highlighting a major genetic influence on cannabinoid profiles. These insights offer valuable guidance for Cannabis breeding programs, enabling the use of precise genetic markers to select and refine promising Cannabis varieties. This approach promises to speed up the breeding process, reduce costs significantly compared to traditional methods, and ensure that the resulting Cannabis varieties are optimized for specific medical and recreational needs. This study marks a significant stride toward fully integrating Cannabis into modern agricultural practices and genetic research, paving the way for future innovations.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 2","pages":"e70031"},"PeriodicalIF":3.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12104491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Discovering leaf and stripe rust resistance in soft red winter wheat through genome-wide association studies. 通过全基因组关联研究发现软红冬小麦叶片和条锈病抗性。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70055

John W Bagwell, Mohamed Mergoum, Madhav Subedi, Suraj Sapkota, Bikash Ghimire, Benjamin Lopez, James W Buck, Bochra A Bahri

{"title":"Discovering leaf and stripe rust resistance in soft red winter wheat through genome-wide association studies.","authors":"John W Bagwell, Mohamed Mergoum, Madhav Subedi, Suraj Sapkota, Bikash Ghimire, Benjamin Lopez, James W Buck, Bochra A Bahri","doi":"10.1002/tpg2.70055","DOIUrl":"10.1002/tpg2.70055","url":null,"abstract":"Leaf rust (LR) and stripe rust (YR), which are caused by Puccinia triticina and Puccinia striiformis, respectively, are among the most devastating wheat rusts worldwide. These diseases can be managed by using genetically resistant cultivars, an economical and environmentally safer alternative to fungicides. Over 100 and 80 Lr and Yr resistance genes have been discovered, respectively; however, rust pathogens are overcoming introduced resistance genes in the southeastern United States. Genome-wide association study has emerged as a valuable tool to identify new LR and YR resistance loci. In this study, a panel of 263 soft red winter wheat genotypes was evaluated for LR and YR severity in Plains, GA, and Williamson, GA, in a randomized complete block design of two replicates during 2019 and 2021-2023. Also, LR and YR infection types were assessed on seedlings at the three leaf stage in three greenhouse trials. A total of 26 significant quantitative trait loci (QTL) explaining 0.6%-30.8% phenotypic variance (PV) was detected by at least two of the five GAPIT models (BLINK, CMLM, FarmCPU, GLM, and MLM) tested. Nine major QTL included QLrYr-2A.1 linked to single-nucleotide polymorphism S2A_20855466, which had the highest overall PV (30.8%) for response to both rust pathogens in the field. Using the Chinese Spring Reference Genome Version 1.0, we detected 16 candidate genes, and four known R genes and QTL overlapped two major QTL. Of these QTL, 16 are likely novel genetic loci with potential for marker-assisted selection.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 2","pages":"e70055"},"PeriodicalIF":3.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12152529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Low density marker-based effectiveness and efficiency of early-generation genomic selection relative to phenotype-based selection in dolichos bean (Lablab purpureus L. Sweet). 基于低密度标记的早代基因组选择的有效性和效率相对于基于表型的选择。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70039

Mugali Pundalik Kalpana, Sampangi Ramesh, Chindi Basavaraj Siddu, Gonal Basanagouda, K Madhusudan, Hosakoti Sathish, Dinesh Sindhu, Munegowda Kemparaju, C Anilkumar

{"title":"Low density marker-based effectiveness and efficiency of early-generation genomic selection relative to phenotype-based selection in dolichos bean (Lablab purpureus L. Sweet).","authors":"Mugali Pundalik Kalpana, Sampangi Ramesh, Chindi Basavaraj Siddu, Gonal Basanagouda, K Madhusudan, Hosakoti Sathish, Dinesh Sindhu, Munegowda Kemparaju, C Anilkumar","doi":"10.1002/tpg2.70039","DOIUrl":"10.1002/tpg2.70039","url":null,"abstract":"Genomic prediction has been demonstrated to be an efficient approach for the selection of candidates based on marker information in many crops. However, efforts to understand the efficiency of genomic selection over phenotype-based selection in understudied crops such as dolichos bean (Lablab purpureus L. Sweet) are limited. Our objectives were to (i) explore the effective marker density for achieving high prediction accuracy and (ii) assess the effectiveness and efficiency of genomic selection over phenotype-based selection on seed yield at early segregating generations in dolichos bean. In this study, the training population, which consisted of F5:6 recombinant inbreds, had a shared common parent with the breeding population, which consisted of F2 generation breeding population. The populations were genotyped with newly synthesized genomic simple sequence repeat-based markers. The effective marker density for genomic prediction was assessed by using a varying number of markers in predictions using 11 different models. Furthermore, the effectiveness of genomic selection was assessed by comparing the genetic gains in progenies between genotypes selected based on predicted seed yield and phenotypically selected genotypes. Our results indicate that low-density markers that are evenly distributed throughout the genome are sufficient for the integration of genomic selection in dolichos breeding programs. The genomic selection was proved to be two times more effective than phenotypic selection in early-generation selection in dolichos beans. The results have a significant impact on adopting genomic selection in regular breeding programs of Dolichos beans at a low cost.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 2","pages":"e70039"},"PeriodicalIF":3.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144152305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic and biochemical comparison of allelic triple-mutant lines derived from conventional breeding and multiplex gene editing. 传统育种和多重基因编辑获得的等位基因三突变系的基因组和生化比较。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70056

Junqi Liu, Ritesh Kumar, Samatha Gunapati, Steven Mulkey, Yinjie Qiu, Yer Xiong, Vishnu Ramasubramanian, Jean-Michel Michno, Praveen Awasthi, Daniel D Gallaher, Thi Thao Nguyen, Won-Seok Kim, Hari B Krishnan, Aaron J Lorenz, Robert M Stupar

{"title":"Genomic and biochemical comparison of allelic triple-mutant lines derived from conventional breeding and multiplex gene editing.","authors":"Junqi Liu, Ritesh Kumar, Samatha Gunapati, Steven Mulkey, Yinjie Qiu, Yer Xiong, Vishnu Ramasubramanian, Jean-Michel Michno, Praveen Awasthi, Daniel D Gallaher, Thi Thao Nguyen, Won-Seok Kim, Hari B Krishnan, Aaron J Lorenz, Robert M Stupar","doi":"10.1002/tpg2.70056","DOIUrl":"10.1002/tpg2.70056","url":null,"abstract":"Multiplex gene editing allows for the simultaneous targeting and mutagenesis of multiple loci in a genome. This tool is particularly valuable for plant genetic improvement, as plant genomes often require mutations at multiple loci to confer useful and/or novel traits. However, the regulation of gene editing can vary depending on the number of loci targeted. In this study, we developed triple-mutant soybean (Glycine max (L.) Merrill) lines using different crop improvement strategies, including conventional backcross breeding of standing variant alleles and clustered regularly interspaced short palindromic repeats-based multiplex editing to introduce new alleles. The mutations were targeted to genes encoding seed antinutritional components, as previously described in a triple null soybean carrying knockout alleles for a Kunitz trypsin inhibitor, a soybean agglutinin, and the allergen P34 protein. The products developed from these respective genetic improvement pipelines were tested for differences between the triple-mutant lines and their parental lines. Analyses included genomics, seed proteomics, trypsin inhibition, seed protein digestibility, and harvestable yield of the different lines. We observed that both multiplex gene editing and conventional breeding approaches produced essentially equivalent products in comparison to their parental lines. We conclude that the multiplex gene editing strategy is not inherently riskier than conventional breeding for developing complex mutant lines of this type.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 2","pages":"e70056"},"PeriodicalIF":3.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12141651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic dissection of crown rust resistance in oat and the identification of key adult plant resistance genes. 燕麦冠锈病抗性的遗传解剖及关键成株抗性基因的鉴定。

IF 3.9 2区生物学

Plant Genome Pub Date : 2025-06-01 DOI: 10.1002/tpg2.70059

Nikwan Shariatipour, Mahboobeh Yazdani, Anders Carlsson, Therése Bengtsson, Shahryar F Kianian, Marja Jalli, Mahbubjon Rahmatov

{"title":"Genetic dissection of crown rust resistance in oat and the identification of key adult plant resistance genes.","authors":"Nikwan Shariatipour, Mahboobeh Yazdani, Anders Carlsson, Therése Bengtsson, Shahryar F Kianian, Marja Jalli, Mahbubjon Rahmatov","doi":"10.1002/tpg2.70059","DOIUrl":"10.1002/tpg2.70059","url":null,"abstract":"Crown rust (Puccinia coronata f. sp. Avenae Erikss.) poses a significant threat to oat production worldwide. The most effective strategy for managing this disease involves identifying, mapping, and deploying resistance genes to develop cultivars with enhanced resistance. In this study, we conducted a meta-analysis of quantitative trait loci (QTLs) linked to crown rust resistance across diverse oat populations and environments. From 11 studies conducted between 2003 and 2024, we selected 167 QTLs, of which 127 were successfully mapped onto an oat consensus linkage map. These QTLs were mainly located on chromosomes of the D and C sub-genomes, showing considerable variation in genetic distances and marker associations. Based on the integration of these QTLs in a meta-QTL (MQTL) analysis, 23 MQTLs were identified for crown rust resistance in the oat genome. Gene mining within the MQTL intervals identified 1526 candidate genes, most of which were located in the D sub-genome. Functional analysis revealed that these genes play key roles in stress response, hormonal regulation, and polyamine metabolism, which are crucial for plant defense. Conserved regulatory elements (cis-acting regulatory element [CAREs]) were also identified in the promoter regions of key resistance genes, indicating their involvement in light response, stress regulation, and hormone signaling. This study represents a significant advancement in understanding the genetic architecture of crown rust resistance in oat and provides a valuable resource for breeding programs focused on improving disease resistance.","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 2","pages":"e70059"},"PeriodicalIF":3.9,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12163869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144286850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0