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Genome-wide association analysis of winter survival in a diverse Canadian winter wheat population. 不同加拿大冬小麦群体冬季生存的全基因组关联分析。
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70091
Rachel Whiting, Alexandra Ficht, Yi Chen, Davoud Torkamaneh, Joseph Colasanti, Eric M Lyons
{"title":"Genome-wide association analysis of winter survival in a diverse Canadian winter wheat population.","authors":"Rachel Whiting, Alexandra Ficht, Yi Chen, Davoud Torkamaneh, Joseph Colasanti, Eric M Lyons","doi":"10.1002/tpg2.70091","DOIUrl":"https://doi.org/10.1002/tpg2.70091","url":null,"abstract":"<p><p>Vrn-A1 (VERNALIZATION A1) and Fr-A2 (FROST RESISTANCE A2) have been associated with variation in winter survival of wheat (Triticum aestivum L.). The beneficial alleles of Vrn-A1 and Fr-A2 are largely fixed in Canadian winter wheat germplasm, rendering the associated molecular markers ineffective for marker-assisted selection (MAS) in elite populations. The objectives were to (i) identify quantitative trait loci (QTLs) for winter survival in eastern Canada and determine their usefulness for MAS and (ii) explore the underlying genetic mechanisms of superior winter survival in the region. A subpopulation (n = 321) of the Canadian Winter Wheat Diversity Panel, consisting of genotypes that were fixed for the beneficial alleles of vrn-A1 and Fr-A2, was previously evaluated for winter survival in three eastern Canadian environments (Elora 2016-2017, CÉROM 2017-2018, and Elora 2017-2018). Genome-wide association mapping identified three significant QTLs for winter survival, a previously identified QTL on chromosome 5A, and two novel QTLs on chromosomes 5D and 7B. These QTLs were of low-to-moderate marker utility (0.1473-0.4796) and conferred a 0.7%-1.8% increase in mean winter survival. In silico analyses revealed that an array of biotic and abiotic stress responses are implicated in winter survival in eastern Canada, which challenges the notion that lethal temperature is the primary cause of winterkill in some regions. As significant winterkill events are sporadic in the region, it may be beneficial to identify individual components of winter survival that can be examined in artificial environments.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70091"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12365865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975583","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
Integration of physiological and remote sensing traits for improved genomic prediction of wheat yield. 结合生理和遥感性状改进小麦产量基因组预测。
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70110
Guillermo García-Barrios, Carlos A Robles-Zazueta, Abelardo Montesinos-López, Osval A Montesinos-López, Matthew P Reynolds, Susanne Dreisigacker, José A Carrillo-Salazar, Liana G Acevedo-Siaca, Margarita Guerra-Lugo, Gilberto Thompson, José A Pecina-Martínez, José Crossa
{"title":"Integration of physiological and remote sensing traits for improved genomic prediction of wheat yield.","authors":"Guillermo García-Barrios, Carlos A Robles-Zazueta, Abelardo Montesinos-López, Osval A Montesinos-López, Matthew P Reynolds, Susanne Dreisigacker, José A Carrillo-Salazar, Liana G Acevedo-Siaca, Margarita Guerra-Lugo, Gilberto Thompson, José A Pecina-Martínez, José Crossa","doi":"10.1002/tpg2.70110","DOIUrl":"10.1002/tpg2.70110","url":null,"abstract":"<p><p>Genomic selection is an extension of marker-assisted selection by leveraging thousands of molecular markers distributed across the genome to capture the maximum possible proportion of the genetic variance underlying complex traits. In this study, genomic prediction models were developed by integrating phenological, physiological, and high-throughput phenotyping traits to predict grain yield in bread wheat (Triticum aestivum L.) under three environmental conditions: irrigation, drought stress, and terminal heat stress. Model performance was evaluated using both five-fold cross-validation and leave-one-environment-out (LOEO) schemes. Under five-fold cross-validation, the model incorporating vegetation indices derived from spectral datasets from the grain-filling phase achieved the highest accuracy. In LOEO validation, the model that included days to heading performed best under irrigation, whereas under drought stress, the model utilizing vegetation indices from the vegetative stage showed the highest accuracy. Under terminal heat stress, three models performed best: one incorporating genotype by environment interaction, one using vegetation indices during the vegetative stage, and one integrating spectral reflectance data from both the vegetative and grain-filling phases. Although incorporating multiple covariates can improve prediction accuracy or reduce the normalized root mean square error, using an extended model with all available covariates is not recommended due to the marginal predictive accuracy gains, increases in phenotyping, costs and complexity of data collection analysis. Overall, our findings show the importance of tailored phenomic inputs to specific environmental contexts to optimize genomic prediction of wheat yield.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70110"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12409263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994196","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 exploration of durable wheat rust resistance by integrating data from multiple worldwide populations. 通过整合来自世界各地多个种群的数据,对小麦耐久抗锈病的基因组探索。
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70093
Reem Joukhadar, Richard M Trethowan, Urmil Bansal, Rebecca Thistlethwaite, Josquin Tibbits, Harbans Bariana, Matthew J Hayden
{"title":"Genomic exploration of durable wheat rust resistance by integrating data from multiple worldwide populations.","authors":"Reem Joukhadar, Richard M Trethowan, Urmil Bansal, Rebecca Thistlethwaite, Josquin Tibbits, Harbans Bariana, Matthew J Hayden","doi":"10.1002/tpg2.70093","DOIUrl":"10.1002/tpg2.70093","url":null,"abstract":"<p><p>Global wheat (Triticum aestivum L.) production faces significant challenges due to the destructive nature of leaf (Puccinia triticina; leaf rust [Lr]), stem (Puccinia graminis; stem rust [Sr]), and stripe (Puccinia striiformis; stripe rust [Yr]) rust diseases. Despite ongoing efforts to develop resistant varieties, these diseases remain a persistent challenge due to their highly evolving nature. Overcoming these challenges requires the identification and deployment of genetically diverse resistance genes in future cultivars. This study explored durable resistance against rust diseases by integrating data from five global populations. The populations exhibit diverse origins and were phenotypically evaluated in 16, 13, and 19 global field experiments, with total phenotypic observations of 12,694, 10,725, and 16,281 for Lr, Sr, and Yr, respectively. Field experiments showed moderate heritability of 0.43, 0.62, and 0.41 for Lr, Sr, and Yr, respectively. Genetic correlations were moderate among experiments for the same disease (0.34-0.59), but low among the three diseases (<0.21). The meta-genome-wide association studies (metaGWAS) analysis identified 19 quantitative trait loci (QTLs) associated with the resistance to Lr, 17 with the resistance to Sr, and five with the resistance to Yr. Six QTLs controlling resistance to more than one rust disease were also identified. Additionally, the study unveiled 13 potentially new QTLs (five for Lr and Yr each and three for Yr), contributing valuable insights into the genetic basis of wheat rust resistance. The integration of diverse populations and environments through metaGWAS enhanced the detection of stable QTL. This research provides breeders with additional resistance loci to combat rust pathogens.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70093"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024589","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 prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole-genome resequence and multi-environmental data. 利用全基因组重测序和多环境数据预测玉米茎秆抗倒伏及其相关中间表型
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70125
Caique Machado E Silva, Bharath Kunduru, Norbert Bokros, Kaitlin Tabaracci, Yusuf Oduntan, Manwinder S Brar, Rohit Kumar, Christopher J Stubbs, Maicon Nardino, Christopher S McMahan, Seth DeBolt, Daniel J Robertson, Rajandeep S Sekhon, Gota Morota
{"title":"Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole-genome resequence and multi-environmental data.","authors":"Caique Machado E Silva, Bharath Kunduru, Norbert Bokros, Kaitlin Tabaracci, Yusuf Oduntan, Manwinder S Brar, Rohit Kumar, Christopher J Stubbs, Maicon Nardino, Christopher S McMahan, Seth DeBolt, Daniel J Robertson, Rajandeep S Sekhon, Gota Morota","doi":"10.1002/tpg2.70125","DOIUrl":"10.1002/tpg2.70125","url":null,"abstract":"<p><p>Breeding for stalk lodging resistance is of paramount importance to maintain and improve maize (Zea mays L.) yield and quality and meet increasing food demand. The integration of environmental, phenotypic, and genotypic information offers the opportunity to develop genomic prediction strategies that can improve the genetic gain for complex traits such as stalk lodging. However, implementation of genomic predictions for stalk lodging resistance has been sparse primarily due to the lack of reliable and reproducible phenotyping strategies. In this study, we measured 10 traits related to stalk lodging resistance obtained from a novel phenotyping platform on approximately 31,000 individual stalks. These traits were combined with environmental information and whole-genome resequence data to investigate the predictive ability of different single and multi-environment genomic prediction models. In total, 555 maize inbred lines from the Wisconsin diversity panel were evaluated in four environments. The multi-environment models more than doubled the prediction accuracy compared to the single-environment model for most traits, particularly when predicting lines in a sparse testing design. Predictive correlations for stalk bending strength and stalk flexural stiffness, a nondestructive method for assessment of stalk lodging resistance, were moderately high and ranged between 0.32-0.89 and 0.26-0.88, respectively. In contrast, rind thickness was the most difficult trait to predict. Our results show that the use of multi-environmental data could improve genomic prediction accuracy for stalk lodging resistance and its intermediate phenotypes. This study will serve as a first step toward genetic improvement and the development of maize varieties resistant to stalk lodging.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70125"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126330","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
Development and characterization of a wild emmer wheat backcross introgression population for hard winter wheat improvement. 硬冬小麦改良野生二粒小麦回交渐渗群体的建立与特性研究。
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70104
John H Price, Mary J Guttieri, Moses Nyine, Eduard Akhunov
{"title":"Development and characterization of a wild emmer wheat backcross introgression population for hard winter wheat improvement.","authors":"John H Price, Mary J Guttieri, Moses Nyine, Eduard Akhunov","doi":"10.1002/tpg2.70104","DOIUrl":"10.1002/tpg2.70104","url":null,"abstract":"<p><p>Wild emmer wheat (Triticum turgidum subsp. dicoccoides) is the tetraploid progenitor of hexaploid bread wheat (Triticum aestivum L.) and is known to be a valuable source of genetic variation for wheat improvement. However, direct evaluation of wild emmer diversity for agronomic potential has limited value unless performed in the backgrounds of adapted cultivars. Here, we present a genetic characterization of a population of 1601 backcross recombinant inbred lines, with an average genome composition of 75% bread wheat and 25% wild emmer. Low-coverage whole-genome sequencing allowed introgressions and aneuploidies to be identified at a relatively low cost per sample. We identified a relatively large proportion of small introgressions (median length 38 Mb), and we found introgressions to be distributed across all chromosomes. Approximately 44% of genotyped progeny carried at least one aneuploidy, with monosomies being by far the most common. This population, which we have denoted as the Great Plains Wild Emmer/Hard Winter Wheat introgression population (GPWEW-IP), is, to our knowledge, the first introgression population developed through the direct hybridization of wild emmer wheat and US-adapted hard winter wheat. We believe that this population represents a valuable resource for wheat breeders and will accelerate the discovery and integration of useful variation from wild emmer wheat.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70104"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12402295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975518","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
Analysis of candidate genes identified via genome-wide association analysis of sugar-related traits in maize kernels. 玉米籽粒糖相关性状全基因组关联分析鉴定的候选基因分析。
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70101
Dan Lv, Jingyun Luo, Songqin Liu, Ran Zheng, Aoni Zhang, Bo Tong, Qingping Zeng, Xinyi Liu, Hongbing Luo, Min Deng
{"title":"Analysis of candidate genes identified via genome-wide association analysis of sugar-related traits in maize kernels.","authors":"Dan Lv, Jingyun Luo, Songqin Liu, Ran Zheng, Aoni Zhang, Bo Tong, Qingping Zeng, Xinyi Liu, Hongbing Luo, Min Deng","doi":"10.1002/tpg2.70101","DOIUrl":"10.1002/tpg2.70101","url":null,"abstract":"<p><p>Maize (Zea mays L.) is a globally significant crop, with its kernel sugar content playing a crucial role in determining nutritional quality and industrial applications. This study aimed to elucidate the genetic mechanisms underlying sugar-related traits in maize kernels through genome-wide association studies. We evaluated 495 maize inbred lines for reducing sugar content, soluble sugar content, and the reducing/soluble sugar ratio. Phenotypic analysis revealed substantial variation, with coefficients of variation ranging from 28.84% to 53.86%, and high broad-sense heritability (87.90%-93.98%). Using 12,617,573 high-quality single-nucleotide polymorphisms, we identified 93 significant quantitative trait nucleotides associated with these traits. Transcriptomic data from the maize inbred line B73 highlighted six candidate genes (Zm00001d040189, Zm00001d032517, Zm00001d052399, Zm00001d028974, Zm00001d036971, and Zm00001d022316) with high expression during kernel development. Protein-protein interaction and coexpression network analyses suggested that these genes are involved in metabolic processes, cell communication, and carbohydrate metabolism. Haplotype analysis further revealed that the optimal haplotypes of the six candidate genes could increase the kernel sugar content without affecting the yield traits of maize. These findings advance our understanding of the genetic basis of sugar-related traits in maize and offer valuable molecular markers for future breeding programs.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70101"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12411998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145001782","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
Better together: Subgenomes for allotetraploid potato wild relative Solanum acaule Bitt. reveal origins in Petota Clade 3 and 4. 更好地在一起:异源四倍体马铃薯野生近缘种龙葵的亚基因组。揭示了Petota Clade 3和4的起源。
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70095
S Achakkagari, J C Camargo-Tavares, D Praslickova, C Martini, B Bizimungu, N L Anglin, N Manrique-Carpintero, H Lindqvist-Kreuze, H H Tai, M V Strömvik
{"title":"Better together: Subgenomes for allotetraploid potato wild relative Solanum acaule Bitt. reveal origins in Petota Clade 3 and 4.","authors":"S Achakkagari, J C Camargo-Tavares, D Praslickova, C Martini, B Bizimungu, N L Anglin, N Manrique-Carpintero, H Lindqvist-Kreuze, H H Tai, M V Strömvik","doi":"10.1002/tpg2.70095","DOIUrl":"https://doi.org/10.1002/tpg2.70095","url":null,"abstract":"<p><p>Potato wild relatives (Solanum section Petota) are a source of genetic diversity for climate-smart improvement of modern cultivars (Solanum tuberosum). The allotetraploid Solanum acaule Bitter. has been previously used to introgress frost tolerance into potato cultivars such as Yukon Gold and Viking. The current study presents the subgenomes of S. acaule. In a phylogenetic context, the placement of the individual subgenomes shows that Solanum megistacrolobum (Clade 4) is the progenitor species of S. acaule subgenome 2, while the progenitor species of subgenome 1 (mapping to Clade 3) is still unknown and may be extinct. The genome assembly is 1.34 Gb in 24 chromosomes with an N50 of 56.2 Mb, making the theoretical tetraploid S. acaule genome 2.68 Gb. The C-repeat binding factor (CBF) cold response genes were identified in the subgenomes, and in a freeze-challenged transcriptome analysis of S. acaule compared with autotetraploid S. tuberosum 'Atlantic', CBF1 was induced in both species, while CBF4 (subgenome 2) was induced only in S. acaule. A general subgenome expression bias was not detected in a set of homoeologous genes, though the subgenomes diverged in the number of differentially expressed genes and their functional roles.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70095"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12368328/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975556","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
Pangenome insights into structural variation and functional diversification of barley CCT motif genes. 大麦CCT基序基因结构变异和功能多样化的泛基因组研究。
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70098
Zihao Zhu, Nils Stein
{"title":"Pangenome insights into structural variation and functional diversification of barley CCT motif genes.","authors":"Zihao Zhu, Nils Stein","doi":"10.1002/tpg2.70098","DOIUrl":"https://doi.org/10.1002/tpg2.70098","url":null,"abstract":"<p><p>CONSTANS, CONSTANS-LIKE, TIMING OF CAB EXPRESSION1 (CCT) motif genes play a key role in barley (Hordeum vulgare L.) development and flowering, yet their genetic diversity remains underexplored. Leveraging a barley pangenome (76 genotypes) and pan-transcriptome (subset of 20 genotypes), we examined CCT gene variation and evolutionary dynamics. Motif-based searches, combined with genome assembly validation, revealed annotation limitations and novel frameshift variants (e.g., HvCO10, where Hv is Hordeum vulgare L.), indicating active diversification. Pangenome-wide phylogenetic analysis identified clade-specific domain expansions, including B-box domain additions in HvCO clades. Tissue-specific expression patterns further supported functional divergence among paralogs. Notably, VRN2, a canonical floral repressor associated with winter growth, was retained in spring genotypes, challenging its presumed exclusive role in vernalization. Discrepancies between VRN1 expression, VRN2 deletion, and growth habit implicated additional regulatory mechanisms. These findings highlight the power of pangenomes in resolving gene family complexity, refining annotations, and advancing the understanding of CCT genes to enhance barley resilience and adaptability.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70098"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12381546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975601","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
Marker-trait association mapping for perpetual flowering habit in an octoploid ancestral strawberry, Fragaria virginiana. 八倍体草莓祖先永久开花习性的标记-性状关联定位。
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70108
Samikshya Rijal, Lise L Mahoney, Yilong Yang, Thomas M Davis
{"title":"Marker-trait association mapping for perpetual flowering habit in an octoploid ancestral strawberry, Fragaria virginiana.","authors":"Samikshya Rijal, Lise L Mahoney, Yilong Yang, Thomas M Davis","doi":"10.1002/tpg2.70108","DOIUrl":"https://doi.org/10.1002/tpg2.70108","url":null,"abstract":"<p><p>Cultivated strawberry Fragaria × ananassa (Duch.) is an economically important small fruit. Flowering habit is a key trait of interest in cultivar development and agricultural production. Two cultivar types are distinguished: seasonal flowering (SF) varieties, which require a sufficiently short day length to initiate flowering; and perpetual flowering (PF) varieties, which are photoperiod-insensitive and continuously flowering at permissive temperatures. Identifying marker-trait associations (MTAs) and genes related to flowering time is an ongoing goal. SF and PF accessions of the ancestral octoploid Fragaria virginiana were used in crossing and backcrossing to generate a BC<sub>1</sub>F<sub>1</sub> mapping population, which was genotyped on the IStraw90 SNP array to develop a linkage map using JoinMap 4.1. MTA analysis was done by chi-square test for independence and compared with analyses done using FlexQTL and WinQTLCart. Six MTAs for PF were mapped, suggesting complex genetic regulation. These MTAs were distributed across five linkage groups (LGs) representing four chromosomal homeology groups. Surprisingly, none of these six MTAs were assigned to a member of the F. virginiana subgenome A, the octoploid strawberry subgenome widely agreed to descend from the ancestral diploid Fragaria vesca. This important distinction extended to the strong MTAs on LG14, which our analysis assigned to the same homeology group but not the same homeolog previously assigned to the well-studied FaPFRU locus conferring continuous flowering in F. × ananassa. This alternative localization may help to explain why the gene(s) underlying FaPFRU have remained unidentified in the 13 years since its discovery.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70108"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12375845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975624","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
The NPGS Sudan sorghum germplasm collection reveals a novel cluster of R genes associated with rust resistant. NPGS苏丹高粱种质资料揭示了一个与抗锈病相关的新R基因簇。
IF 3.8 2区 生物学
Plant Genome Pub Date : 2025-09-01 DOI: 10.1002/tpg2.70113
Hugo E Cuevas, Louis K Prom
{"title":"The NPGS Sudan sorghum germplasm collection reveals a novel cluster of R genes associated with rust resistant.","authors":"Hugo E Cuevas, Louis K Prom","doi":"10.1002/tpg2.70113","DOIUrl":"10.1002/tpg2.70113","url":null,"abstract":"<p><p>Leaf rust, caused by the obligate fungal pathogen Puccinia purpurea, poses a serious threat to sorghum [Sorghum bicolor (L.) Moench] production leading to significant yield losses and undermining its values as renewable fuel crop. In this study, the United States Department of Agriculture-Agriculture Research Service, National Plant Germplasm System (NPGS) Sudan core collection was evaluated for rust-resistant response across four tropical environments. The analysis identified 18 accessions with rust resistant, among which four accessions (PI 568621, PI 569393, PI 570548, and PI 570974) consistently showed no rust pustules across all environments. Genome-wide association analysis led to the identification of a 57 kbp genomic region on chromosome 8 that encompasses a cluster of five homologous R genes. The resequencing analysis of the first exon from one candidate gene (Sobic.008G178200) found 61 point mutations that generate seven haplotypes. The high homology of these five genes and seven haplotypes indicates that this cluster might be acting as a single locus (Rp2) against P. purpurea. Comparative genome analysis found that the orthologs of Rp2 locus in maize (Zm00001d023311) are associated with the resistant response to Puccinia polysora, the causal agent of southern corn rust and in rice (Os12G29690), with resistance to the brown planthopper (Nilaparvata lugens). The introgression of the Rp2 locus into elite varieties or the inclusion of top-performing Sudanese tropical accessions in pre-breeding germplasm can accelerate the development of improved sorghum germplasm with durable rust resistant.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 3","pages":"e70113"},"PeriodicalIF":3.8,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12438027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071038","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}
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