Theoretical and Applied Genetics最新文献

{"title":"QTL mapping and candidate genes prediction for plant height and brix content in sorghum [Sorghum bicolor (L.) Moench].","authors":"Xing Shi, Youhou Duan, Shaohua Chai, Yan Guo, Shuqing Guo, Chuanxing Wang, Shiru Li, Delong Liu, Baili Feng, Feng Lu, Pu Yang","doi":"10.1007/s00122-025-05024-5","DOIUrl":"10.1007/s00122-025-05024-5","url":null,"abstract":"<p><strong>Key message: </strong>By constructing a high-density genetic linkage map using a recombinant inbred line (RIL) population from two sorghum lines with distinct variations in plant height and brix content, eight genetic loci were identified, and candidate genes associated with these traits were predicted. Sorghum, recognized as a crucial forage and energy crop, exhibits yield and quality influenced by plant height and sugar content traits. Considering the complex genetic architecture of plant height and sugar content, this study utilized a sorghum recombinant inbred line population comprising 250 lines to elucidate the phenotypic variation and genetic foundations of these traits. Utilizing streamlined genome sequencing technology, the genotypes of each line were scrutinized, culminating in the construction of a sorghum genetic linkage map spanning 1129.97 centi-Morgans (cM) and encompassing 2101 bin markers. This population was planted in Liaoning during the growing seasons from 2014 to 2020, and the phenotypes of plant height and brix content were characterized across six different environments. Simultaneously, optimal genetic models for sorghum plant height and brix content were analyzed. Eight QTLs significantly associated with plant height and brix content were identified on chromosomes 1, 5, 6, 7, and 8, using QTL mapping. In this study, two QTLs associated with plant height and one QTL associated with brix content were identified across at least two different environments. The confidence intervals of the identified major effect QTL loci were utilized to predict candidate genes. Sobic.007G163200.1 was identified as a significant candidate gene for plant height, involved in tryptophan metabolism. Two genes associated with ABC transporter-related pathways were also identified as significant candidate genes for plant height. Furthermore, three genes involved in carbon fixation in photosynthetic organisms were identified as significant candidate genes for brix content.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"238"},"PeriodicalIF":4.2,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970202","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}

{"title":"The transcription factor BoMYC2 negatively regulates seed size by activating cytokinin dehydrogenase BoCKX5 in Broccoli.","authors":"Xiaomei Wu, Yuxiao Tian, Weihuan Li, Jiaqing An, Zhijian Wu, Lu Huang, Junwei Wang, Zhenzhu Hu, Ke Huang, Qiuyun Wu","doi":"10.1007/s00122-025-05027-2","DOIUrl":"https://doi.org/10.1007/s00122-025-05027-2","url":null,"abstract":"<p><p>Broccoli is an economically significant vegetable with high nutritional and medicinal value. Seed size/weight is one of the important agronomic traits that determine crop yield, which is regulated by multiple plant hormones. However, limited information is known about the regulation of seed size control in broccoli. Here, we report that the basic helix-loop-helix transcription factor BoMYC2 exerts a negative regulatory influence on seed-related traits in broccoli. The overexpression of BoMYC2 in Arabidopsis and broccoli led to notably decreased seed size and seed weight, likely by repressing cell proliferation of embryonic. Besides, overexpression of BoMYC2 increased the fatty acid accumulation while reducing the protein and soluble sugar levels in stably transgenic broccoli seeds, affecting seed storage compounds composition and seed size. Based on DNA affinity purification sequencing, BoMYC2 targeted the cytokinin oxidase gene BoCKX5 by binding to the G-box motif in its promoter regions. BoMYC2 activated the expression of BoCKX5 to modulate cytokinin metabolism. The expression levels of cytokinin-related genes and jasmonic acid-related genes were further analyzed in transgenic broccoli seeds, implying that BoMYC2 leads to higher jasmonic acid and lower cytokinin hormone content, which might affect the cell proliferation in seeds. Furthermore, cytokinin levels were significantly lower in BoMYC2-overexpressing broccoli than in wild-type plants. Collectively, these findings reveal a BoMYC2-BoCKX5 regulatory module that controls seed size/weight, enriching our understanding of the internal mechanism in seed size regulation and providing promising targets for high-yield broccoli breeding.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"236"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970271","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}

{"title":"Identification of new genomic loci for seed protein and oil content in the soybean pangenome using genome-wide association and haplotype analyses.","authors":"Tri D Vuong, Guangqi He, Haifei Hu, Babu Valliyodan, Dongho Lee, Philipp E Bayer, William T Schapaugh, Rene Hessel, David Edwards, Henry T Nguyen","doi":"10.1007/s00122-025-05020-9","DOIUrl":"https://doi.org/10.1007/s00122-025-05020-9","url":null,"abstract":"<p><p>The soybean [Glycine max (L.) Merr.] pangenome has been studied and shown to be an invaluable resource for investigating structural variations (SVs), from which different genomic markers were successfully developed and employed for genome-wide association studies (GWAS). Among the SVs markers, gene presence-and-absence variations (PAVs) have been developed in soybean, but have not been widely utilized for association analyses. Here, we reported GWAS and haplotype analysis of seed protein and oil content for two diverse panels, comprised over 500 soybean accessions evaluated in multiple field environments using three marker datasets, whole genome sequence (WGS)-single-nucleotide polymorphisms (SNPs), 50 K-SNPs, and PAVs. The analyses identified new quantitative trait loci (QTL) for protein and oil content, along with the validation of previously reported QTL for these traits. This includes a well-studied QTL on chromosome (Chr.) 20 and another one on Chr. 05 for protein and/or oil. Importantly, this study is the first to report a new genomic locus for both protein and oil mapped to Chr. 08. Gene ontology annotations and expression profiles suggested candidate genes. Further analyses using haplotype-based markers led to the identification of multiple haplotype blocks encompassing candidate genes. Among these, Glyma.05G243400 on Chr. 05 and Glyma.08G109900 and Glyma.08G110000 on Chr. 08 were identified as promising targets. These genes can be incorporated into soybean breeding programs to enhance the selection of desirable protein and oil phenotypes through a haplotype-based breeding approach.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"237"},"PeriodicalIF":4.2,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970243","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}

{"title":"A single-base mutation on the 5' UTR of BrATG5 confers the premature leaf senescence phenotype in Chinese cabbage.","authors":"Zifan Zhao, Xianlei Zhao, Siyu Wu, Yilong Zhang, Hui Feng, Zhiyong Liu, Chong Tan, Xueling Ye","doi":"10.1007/s00122-025-05026-3","DOIUrl":"https://doi.org/10.1007/s00122-025-05026-3","url":null,"abstract":"<p><strong>Key message: </strong>BrATG5 encoding autophagy protein was fine-mapped through MutMap and KASP analysis, and its function in regulating leaf senescence was verified using virus-induced gene silencing and functional complementation assays in Chinese cabbage. Leaf senescence is the final stage of leaf development, and is accompanied by the breakdown of organelle and catabolism of chlorophyll and macromolecules. The generated nutrients are supplied to developing seeds or other growing organs. However, premature leaf senescence will cause a decrease in the yield and quality of leafy head in Chinese cabbage. In this study, a premature leaf senescence mutant M1684 was screened from an ethyl methane sulfonate (EMS) mutagenized population of Chinese cabbage 'FT'. The outer whorl leaves of M1684 showed a premature senescence phenotype from seedling stage, and the yield of leafy head and seed was reduced in M1684. The chloroplast structure and photosynthetic activity of the leaves of M1684 were impaired and programmed cell death (PCD) occurred earlier in M1684 than in 'FT'. Genetic analysis, MutMap and kompetitive allele-specific PCR (KASP) genotyping showed that BraA10g022760.3.5C, which encodes an autophagy protein, was the candidate gene, named BrATG5. The function of BrATG5 in regulating leaf senescence was verified by virus-induced gene silencing (VIGS) and functional complementation assays. 5' rapid amplification of complementary DNA ends (5' RACE) clone, and quantitative real-time PCR (qRT-PCR) assays showed that the single nucleotide polymorphism on the 5' untranslated region (5' UTR) decreased the expression level of BrATG5. BrATG5 interacted with BrATG12 to form a complex. These results suggest that BrATG5 is involved in leaf senescence in Chinese cabbage, and provide a better understanding of the molecular mechanisms of leaf senescence and a clearer theoretical basis for anti-senescence research in Chinese cabbage.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"235"},"PeriodicalIF":4.2,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970082","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}

{"title":"Evolution of population structure in a commercial European hybrid dent maize breeding program and consequences on genetic diversity.","authors":"Romain Kadoumi, Nicolas Heslot, Fabienne Henriot, Alain Murigneux, Mathilde Berton, Laurence Moreau, Alain Charcosset","doi":"10.1007/s00122-025-05008-5","DOIUrl":"https://doi.org/10.1007/s00122-025-05008-5","url":null,"abstract":"<p><strong>Key message: </strong>Differentiation between Stiff Stalk and Non-Stiff Stalk heterotic groups increased significantly over time, while genetic diversity within both groups declined, highlighting the impact of long-term selection in hybrid maize breeding. Differentiation between Stiff Stalk and Non-Stiff Stalk heterotic groups increased significantly over time, while genetic diversity within both groups declined, highlighting the impact of long-term selection in hybrid maize breeding. The separation of germplasm into complementary heterotic genetic pools is fundamental to modern hybrid breeding programs. This approach facilitates the development of high-performing hybrids by maximizing heterosis through crosses of divergent inbred lines. Maintaining heterotic structure ensures continuous genetic gain and selection of divergent alleles, but introducing novel germplasm is equally important to mitigate the risks of diversity loss from repeated selection of elite material. This study presents a large-scale assessment of the evolution of genetic diversity, population structure, and differentiation between heterotic groups, within a private European hybrid dent maize breeding program. Forty years of breeding data and 84,000 genotypes were used. Clustering methods revealed two main heterotic groups in modern germplasm: Stiff Stalks and Non-Stiff Stalks. These two groups originated from Stiff Stalk, Iodent, and Lancaster founders, forming three ancestral groups. Differentiation between heterotic groups was low for early founder inbreds and increased over time. Consistently, intragroup diversity decreased over time, and marker fixation and linkage disequilibrium increased. The main cause of diversity loss germplasm-wide was the merging and genetic homogenization of the ancestral Iodent and Lancaster groups into the modern Non-Stiff Stalk heterotic group. Insights into the genetic relationship between hybrid heterotic group population structure and intragroup diversity can assist breeders in enhancing heterotic group divergence, while preserving diversity across selection cycles. This study provides an overview of the evolution of key genetic metrics, to inform strategies for managing diversity and differentiation in commercial hybrid breeding programs.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"233"},"PeriodicalIF":4.2,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12397178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a dominant stripe rust resistance gene YrXY on chromosome 6R in hexaploid triticale.","authors":"Yu Lin, Yahan Yang, Yichang Gou, Zhenzhen Xue, Genxi Huang, Hongshen Wan, Zhiqiang Wang, Lin Huang, Houyang Kang, Yi Wang, Yonghong Zhou, Haiqin Zhang","doi":"10.1007/s00122-025-05025-4","DOIUrl":"https://doi.org/10.1007/s00122-025-05025-4","url":null,"abstract":"<p><p>Breeding resistant cultivars is the most effective strategy to control stripe rust in cereal crops. The hexaploid triticale line Xinyi is highly resistant to stripe rust at the seedling and adult plant stages. A segregating F₂ population derived from a cross between Xinyi and the susceptible hexaploid triticale cultivar Zhongsi1048 was assessed to understand the genetic architecture of stripe rust resistance. Genetic analysis revealed that an all-stage resistance in Xinyi, temporarily designated YrXY, was caused by a single dominant gene. Based on bulked segregant RNA sequence (BSR-seq) analysis, YrXY was identified at 868.82-883.98 Mb on chromosome 6R. By constructing a genetic map based on newly developed KASP markers, the YRXY locus was reconfirmed and narrowed to a 1.4 cM genetic interval, correspondingly to a 2.03 Mb genomic interval (871.47-873.50 Mb). Thirty-two high-confidence genes were predicted in this genomic region, and the non-specific serine/threonine protein kinase gene SECCE6Rv1G0451190 was the most likely candidate gene based on sequence and expression analysis. Genotyping using KASP markers closely linked to YRXY in a segregating population (F₅) derived from a cross of Xinyi and common wheat line L83 revealed that the stripe rust resistance gene YrXY was stably expressed in a wheat-triticale background. We developed a closely linked, breeder-friendly PCR marker that can be used in marker-assisted breeding for stripe rust resistance in both triticale and wheat.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"234"},"PeriodicalIF":4.2,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970113","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}

{"title":"Foliar disease resistance phenomics of fungal pathogens: image-based approaches for mapping quantitative resistance in cereal germplasm.","authors":"Matthew Ulrich, Linda Brain, Jianqiao Zhang, Anthony R Gendall, Stefanie Lück, Dimitar Douchkov, Eden Tongson, Peter M Dracatos","doi":"10.1007/s00122-025-05017-4","DOIUrl":"https://doi.org/10.1007/s00122-025-05017-4","url":null,"abstract":"<p><p>Host plant resistance is the most effective and environmentally sustainable means of reducing yield losses caused by fungal foliar pathogens of cereal species. Cereal genebank collections hold diverse pools of potentially underutilized disease resistance alleles, and cereal genomic resources are well advanced due to large-scale sequencing and genotyping efforts. Genome-Wide Association Studies (GWAS) have emerged as the predominant association genetics technique to initially discover novel disease resistance loci or alleles in these diverse collections. Traditional disease resistance phenotyping methods are reliant on visual estimation of disease symptom severity and have successfully supported genetic mapping studies either via GWAS or QTL mapping in biparental populations facilitating both marker development and gene cloning efforts. Due to foliar pathogens having a high capacity to evolve, there is a need to pyramid disease resistance genes with diverse mechanisms for durable control. Resistance expressed as a quantitative trait, known as quantitative resistance (QR), is hypothesized to be more durable, unlike major R-gene resistance that is race-specific and can be vulnerable to breaking down without gene stewardship. However, assessing QR visually is challenging, particularly when complicated by complex genotype × environment (G × E) effects in the field. High-throughput image-based phenotyping provides accurate and unbiased data that can support foliar disease resistance screening efforts of genebank collections using GWAS. In this review, we discuss image-based disease phenotyping based on macroscopic (visible symptoms) and microscopic features during the host-pathogen interaction. Quantitative image analysis approaches using conventional and artificial intelligence (AI) algorithms are also discussed.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"232"},"PeriodicalIF":4.2,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12394310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of three quantitative trait loci conferring robust resistance to wheat yellow mosaic virus in the wheat cultivar Shunyou.","authors":"Shota Takata, Goro Ishikawa, Hidekazu Maejima, Yasushi Uehara, Kenta Tsunekawa, Ryoji Suzuki, Shuhei Kato, Norikuni Saka, Chihiro Souma, Mikiko Yanaka, Kazuhiro Nakamura, Hitoshi Matsunaka, Chikako Kiribuchi-Otobe, Koichi Hatta, Hisayo Kojima, Fuminori Kobayashi","doi":"10.1007/s00122-025-05016-5","DOIUrl":"https://doi.org/10.1007/s00122-025-05016-5","url":null,"abstract":"<p><strong>Key message: </strong>Three QTLs for resistance to WYMV were mapped, and the effects of each QTL on three pathotypes were evaluated. The KASP markers identified different origins of these QTLs. Wheat yellow mosaic virus (WYMV) is a soil-borne pathogen, which hampers wheat production in Japan. WYMV is classified into three pathotypes (I-III), with different geographical distributions in Japan. Breeding wheat lines that are resistant to all three pathotypes is crucial for developing broadly adapted cultivars. To elucidate the genetic basis of resistance against WYMV pathotypes I-III, doubled haploid (DH) lines derived from a susceptible cultivar Kitahonami and a resistant cultivar Shunyou that exhibit resistance to all pathotypes were analyzed. Quantitative trait locus (QTL) analysis using phenotypic data from nursery fields, where pathotype I predominates, identified three resistance QTLs, QYm.naro-2A, QYm.naro-6D, and QYm.naro-7A, located on chromosome arms 2AL, 6DL, and 7AS, respectively. Shunyou and DH lines carrying all three QTLs exhibited robust resistance to all pathotypes, whereas partial resistance was observed with one or two QTLs. To facilitate the utilization of these QTLs in breeding programs, three Kompetitive allele-specific PCR (KASP) markers were developed for each QTL. Pedigree analysis of Shunyou suggested that the resistant allele on 2AL originated from domestic parental cultivars, while those on 6DL and 7AS were introduced from foreign cultivars. These KASP markers may be valuable tools for marker-assisted selection, offering the potential to develop wheat cultivars with durable and broad-spectrum resistance to WYMV.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"230"},"PeriodicalIF":4.2,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970100","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}

{"title":"Introgression of stem rust resistance gene Sr68 from Thinopyrum junceum into wheat.","authors":"Swarupa Nanda Mandal, Baljeet K Gill, Zhixia Niu, Qijun Zhang, Daryl L Klindworth, Santiago Bataller, Matthew N Rouse, Yue Jin, Richard R C Wang, Xiwen Cai, Xiaofei Zhang, Roger Thilmony, Yong-Qiang Gu, Amanda Peters Haugrud, Steven S Xu","doi":"10.1007/s00122-025-05005-8","DOIUrl":"https://doi.org/10.1007/s00122-025-05005-8","url":null,"abstract":"<p><strong>Key message: </strong>A new stem rust resistance gene, Sr68, from Thinopyrum junceum was transferred to chromosome arm 1BS of wheat using monosomic-induced Robertsonian translocation and ph1b-induced homoeologous recombination. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is one of the most destructive diseases of wheat (Triticum aestivum L.). Identifying and deploying stem rust resistance (Sr) genes continues as a key strategy for managing this disease. Here, we report the identification and introgression of a novel Sr gene from wheat 'Chinese Spring' (CS)-Thinopyrum junceum group-4 chromosome (designated 4E) disomic addition line HD3505 (2n = 44) to a wheat chromosome. We first developed an F₂ population by crossing HD3505 to a CS line monosomic for chromosome 4D (CS M4D). A stem rust-resistant F₂ plant carrying a Robertsonian translocation chromosome was identified and consecutively backcrossed to CS ph1b and CS to produce a population of 1209 BC₂F₁ plants. Three BC₂F₁ plants with reduced Th. junceum chromatin (BG2133, BG5136, and BG2161) carrying the Sr gene were identified. Genomic and oligonucleotide multiplex fluorescence in situ hybridization analysis revealed that Th. junceum chromosome segments carrying the Sr gene in the three translocation lines were in the distal region of chromosome arm 1BS, with sizes of 33.22-34.51% of the translocation chromosomes. The Sr gene in the translocation lines was designated Sr68. Additionally, the translocation replaced the Gli-B1 locus, eliminating ω-gliadins that encode immunoreactive epitopes, potentially reducing gluten immunogenicity. The newly developed wheat lines with Sr68 and associated molecular markers provide new resistance resources against Ug99 and other Pgt races for wheat improvement.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"229"},"PeriodicalIF":4.2,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970151","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}

{"title":"Climate change and plant genomic plasticity.","authors":"Carlo M Pozzi, Angelo Gaiti, Alberto Spada","doi":"10.1007/s00122-025-05010-x","DOIUrl":"https://doi.org/10.1007/s00122-025-05010-x","url":null,"abstract":"<p><strong>Key message: </strong>Genome adaptation, driven by mutations, transposable elements, and structural variations, relies on plasticity and instability. This allows populations to evolve, enhance fitness, and adapt to challenges like climate change. Genomes adapt via mutations, transposable elements, DNA structural changes, and epigenetics. Genome plasticity enhances fitness by providing the genetic variation necessary for organisms to adapt their traits and survive, which is especially critical during rapid climate shifts. This plasticity often stems from genome instability, which facilitates significant genomic alterations like duplications or deletions. While potentially harmful initially, these changes increase genetic diversity, aiding adaptation. Major genome reorganizations arise from polyploidization and horizontal gene transfer, both linked to instability. Plasticity and restructuring can modify Quantitative Trait Loci (QTLs), contributing to adaptation. Tools like landscape genomics identify climate-selected regions, resurrection ecology reveals past adaptive responses, and pangenome analysis examines a species' complete gene set. Signatures of past selection include reduced diversity and allele frequency shifts. Gene expression plasticity allows environmental adaptation without genetic change through mechanisms like alternative splicing, tailoring protein function. Co-opted transposable elements also generate genetic and regulatory diversity, contributing to genome evolution. This review consolidates these findings, repositioning genome instability not as a mere source of random error but as a fundamental evolutionary engine that provides the rapid adaptive potential required for plant survival in the face of accelerating climate change.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"231"},"PeriodicalIF":4.2,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12390881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}