Theoretical and Applied Genetics最新文献

{"title":"Tuning starch granule size distributions in durum wheat using genetic variation at a single locus.","authors":"Brendan Fahy, Jiawen Chen, David Seung","doi":"10.1007/s00122-025-05013-8","DOIUrl":"https://doi.org/10.1007/s00122-025-05013-8","url":null,"abstract":"<p><strong>Key message: </strong>Different missense mutations in TtMRC-A1 can be used to fine-tune granule size distributions in durum wheat grains, creating useful alterations in starch properties. The size distribution of starch granules in wheat grains influences bread- and pasta-making quality, as well as nutritional properties. Here, we demonstrate that in durum wheat, wide variation in starch granule size distributions can be induced through missense mutations at a single genetic locus encoding the MYOSIN RESEMBLING CHLOROPLAST PROTEIN on chromosome 6A (TtMRC-A1). We isolated 29 independent TILLING mutants in durum cultivar Kronos, each harbouring a different missense mutation that causes an amino acid substitution in the MRC protein. Compared to the B-type granule content of wild-type Kronos (24%), six of the missense lines had significant increases in B-type granule content (33-42%), although not to the extent observed in the mrc-1 mutant (58%) which carries a premature stop codon mutation. Notably, one missense line had significantly decreased B-type granule content (15%), demonstrating that mutations in TtMRC-A1 can achieve both increases and decreases in B-type granule content. In these lines, A-type granule size decreased as B-type granule content increased, and Rapid Visco Analysis on selected lines demonstrated that both B-type granule content and A-type granule size strongly correlated with pasting parameters (e.g. peak viscosity and pasting temperature). However, strong correlations between pasting properties and A-type granule size were still observed after removing most of the B-type granules via sieving, indicating that A-type granule size is the primary contributor to the observed variation in pasting properties. Overall, we demonstrate that mutations at TtMRC-A1 can greatly extend the range of granule size distributions in durum wheat, creating useful alterations in starch properties.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"227"},"PeriodicalIF":4.2,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12379660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970294","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":"Homoeologous recombination-based transfer and cytological mapping of the novel powdery mildew resistance gene Pm7C from Aegilops caudata.","authors":"Yueming Ren, Mengzhen Luo, Yajun Feng, Qifan Chen, Chao Ma, Wenxuan Liu, Fu Guo, Qianwen Liu, Muhammad Amjad, Ranran Jia, Xinpei He, Xiang Ji, Yanlong Zhao, Weixiu Kong, Mengqing Guo, Luna Tao, Zheng Yang, Kai Han, Guihong Yin, Sunish K Sehgal, Yue Zhao, Jinpeng Zhang, Huanhuan Li","doi":"10.1007/s00122-025-05015-6","DOIUrl":"https://doi.org/10.1007/s00122-025-05015-6","url":null,"abstract":"<p><strong>Key message: </strong>A novel powdery mildew resistance gene Pm7C from Aegilops caudata was introgressed into common wheat through ph1b-induced homoeologous recombination and mapped to the 7CL bin FL 0.90-0.96 on chromosome 7C. Wheat powdery mildew poses a significant threat to wheat grain yield and quality. Developing resistant wheat varieties through the deployment of resistance genes is the most effective, economically feasible, and environmentally sustainable strategy to combat this disease. Aegilops caudata (2n = 2x = 14, CC), a wild relative of common wheat, has been identified as a valuable genetic resource harboring novel resistance loci. Specifically, chromosome 7C of Ae. caudata carries a novel broad-spectrum resistance gene, tentatively designated as Pm7C. However, the structural variations in chromosome 7C, coupled with the unavailability of a reference genome for Ae. caudata, have hindered the introgression of this resistance gene into common wheat and its mapping. In this study, we report the development of wheat-Ae. caudata 7C recombinants via ph1b-induced homoeologous recombination and the cytological mapping of the resistance gene Pm7C. By integrating the analysis of 69 7C-specific markers with breakpoint mapping of 7C recombinants using in situ hybridization, we characterized 35 wheat-Ae. caudata 7C recombinants, categorizing them into 10 distinct types. This enabled the construction of a physical map of 7C, comprising nine chromosomal bins defined by 69 specific markers. Subsequent evaluation of powdery mildew resistance in these recombinants mapped Pm7C to the long arm of 7C within the interval of FL 0.90-0.96. Additionally, terminal recombinant 7CT1 (T7DL.7DS-7CL) and intercalary recombinant 7CT4 (Ti7DL.7DS-7CL-7DS) were identified as containing small 7CL segments that harbor Pm7C. These resources are expected to facilitate wheat disease-resistant breeding and further efforts in cloning and elucidating the resistance mechanism of Pm7C.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"228"},"PeriodicalIF":4.2,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970130","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":"Harnessing big data for enhanced genome-wide prediction in winter wheat breeding.","authors":"Ravindra Reddy Gundala, Ulrike Avenhaus, Jost Doernte, Wera Maria Eckhoff, Jutta Foerster, Mario Gils, Michael Koch, Martin Kirchhoff, Sonja Kollers, Nina Pfeiffer, Matthias Rapp, Monika Spiller, Valentin Wimmer, Markus Wolf, Yusheng Zhao, Jochen Christoph Reif","doi":"10.1007/s00122-025-05007-6","DOIUrl":"https://doi.org/10.1007/s00122-025-05007-6","url":null,"abstract":"<p><strong>Key message: </strong>By combining data from different public and private breeding programs for genomic selection, we have increased the size and diversity of the training population, which has led to better predictions of grain yield and plant height in winter wheat compared to using individual training sets. The accuracy of genome-wide prediction is anticipated to improve with an increase in training population size. In our study, we assembled a comprehensive wheat data set consisting of about 18,000 inbred lines and phenotypic data from about 250,000 plots. We evaluated the potential to train genome-wide prediction models using this big data set through data from post-registration trials conducted across a wide range of environments. Our findings demonstrated that using big data can enhance the prediction ability by up to 97% for grain yield and 44% for plant height, outperforming individual training sets. This improvement is primarily attributed to the expansion of the training set size relative to the genetic diversity. In conclusion, big data holds significant potential to accelerate genetic gain in winter wheat predictive breeding, making it a compelling option.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"224"},"PeriodicalIF":4.2,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12373547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970059","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":"Molecular characterization of a new wheat-Thinopyrum ponticum translocation line with resistance to stripe rust.","authors":"Chengzhi Jiang, Yujie Luo, Yile Qi, Li Li, Tingting Jiang, Ennian Yang, Guangrong Li, Zujun Yang","doi":"10.1007/s00122-025-05018-3","DOIUrl":"https://doi.org/10.1007/s00122-025-05018-3","url":null,"abstract":"<p><p>Stripe rust (Puccinia striiformis f. sp. tritici) is a globally devastating foliar disease affecting common wheat. The development of new wheat varieties with novel and durable stripe rust resistance through wide hybridization represents a sustainable and cost-effective strategy for controlling the disease. Thinopyrum ponticum (Podp.) Barkworth & D.R. Dewey, a polyploid species in the tertiary genetic pool of wheat, harbors multiple disease resistance genes, and has been widely utilized for wheat improvement. We previously identified a wheat-Th. ponticum 6J^S (6B) substitution line X005 with novel stripe rust resistance, which was derived from the wheat-Th. ponticum partial amphiploid Xiaoyan7430. In the present study, the chromosome compositions of Xiaoyan7430 and X005 were precisely characterized using non-denaturing - fluorescence in situ hybridization (ND-FISH) and Oligo-FISH painting. Notably, chromosome 6J^S in X005 displayed distinctly different ND-FISH patterns compared to other reported Th. ponticum-derived 6Ae chromosomes introduced into various wheat backgrounds. To physically localize the 6J^S-derived stripe rust resistance gene from X005, we isolated a set of wheat-6J^S deletion and translocation lines after extensive screening of the progenies of crosses between X005 and susceptible wheat cultivars. Using 75 molecular markers, we established a cytological bin map for chromosome 6J^S of X005. Resistance evaluation combined with molecular mapping revealed that the critical resistance locus resides in bin 6J^SS-2 (FL 0.53-0.67) on the 6J^S short arm, corresponding to the 74.51-135.61 Mb genome region of Th. elongatum chromosome 6E. This locus confers stripe rust resistance at both the seedling and adult-plant stages. Translocation T6J^SS·6BL had enhanced Yr resistance and increased tiller numbers without any obvious negative effect on agronomic traits. Thus, the newly developed wheat-Th. ponticum 6J^S translocation lines represent novel germplasm resources for the breeding of disease-resistant wheat cultivars.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"226"},"PeriodicalIF":4.2,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970231","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 and utilization of a novel large-effect QTL and linked markers for enhancing protein concentration in peanut.","authors":"Mingjun Wang, Jianbin Guo, Gaorui Jin, Taihua Yang, Weigang Chen, Yuning Chen, Li Huang, Huaiyong Luo, Xiaojing Zhou, Boshou Liao, Huifang Jiang, Nian Liu, Yong Lei","doi":"10.1007/s00122-025-05000-z","DOIUrl":"https://doi.org/10.1007/s00122-025-05000-z","url":null,"abstract":"<p><strong>Key message: </strong>A novel large-effect QTL qPCB03 for protein concentration was identified, and a KASP marker linked to qPCB03 was developed and validated to enhance protein concentration by 1.23 to 1.57 percentage points in the RIL populations. Peanut is a vital source of protein for humans, playing a key role in maintaining a steady protein supply. In this study, the high-protein cultivar Zhonghua6 (29.14 ± 1.69%) was crossed with Xuhua13 (24.55 ± 1.84%) to construct a recombinant inbred line (RIL) population. The protein concentration of the RIL population exhibited significant variation, ranging from 21.05 to 30.28%. To discover genomic regions associated with protein concentration, four libraries were constructed (two parents and two extreme bulks) for bulked segregant sequencing (BSA-seq). The results revealed significant associations between protein concentration and the genomic regions on chromosomes A07, A10, B03, and B10. Through linkage analysis, nine QTLs (quantitative trait loci) for protein concentration were identified, among which the large-effect and stable QTL qPCB03 on chromosome B03 (125.92-127.94 Mb) explained 11.03-12.86% of the phenotypic variation. This QTL (qPCB03), simultaneously identified by both BSA-Seq and linkage mapping, had not been documented in prior studies. Within the ~ 2 Mb interval of qPCB03, a total of 349 genomic variants were discovered, including six single nucleotide polymorphisms (SNPs) that resulted in nonsynonymous mutations in six genes. Based on genomic variants of the target region, KASP markers were developed and validated in 147 peanut varieties exhibiting variable seed protein concentration. According to the marker-assisted selection, favorable genotypes could potentially enhance protein concentration by 1.23-1.57 percentage points in the RIL populations. The identification of stable loci and the development of markers facilitate marker-assisted breeding in peanuts, while the discovery of candidate genes lays the groundwork for the fine mapping of key genes regulating protein concentration.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"223"},"PeriodicalIF":4.2,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970140","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":"Improved bivariate analysis of canola survivability against blackleg disease.","authors":"Timothy Thavarajah, James Walter, Julian Taylor","doi":"10.1007/s00122-025-04993-x","DOIUrl":"https://doi.org/10.1007/s00122-025-04993-x","url":null,"abstract":"<p><strong>Key message: </strong>The bivariate analysis of canola survivability against blackleg disease with marker-based genomic information, a flexible residual variance model, and a novel selection measure can improve genetic gain for blackleg resistance. Canola (Brassica napus) is an important oilseed crop grown extensively worldwide. It is deleteriously affected by the pathogen Leptosphaeria maculans, commonly known as blackleg, causing up to 15% yield loss in Australia annually. The most effective way to manage this disease is by growing resistant varieties. Screening genotypes for blackleg resistance has typically involved deriving percentage survivability against blackleg (from plant counts at emergence and maturity) and conducting a univariate analysis. More comprehensive approaches have involved a bivariate analysis that accounts for the correlation between plant counts. In this research, we have collated a new dataset from disease nurseries within a commercial breeding programme, comprised of related genotypes evaluated over 3 years at four locations across Australia, and outlined an innovative bivariate analysis approach. The research objectives were to (1) incorporate genomic marker information; (2) apply a more flexible residual model; and (3) develop a novel selection measure, responsiveness to blackleg disease, from the bivariate regression. Moderate to strong genetic correlations were found between traits, ranging between 0.49 and 0.91. The incorporation of genomic markers benefitted the maturity count more than emergence count. Furthermore, the more flexible residual model significantly improved model fit in five experiments. Using responsiveness as a selection measure produced comparable rankings with the univariate analysis of per cent survivability, with some re-ranking of genotypes which reflects the improved analysis through the bivariate approach. Ultimately, these results demonstrate an improvement over historic analyses, thus encouraging their adoption in canola breeding programmes to accelerate genetic gain for blackleg resistance.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"225"},"PeriodicalIF":4.2,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12373551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970220","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 an adaptor protein 2σ gene for OsTGW12 to determine grain weight and potentiate quality breeding in rice.","authors":"Xiaoqiong Li, Huangai Li, Ke Xie, Jinling Han, Kaiqiang Liu, Ying Chen, Jingang Qi, Hongpei Jin, Hanhua Tong, Aihua Sha, Sibin Guo","doi":"10.1007/s00122-025-05022-7","DOIUrl":"https://doi.org/10.1007/s00122-025-05022-7","url":null,"abstract":"<p><strong>Key message: </strong>This study identified an adaptor protein gene OsAP2σ (LOC_Os12g10560) as a causal gene for OsTGW12, a major QTL on rice chromosome to determine the thousand-grain weight (TGW), elucidated the role of a specific SNP (G266A) within this gene in determining grain size by affecting cell number, and the demonstrated interaction between OsAP2σ and OsSAMS1 suggested a novel regulatory mechanism linking clathrin-mediated endocytosis (CME) to S-adenosylmethionine metabolism in rice grain development. In rice, many quantitative trait loci/genes of thousand-grain weight (TGW) have been identified and applied to breed rice varieties with high yield. Here, we identified an allele OsAP2σ^89G from a small grain indica rice variety G1025, a causal gene for OsTGW12 on rice chromosome 12 to determine grain weight. AP2σ is an adaptor protein (AP) subunit 2σ involved in the clathrin-mediated endocytosis (CME) in eukaryotic cells. Moreover, overexpression of the allele K1561-OsAP2σ^89E but not the allele G1025-OsAP2σ^89G increased grain length, grain width and grain weight than the wild type G1025 whereas the RNAi-mediated OsAP2σ mutant showed the opposites. Co-immunoprecipitation mass spectrometry (Co-IP-MS), yeast two-hybrid (Y2H), and luciferase implementation (LUC) assays demonstrated the interaction between OsAP2σ and S-adenosylmethionine synthetase (OsSAMS1), a key enzyme involved in methionine metabolism pathway. In addition, both OsAP2σ and OsSAMS1 were localized into the plasma membrane (PM) and nucleus. Transcriptomic analysis revealed that OsAP2σ regulated the expressions of related genes to CME, mitogen activated protein kinase (MAPK) signaling, and auxin transport and transcriptional regulation during rice grain development. Thus, this study reveals a new role of OsAP2σ and provides a potential in further breeding programs of the quality improvement in rice.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"221"},"PeriodicalIF":4.2,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970086","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":"Genetic control of stem elongation in common bean and the influence of age and flowering time.","authors":"Chantelle J Beagley, Jacqueline K Vander Schoor, Jakob B Butler, James L Weller","doi":"10.1007/s00122-025-04996-8","DOIUrl":"https://doi.org/10.1007/s00122-025-04996-8","url":null,"abstract":"<p><strong>Key message: </strong>Genetic analysis of stem elongation in common bean identified loci acting at different developmental stages and reveals interactions with flowering time. Stem internode elongation is a major determinant of growth habit and plant height, and is often responsive to environmental signals, making it an integral component of plant architecture and a core characteristic targeted for crop improvement. More effective exploitation of stem elongation requires increased understanding of not only major determinants, but also of more subtle, specific influences as breeders seek to further refine adaptation to local growing environments. Common bean is a globally important legume crop and exhibits extensive variation in stem elongation, but there is little knowledge about the underlying genetic control. To better understand this trait, we performed a comprehensive genetic analysis in a wide F₂ cross between wild and domesticated bean. By conducting quantitative trait locus (QTL) analyses of the length of individual internodes, we discovered four main genomic regions influencing internode length at different stages of development. Of these, one demonstrated strong association with the two known flowering genes Fin and Ppd on chromosome 1, while two other regions were validated in subsequent F₃ and F₄ generations and were demonstrated to be independent of flowering time. These results highlight the complex dynamic nature and potential pleiotropic interactions of elongation genes throughout development, and indicate new avenues of inquiry towards improving crop adaptation to specific environments.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"222"},"PeriodicalIF":4.2,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12370798/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970145","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":"The National Plant Germplasm System cotton collection-a review of germplasm resources, phenotypic characterization, and genomic variation.","authors":"Lori L Hinze, Joshua A Udall, John Z Yu, James E Frelichowski","doi":"10.1007/s00122-025-05009-4","DOIUrl":"https://doi.org/10.1007/s00122-025-05009-4","url":null,"abstract":"<p><p>This review is an investigation of the status of phenotypic and molecular characterization efforts in the National Plant Germplasm System (NPGS) cotton collection, highlighting progress to date to maximize the efficiency and effectiveness of future characterization efforts. We considered recent publications of large-scale characterization activities involving the cotton collection. Reports of qualitative descriptors and quantitative phenotypes were considered as well as reports of molecular genotypes. Approximately 80% of cotton accessions are characterized with standardized descriptors and digital images; in addition, large numbers of accessions have recently been screened for resistance to Fusarium wilt, bacterial blight, and cotton leaf curl virus. Many studies have measured genotypes of accessions using a range of technologies-31% of accessions have been genotyped using simple sequence repeat markers, 5% have been genotyped with single nucleotide polymorphism (SNP) arrays, 7% have been genotyped with SNPs from resequencing, and 0.2% of accessions have been sequenced genomically de novo. These efforts ensure that valuable genetic resources are well-characterized, although only a small fraction of the genetic variability in the cotton collection has been surveyed to date. The integration of NPGS cotton collection resources with phenotypic and genotypic information has illuminated the value of cotton genetic variation and genes associated with important traits such as disease resistance and stress tolerance. The cotton collection is a premier information source and critical foundation of variation essential for cotton research and breeding programs aimed at developing resilient cultivars with superior yield and fiber quality in support of U.S. cotton production.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"220"},"PeriodicalIF":4.2,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970166","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":"Transferability of genomic prediction models across market segments in potato and the effect of selection.","authors":"Kathrin Thelen, Po-Ya Wu, Nadia Baig, Vanessa Prigge, Julien Bruckmüller, Katja Muders, Bernd Truberg, Stefanie Hartje, Juliane Renner, Delphine Van Inghelandt, Benjamin Stich","doi":"10.1007/s00122-025-05004-9","DOIUrl":"https://doi.org/10.1007/s00122-025-05004-9","url":null,"abstract":"<p><p>Genomic prediction (GP) can help increase the efficiency of breeding programs, as genotypes can be selected based on their predicted performance. However, to the best of our knowledge, this procedure is not yet routine in commercial breeding programs in tetraploid organisms like potato (Solanum tuberosum L.). The objectives of this study were to (i) Estimate the prediction accuracy for 26 different potato traits in a panel of about 1000 genotypes based on 202,008 single nucleotide polymorphisms, (ii) Evaluate the influence of the size and constitution of the training set on the prediction accuracy, and (iii) Investigate how the effect of selection in the training set influences the outcome of GP. GP revealed high prediction accuracies using genomic best linear unbiased prediction. Our results indicated that a training set of 280-480 clones and 10,000 markers was sufficient. Prediction within a specific market segment led to a higher prediction accuracy compared to adding clones from other market segments to the training set or to predict between different market segments. Lastly, we found a higher prediction accuracy when in a training set of selected clones, i.e., a training set that consists of clones with high trait values, 20% of the clones were replaced by clones that were sampled from the clones that showed the lowest 10% trait values. This observation shows that clones from advanced breeding stages can be used as training set, if some clones specifically from the other side of the distribution range are added to the training set.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 9","pages":"219"},"PeriodicalIF":4.2,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12367938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144970329","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}