Plant Genome最新文献

{"title":"Optimization of high-throughput marker systems for genomic prediction in alfalfa family bulks.","authors":"Pablo Sipowicz, Mario Henrique Murad Leite Andrade, Claudio Carlos Fernandes Filho, Juliana Benevenuto, Patricio Muñoz, L Felipe V Ferrão, Marcio F R Resende, C Messina, Esteban F Rios","doi":"10.1002/tpg2.20526","DOIUrl":"10.1002/tpg2.20526","url":null,"abstract":"<p><p>Alfalfa (Medicago sativa L.) is a perennial forage legume esteemed for its exceptional quality and dry matter yield (DMY); however, alfalfa has historically exhibited low genetic gain for DMY. Advances in genotyping platforms paved the way for a cost-effective application of genomic prediction in alfalfa family bulks. In this context, the optimization of marker density holds potential to reallocate resources within genomic prediction pipelines. This study aimed to (i) test two genotyping platforms for population structure discrimination and predictive ability (PA) of genomic prediction models (G-BLUP) for DMY, and (ii) explore optimal levels of marker density to predict DMY in family bulks. For this, 160 nondormant alfalfa families were phenotyped for DMY across 11 harvests and genotyped via targeted sequencing using Capture-seq with 17K probes and the DArTag 3K panel. Both platforms discriminated similarly against the population structure and resulted in comparable PA for DMY. For genotyping optimization, different levels of marker density were randomly extracted from each platform. In both cases, a plateau was achieved around 500 markers, yielding similar PA as the full set of markers. For phenotyping optimization, models with 500 markers built with data from five harvests resulted in similar PA compared to the full set of 11 harvests and full set of markers. Altogether, genotyping and phenotyping efforts were optimized in terms of number of markers and harvests. Capture-seq and DArTag yielded similar results and have the flexibility to adjust their panels to meet breeders' needs in terms of marker density.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20526"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787441","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}

{"title":"Optimal implementation of genomic selection in clone breeding programs exemplified in potato: II. Effect of selection strategy and cross-selection method on long-term genetic gain.","authors":"Po-Ya Wu, Benjamin Stich, Stefanie Hartje, Katja Muders, Vanessa Prigge, Delphine Van Inghelandt","doi":"10.1002/tpg2.70000","DOIUrl":"10.1002/tpg2.70000","url":null,"abstract":"<p><p>Different cross-selection (CS) methods incorporating genomic selection (GS) have been used in diploid species to improve long-term genetic gain and preserve diversity. However, their application to heterozygous and autotetraploid crops such as potato (Solanum tuberosum L.) is lacking so far. The objectives of our study were to (i) assess the effects of different CS methods and the incorporation of GS and genetic variability monitoring on both short- and long-term genetic gains compared to strategies using phenotypic selection (PS); (ii) evaluate the changes in genetic variability and the efficiency of converting diversity into genetic gain across different CS methods; and (iii) investigate the interaction effects between different genetic architectures and CS methods on long-term genetic gain. In our simulation results, implementing GS with optimal selected proportions had increased short- and long-term genetic gain compared to any PS strategy. The CS method considering additive and dominance effects to predict progeny mean based on simulated progenies (MEGV-O) achieved the highest long-term genetic gain among the assessed mean-based CS methods. Compared to MEGV-O and usefulness criteria (UC), the linear combination of UC and genome-wide diversity (called EUCD) maintained the same level of genetic gain but resulted in higher diversity and a lower number of fixed QTLs. Moreover, EUCD had a relatively high degree of efficiency in converting diversity into genetic gain. However, choosing the most appropriate weight to account for diversity in EUCD depends on the genetic architecture of the target trait and the breeder's objectives. Our results provide breeders with concrete methods to improve their potato breeding programs.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70000"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11835509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450748","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}

{"title":"A linkage map of Aegilops biuncialis reveals significant genomic rearrangements compared to bread wheat.","authors":"Adam Lampar, András Farkas, László Ivanizs, Kitti Szőke-Pázsi, Eszter Gaál, Mahmoud Said, Jan Bartoš, Jaroslav Doležel, Abraham Korol, Miroslav Valárik, István Molnár","doi":"10.1002/tpg2.70009","DOIUrl":"10.1002/tpg2.70009","url":null,"abstract":"<p><p>Goatgrasses with U- and M-genomes are important sources of new alleles for wheat breeding to maintain yield and quality under extreme conditions. However, the introgression of beneficial traits from wild Aegilops species into wheat has been limited by poor knowledge of their genomes and scarcity of molecular tools. Here, we present the first linkage map of allotetraploid Aegilops biuncialis Vis., developed using 224 F₂ individuals derived from a cross between MvGB382 and MvGB642 accessions. The map comprises 5663 DArTseq markers assigned to 15 linkage groups corresponding to 13 chromosomes. Chromosome 1M^b could not be constructed due to a lack of recombination caused by rearrangements in the MvGB382 accession. The genetic map spans 2518 cM with an average marker density of 2.79 cM. The skeleton map contains 920 segregating markers, divided between the M^b sub-genome (425 markers) and the U^b sub-genome (495 markers). Chromosomes of the M^b sub-genome, originating from Aegilops comosa Sm. in Sibth. et Sm., show well-preserved collinearity with Triticum aestivum L. chromosomes. In contrast, chromosomes of the U^b sub-genome, originating from Aegilops umbellulata Zhuk., exhibit a varying degree of collinearity, with 1U^b, 3U^b, and 5U^b retaining a substantial level of collinearity with Triticum aestivum, while 2U^b, 4U^b, 6U^b, and 7U^b show significant rearrangements. A quantitative trait locus affecting fertility was identified near the centromere on the long arm of chromosome 3M^b, explaining 23.5% of the variance. The genome structure of Aegilops biuncialis, highlighted by the genetic map, provides insights into the speciation within the species and will support alien gene transfer into wheat.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70009"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11863542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143505095","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}

{"title":"A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium.","authors":"Kate E Jaggi, Karol Krak, Helena Štorchová, Bohumil Mandák, Ashley Marcheschi, Alexander Belyayev, Eric N Jellen, John Sproul, David Jarvis, Peter J Maughan","doi":"10.1002/tpg2.70010","DOIUrl":"10.1002/tpg2.70010","url":null,"abstract":"<p><p>The genus Chenopodium L. is characterized by its wide geographic distribution and ecological adaptability. Species such as quinoa (Chenopodium quinoa Willd.) have served as domesticated staple crops for centuries. Wild Chenopodium species exhibit diverse niche adaptations and are important genetic reservoirs for beneficial agronomic traits, including disease resistance and climate hardiness. To harness the potential of the wild taxa for crop improvement, we developed a Chenopodium pangenome through the assembly and comparative analyses of 12 Chenopodium species that encompass the eight known genome types (A-H). Six of the species are new chromosome-scale assemblies, and many are polyploids; thus, a total of 20 genomes were included in the pangenome analyses. We show that the genomes vary dramatically in size with the D genome being the smallest (∼370 Mb) and the B genome being the largest (∼700 Mb) and that genome size was correlated with independent expansions of the Copia and Gypsy LTR retrotransposon families, suggesting that transposable elements have played a critical role in the evolution of the Chenopodium genomes. We annotated a total of 33,457 pan-Chenopodium gene families, of which ∼65% were classified as shell (2% private). Phylogenetic analysis clarified the evolutionary relationships among the genome lineages, notably resolving the taxonomic placement of the F genome while highlighting the uniqueness of the A genome in the Western Hemisphere. These genomic resources are particularly important for understanding the secondary and tertiary gene pools available for the improvement of the domesticated chenopods while furthering our understanding of the evolution and complexity within the genus.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70010"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11869160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143525018","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}

{"title":"Gene mapping and candidate gene analysis of a sorghum sheathed panicle-I mutant.","authors":"Jianling Ao, Ruoruo Wang, Wenzeng Li, Yanqing Ding, Jianxia Xu, Ning Cao, Xu Gao, Bin Cheng, Degang Zhao, Liyi Zhang","doi":"10.1002/tpg2.70007","DOIUrl":"10.1002/tpg2.70007","url":null,"abstract":"<p><p>Panicle exsertion is essential for crop yield and quality, and understanding its molecular mechanisms is crucial for optimizing plant architecture. In this study, the sheathed panicle-I (shp-I) mutant was identified from the ethyl methane sulfonate mutant population of the sorghum [Sorghum bicolor (L.) Moench] variety Hongyingzi (HYZ). While phenotypically similar to the wild type during the seedling stage, shp-I exhibits a significantly shorter peduncle internode at the heading stage. Cytomorphological analysis revealed reduced parenchyma cell size within the mutant's peduncle internode. Phytohormonal profiling showed lower levels of indole-3-acetic acid and higher concentrations of brassinosteroid in the mutant compared to the wild type at the peduncle internode. Genetic analysis confirmed that the mutant phenotype was caused by a recessive single-gene mutation. Through bulked segregant analysis sequencing (BSA-seq) genetic mapping, the causative locus for the mutant phenotype was localized to a 59.65-59.92 Mb interval on chromosome 10, which contains 28 putative genes. Additionally, the gene SbiHYZ.10G230700, which encodes a BTB/POZ and MATH (BPM) domain protein, was identified as a candidate gene. Further analysis revealed that the non-synonymous mutations in the candidate gene were located within the MATH domain, affecting the 3D structure of the protein. In summary, this study provides a new genetic material and candidate genes for future research into the molecular regulation of sorghum peduncle length.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70007"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544198","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}

{"title":"Phytocytokine genes newly discovered in Malus domestica and their regulation in response to Erwinia amylovora and acibenzolar-S-methyl.","authors":"Marie-Charlotte Guillou, Matthieu Gaucher, Emilie Vergne, Jean-Pierre Renou, Marie-Noëlle Brisset, Sébastien Aubourg","doi":"10.1002/tpg2.20540","DOIUrl":"10.1002/tpg2.20540","url":null,"abstract":"<p><p>Phytocytokines belong to a category of small secreted peptides with signaling functions that play pivotal roles in diverse plant physiological processes. However, due to low levels of sequence conservation across plant species and poorly understood biological functions, the accurate detection and annotation of corresponding genes is challenging. The availability of a high-quality apple (Malus domestica) genome has enabled the exploration of five phytocytokine gene families, selected on the basis of their altered expression profiles in response to biotic stresses. These include phytosulfokine, inflorescence deficient in abscission/-like, pathogen-associated molecular pattern induced secreted peptide, plant peptide containing sulfated tyrosine, and C-terminally encoded peptide. The genes encoding the precursors of these five families of signaling peptides were identified using a customized bioinformatics protocol combining genome mining, homology searches, and peptide motif detection. Transcriptomic analyses showed that these peptides were deregulated in response to Erwinia amylovora, the causal agent of fire blight in pome fruit trees, and in response to a chemical elicitor (acibenzolar-S-methyl). Finally, gene family evolution and the orthology relationships with Arabidopsis thaliana homologs were investigated.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20540"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142795947","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}

{"title":"Identification and characterization of a novel QTL for barley yellow mosaic disease resistance from bulbous barley.","authors":"Yi Hong, Hui Zhou, Mengna Zhang, Yuhang Zhang, Juan Zhu, Chao Lv, Baojian Guo, Feifei Wang, Qingliang Li, Jie Sun, Rugen Xu","doi":"10.1002/tpg2.20557","DOIUrl":"10.1002/tpg2.20557","url":null,"abstract":"<p><p>Winter barley (Hordeum vulgare) production areas in the middle and lower reaches of the Yangtze River are severely threatened by barley yellow mosaic disease, which is caused by Barley yellow mosaic virus and Barley mild mosaic virus. Improving barley disease resistance in breeding programs requires knowledge of genetic loci in germplasm resources. In this study, bulked segregant analysis (BSA) identified a novel major quantitative trait loci (QTL) QRym.ZN1-7H for barley yellow mosaic disease resistance in an F₂ population derived from the cross between \"Nongke 1-6\" (H. vulgare) and \"Zaoshu 3\" (H. vulgare). This QTL, originating from bulbous barley (Hordeum bulbosum), demonstrated stability and was further validated in another F₂ population derived from the cross between \"Nongke 2-6\" (H. vulgare) and \"Supi 1\" (H. vulgare). QRym.ZN1-7H accounted for 10.61%-19.34% of the phenotypic variance. The QTL was further fine mapped to the 14- to 39-Mb interval on barley chromosome 7H. Transcriptome analysis identified 53 and 35 differentially expressed genes in roots and leaves (at QRym.ZN1-7H locus), respectively, with nine genes differentially expressing in both tissues. HORVU.MOREX.r3.7HG0650990, a member of the disease resistance protein family (NBS-LRR class), is the most likely candidate gene for QRym.ZN1-7H. Enrichment analysis indicated that QRym.ZN1-7H may be involved in signal transduction in plant innate immune response. This study laid a foundation for barley disease resistance breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e20557"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143056139","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}

{"title":"Assessment of potential candidate genes for partial resistance to Sclerotinia stem rot caused by Sclerotinia sclerotiorum using real-time quantitative PCR.","authors":"Deus Mugabe, Mohsen Yoosefzadeh Najafabadi, Christopher Grainger, Istvan Rajcan","doi":"10.1002/tpg2.20561","DOIUrl":"10.1002/tpg2.20561","url":null,"abstract":"<p><p>Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib) de Bary (S. sclerotiorum), is one of the most important diseases that causes significant soybean [Glycine max (L.) Merr.] seed yield and quality losses in Canada and globally. Initiation of plant defense mechanisms is crucial for establishing partial resistance to the pathogenic fungus. To understand plant response to S. sclerotiorum, we conducted a temporal (1, 3, and 5 days post-inoculation [DPI]) assessment of gene expression changes in the stem of soybean genotypes with contrasting phenotypic response. We focused on four genes that have been previously reported as associated with SSR partial resistance and are known to be involved in defense-related functions such as cell wall modification, signaling, response to wounding, and response to fungus. The results showed a higher and earlier expression of the genes in partially resistant cultivars compared to the susceptible. Expression of some genes increased up to 11- (Glyma.02G059700) to 16-fold (Glyma.09G232100) by 3 DPI in the partially resistant cultivar, OAC Drayton, while the genes were generally downregulated in the susceptible cultivar, OAC Shire, at the same DPI. This study improves our understanding of expression patterns of genes involved in plant defense against fungal pathogens in soybean. More importantly, the knowledge of genes that are essential in defense against S. sclerotiorum can be used to fine-map the quantitative trait loci for SSR resistance and facilitate accelerated breeding of SSR-resistant cultivars through gene-based marker-assisted selection.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e20561"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143256758","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}

{"title":"Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement.","authors":"Amanda R Peters Haugrud, Jyoti Saini Sharma, Qijun Zhang, Andrew J Green, Steven S Xu, Justin D Faris","doi":"10.1002/tpg2.20398","DOIUrl":"10.1002/tpg2.20398","url":null,"abstract":"<p><p>Durum wheat (Triticum turgidum ssp. durum L.) is an important world food crop used to make pasta products. Compared to bread wheat (Triticum aestivum L.), fewer studies have been conducted to identify genetic loci governing yield-component traits in durum wheat. A potential source of diversity for durum is its immediate progenitor, cultivated emmer (T. turgidum ssp. dicoccum). We evaluated two biparental populations of recombinant inbred lines (RILs) derived from crosses between the durum lines Ben and Rusty and the cultivated emmer wheat accessions PI 41025 and PI 193883, referred to as the Ben × PI 41025 (BP025) and Rusty × PI 193883 (RP883) RIL populations, respectively. Both populations were evaluated under field conditions in three seasons with an aim to identify quantitative trait loci (QTLs) associated with yield components and seed morphology that were expressed in multiple environments. A total of 44 and 34 multi-environment QTLs were identified in the BP025 and RP883 populations, respectively. As expected, genetic loci known to govern domestication and development were associated with some of the QTLs, but novel QTLs derived from the cultivated emmer parents and associated with yield components including spikelet number, grain weight, and grain size were identified. These QTLs offer new target loci for durum wheat improvement, and toward that goal, we identified five RILs with increased grain weight and size compared to the durum parents. These materials along with the knowledge of stable QTLs and associated markers can help to expedite the development of superior durum varieties.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20398"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50159101","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}

{"title":"Molecular markers enhance substantially the distinctness of alfalfa varieties for registration and protection.","authors":"Paolo Annicchiarico, Nicolò Franguelli, Barbara Ferrari, Giacomo Campanella, Stefano Gualanduzzi, Margherita Crosta, Chiara Delogu, Giorgia Spataro, Nelson Nazzicari","doi":"10.1002/tpg2.20556","DOIUrl":"10.1002/tpg2.20556","url":null,"abstract":"<p><p>Plant varieties must satisfy distinctness, uniformity, and stability (DUS) requirements for registration. Morphophysiological trait-based distinctness may be challenging for cultivars of major perennial forages. Our study focused on alfalfa (Medicago sativa L. subsp. sativa) with the aims of (a) comparing morphophysiological distinctness with molecular distinctness based on genotyping-by-sequencing (GBS) or the alfalfa DArTag panel, envisaging different statistical criteria for molecular distinctness, and (b) assessing the consistency of morphophysiological and molecular cultivar diversity. The 18 most grown Italian varieties were jointly reevaluated morphophysiologically and were characterized molecularly using three bulked DNA samples of 200 independent genotypes per cultivar. Morphophysiological distinctness was limited by correlations between traits and resulted in 39 non-distinct cultivars in 153 paired comparisons and three cultivars distinct from any other. Best configurations for molecular distinctness featured about 10-fold more polymorphic markers and 10-fold lower average read depth per marker for GBS compared to DArTag. DArTag markers allowed for somewhat better variety distinction than GBS. They reduced to 11 the non-distinct cultivars in paired comparisons and increased to 11 the completely distinct cultivars, based on a principal components analysis of allele frequencies followed by analyses of variance on cultivar principal component scores. This criterion achieved greater variety distinctness than cluster analysis with bootstrap values, discriminant analysis, or analysis of molecular variance. Morphophysiologically distinct cultivars were generally distinct molecularly, but not the reverse. Mantel's test revealed a modest consistency across morphophysiological and DArTag (r = 0.39) or GBS-based (r = 0.46) measures of cultivar Euclidean distance. Our results and other considerations strongly encourage the adoption of molecular distinctness for alfalfa DUS.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e20556"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11795343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190858","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}