Theoretical and Applied Genetics最新文献

{"title":"The knockout of ClaCSLH1 induced dwarfing in watermelon.","authors":"Jiancheng Bao, Jiale Shi, Yuanyuan Qin, Shengqi Hua, Yanhong Wu, Congji Yang, Yige Gu, Wei Dong","doi":"10.1007/s00122-025-04909-9","DOIUrl":"https://doi.org/10.1007/s00122-025-04909-9","url":null,"abstract":"<p><p>In agriculture, selecting ideal plant types with desirable traits, such as dwarfing and upright stem structures, significantly enhances crop yield and quality by optimizing light absorption, spatial efficiency, and nutrient utilization. Developing new varieties of dwarf watermelon is a crucial objective in watermelon breeding. In this study, we constructed an F₂ population using the wild-type V063 as the paternal parent and the dwarf variety dw-n as the maternal parent. The dwarfing trait was found to be governed by a pair of recessive alleles. Through bulk segregant analysis sequencing (BSA-seq) and RNA sequencing (RNA-seq), we identified the gene Cla97C02G035450, which encodes cellulose synthase-like H1 (CSLH1), as a candidate gene associated with the dwarfing phenotype. ClaCLSH1 belongs to the ClaCESA/CSLs family, which is involved in the cell wall formation by regulating the synthesis of cellulose and hemicellulose. Microscopic analyses revealed that dw-n exhibited shorter internode cells, thicker cell walls, and elevated hemicellulose content compared to V063. Subcellular localization studies demonstrated that the CLACSLH1 protein is primarily localized in the nucleus and the cell membrane/wall. Notably, the overexpression of CLACSLH1 in the dw-n background rescued its dwarf phenotype. Furthermore, experiments indicated that knockdown of CLACSLH1 resulted in excessive hemicellulose synthesis, inhibited internode cell elongation, and ultimately led to the stunted phenotype observed in dw-n. This research provides innovative insights into the development of superior dwarf watermelon varieties and advances our understanding of the molecular mechanisms underlying watermelon dwarfism.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"120"},"PeriodicalIF":4.4,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094836","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":"Chromosome-level genome assembly of a high-yield Chinese soybean variety Mengdou1137 unlocks genetic potential of disease and lodging resistance.","authors":"Rujian Sun, Bincheng Sun, Zihao Zheng, Qi Zhang, Xingguo Hu, Rongqi Guo, Lei Feng, Shen Chai, Jingshun Wang, Ping Qiu, Ping Yu, Ying Liu, Wei Song, Yinghui Li, Lijuan Qiu","doi":"10.1007/s00122-025-04881-4","DOIUrl":"https://doi.org/10.1007/s00122-025-04881-4","url":null,"abstract":"<p><strong>Key message: </strong>We assembled the genome of Mengdou1137 with high quality and revealed the specific disease resistance genes and a large number of genomic variations related to agronomic traits. As a cornerstone in the global agricultural landscape, soybean stands as a pivotal oilseed crop, underpinning both nutritional and industrial applications. The burgeoning development of novel soybean varieties significantly propels the crop's industrialization, offering enhanced traits that cater to diverse agricultural and commercial needs. In this study, we present the de novo assembly of the genome a high-yield Chinese soybean variety Mengdou1137, employing an integrated approach of both long-read and short-read sequencing technologies to achieve comprehensive genomic insights. Achieving a notable assembly with a genome size of 999.99 Mb, our work features a contig N50 of 14.92 Mb and a scaffold N50 of 50.26 Mb, successfully anchoring 98.24% of sequences across the 20 chromosomes. Through meticulous comparative analysis with existing soybean genomes, our research unveiled 115 Mengdou1137-specific disease resistance genes alongside a substantial array of agronomical trait-associated genomic variants. Among the salient genomic features, we identified a favorable haplotype of the dwarf gene PH13, a critical determinant of plant stature, underscoring its potential for breeding compact soybean varieties with lodging resistance. This high-quality assembly of the Mengdou1137 genome not only enriches the repository of soybean genetic resources but also paves the way for future innovations in soybean breeding and trait improvement, offering valuable insights for the enhancement of this crucial agricultural commodity.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"119"},"PeriodicalIF":4.4,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144080440","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":"Development of Brassica rapa-nigra monosomic alien addition lines: cytology, genetics, and morphology.","authors":"Pengfei Li, Haiyan Wu, Shizhen Guo, Shunlin Wang, Mimi Zhang, Mengyang Liu, Wei Ma, Jianjun Zhao, Chen Tan, Cheng Cui, Xianhong Ge, Zaiyun Li","doi":"10.1007/s00122-025-04899-8","DOIUrl":"https://doi.org/10.1007/s00122-025-04899-8","url":null,"abstract":"<p><strong>Key message: </strong>Brassica rapa-nigra monosomic alien addition lines (MAALs) were developed and compared with B. oleracea-nigra MAALs containing the same B-genome chromosomes. The diploid Brassica nigra (black mustard) is the donor of the B-genome for two allotetraploids: B. juncea (AABB) and B. carinata (BBCC). To dissect the B-genome of B. nigra within the A-genome background of B. rapa, the progenies of resynthesized B. juncea, successively pollinated by the parental B. rapa, were screened using cytological methods and molecular markers. Seven out of eight B. rapa-nigra MAALs (2n = 21, AA + 1B_1-8) were obtained, except for the AA-B6 MAAL. The additional chromosome appeared as one univalent in 86.76% of pollen mother cells and formed one trivalent with two A-genome chromosomes in 13.24% of cells. Different alien B-genome chromosomes were transmitted to progeny at varying rates, with higher transmission rates via female gametes (averaging 13.59%) than via male gametes (7.31%). These MAALs exhibited significant phenotypic variations which were either of parental origins or novel traits, and chromosomal locations of some traits from B. nigra or genetic interactions were realized from the joint results of B. rapa-nigra and B. oleracea-nigra MAALs with the same additional B-subgenome chromosomes. Comparison analyses of these two sets of MAALs provided new insights into the genetic interplay of the B-genome with A- and C-genomes in these two allotetraploids.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"118"},"PeriodicalIF":4.4,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144049299","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 analysis and fine mapping reveal that AhRt3, which encodes an anthocyanin reductase, is responsible for red testa in cultivated peanuts.","authors":"Yanyan Tang, Xiantao Zhou, Xin Li, Cai Zhou, Wenlin Wang, Mo Zhou, Zhicheng Hu, Xiaobei Li, Kaiyuan Zhang, Siming Wang, Zhihao Zhang, Hao Chen, Jingshan Wang, Lixian Qiao","doi":"10.1007/s00122-025-04903-1","DOIUrl":"https://doi.org/10.1007/s00122-025-04903-1","url":null,"abstract":"<p><strong>Key message: </strong>AhRt3, which governs the red testa of peanut, was narrowed down to a 125.30 kb region, and one gene encoding anthocyanin reductase was identified as the putative candidate gene. Testa color is a special characteristic of peanuts (Arachis hypogaea L.), and those with dark testa have been focused on recent years owing to their high-anthocyanin content and increased antioxidant nutritional value. However, the genetic mechanisms underlying this trait remain limited. To identify the gene responsible for the red testa color in peanuts, an F₂ population was constructed by crossing YH91 (pink testa) with JHT1 (red testa). Genetic analysis revealed that the red testa was controlled by a single dominant gene named AhRt3 (Arachis hypogaea Red Testa 3). Through bulked segregant analysis sequencing, AhRt3 was preliminarily mapped to the chromosome Arahy.03 and subsequently narrowed to a 125.30 kb genomic region containing 12 potential candidate genes. RNA-seq analysis revealed that 4,880 genes were differentially expressed in the seed testa, with only the candidate gene Arahy.W8TDEC exhibiting higher expression levels in JHT1 than in YH91. Additionally, sequence variation, functional annotation, and expression profiling confirmed that Arahy.W8TDEC, which encodes an anthocyanin reductase, may be a candidate gene for AhRt3. The structural variation involving an inversion between the sixth exon and the 3'UTR of Arahy.W8TDEC resulted in altered amino acids closely associated with the red testa phenotype in peanuts. In conclusion, this study highlights the role of a novel gene in regulating red testa and contributes valuable insights into the genetic basis of seed testa in peanuts.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"117"},"PeriodicalIF":4.4,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052542","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":"Molecular characterization and validation of adult-plant stripe rust resistance genes in Yunnan hulled wheat (Triticum aestivum ssp. yunnanense King).","authors":"Linyu Huang, Xinyu Wang, Yan Yan, Li Long, Qiushuo Li, Yuexue Wang, Yongjing Liu, Hao Li, Zhien Pu, Wei Li, Qiantao Jiang, Jian Ma, Houyang Kang, Pengfei Qi, Qiang Xu, Yazhou Zhang, Mei Deng, Yuming Wei, Guoyue Chen, Yunfeng Jiang","doi":"10.1007/s00122-025-04906-y","DOIUrl":"https://doi.org/10.1007/s00122-025-04906-y","url":null,"abstract":"<p><strong>Key message: </strong>Three stable QTLs for adult-plant resistance to stripe rust were identified on chromosomes 2DL, 5B, and 7BS in Yunnan hulled wheat, providing durable high-level resistance through additive effects. Yunnan hulled wheat, a unique subspecies native to China, exhibits excellent adult-plant resistance (APR) to stripe rust. However, the genetic basis of stripe rust resistance in Yunnan hulled wheat remains largely unexplored. In this study, we investigated an accession from Lancang County, which has shown stable APR under field conditions for over 10 years. To identify the stripe rust gene of Lancang hulled wheat (LC), we developed 108 F_5:7 recombinant inbred lines (RILs) from the cross LC × Avocet S, followed by multi-environment phenotypic evaluation of APR to stripe rust. Bulked segregant exome capture sequencing and quantitative trait locus (QTL) analysis identified three stable QTLs on chromosomes 2DL (QYr.LC-2DL), 5B (QYr.LC-5B), and 7BS (QYr.LC-7BS), explaining 11.44-15.74%, 11.27-15.31%, and 12.12-20.00% of the phenotypic variance, respectively. To validate these QTLs, we constructed three independent heterogeneous inbred families (HIF) segregating for QYr.LC-2DL, QYr.LC-5B, and QYr.LC-7BS from the RIL populations using QTL-linked molecular markers. Further molecular mapping of these three HIF populations refined the localization of QYr.LC-2DL, QYr.LC-5B, and QYr.LC-7BS to intervals between markers KP2D-617.34 and KP2D-625.65, KP5B-121.75 and KP5B-262.42, and KP7B-52.54 and KP7B-58.54, respectively. Additionally, additive effects were observed for QYr.LC-2DL, QYr.LC-5B, and QYr.LC-7BS, with lines carrying all three loci showing the highest resistance. Moreover, the linked markers of QYr.LC-2DL and QYr.LC-7BS can be effectively utilized for marker-assisted selection in wheat breeding programs. These findings provide valuable insights into the genetic basis of stripe rust resistance in Yunnan hulled wheat and offer germplasm for breeding wheat varieties with durable resistance.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"116"},"PeriodicalIF":4.4,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144014766","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":"QTL mapping and multi-omics identify candidate genes for protein and oil in soybean.","authors":"Xiaomei Fang, Jiaqi Liu, Aohua Jiang, Xi Li, Pingting Tan, Chen Liu, Xuan Gong, Hao Sun, Chengzhang Du, Jijun Zhang, Xiaochun Zhang, Zelin Yi, Fanjiang Kong, Jian Zhang","doi":"10.1007/s00122-025-04904-0","DOIUrl":"https://doi.org/10.1007/s00122-025-04904-0","url":null,"abstract":"<p><strong>Key message: </strong>QTL mapping, BSA-seq, and RNA-seq revealed key QTL/genes of protein and oil, some of which were aligned with previous QTLs. EMS-mutations and SoyGVD were applied to validate function of candidate genes. Protein and oil are the two principal economic components of soybean seed. Although several related genes regulating soybean protein and oil accumulation have been reported, the regulatory mechanisms remain largely unknown. In this study, quantitative trait loci (QTL) mapping was employed using four generations derived from a cross between Changjiangchun 2 (high protein and oil content) and Yushuxian 2 (low protein and oil content), resulting in the detection of 37 QTLs, including 16 QTLs for protein content and 21 QTLs for oil content. BSA-seq was performed on two parents and two offspring extreme pools from F₂ population individuals. Two QTLs, qOIL1.2 and qPRO14.1, were found to overlap with the BSA-seq mapping interval, in which eight genes exhibited single nucleotide polymorphisms (SNPs) or insertion/deletion (InDel) variations within their coding sequences (CDS). RNA-seq was performed on seeds collected at 20, 30, and 40 days after-pollination (DAP) from two extreme pools of F_2:3 population individuals. A total of 199 deferentially expressed genes (DEGs) were obtained within the QTLs regions. In conjunction with previous research, 10 protein and four oil QTLs intervals were aligned with previously identified QTLs. Notably, based on EMS-induced mutation lines and SoyGVD database, 12 potential candidate genes were screened out and preliminary validated the function for oil and protein in soybeans. These findings lay the groundwork for further research into candidate genes and marker-assisted selection (MAS) in soybean breeding to enhance seed protein and oil content.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"115"},"PeriodicalIF":4.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144014542","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":"Correction: Genetic dissection of flowering time and fine mapping of qFT.A02‑1 in rapeseed (Brassica napus L.).","authors":"Yanling Li, Xin Li, Dezhi Du, Qianru Ma, Zhi Zhao, Long Wang, Yongshun Zhang, Huiqin Shi, Hongping Zhao, Huaxin Li, Damei Pei, Zhigang Zhao, Guoyong Tang, Haidong Liu, Haojie Li, Lu Xiao","doi":"10.1007/s00122-025-04902-2","DOIUrl":"https://doi.org/10.1007/s00122-025-04902-2","url":null,"abstract":"","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"114"},"PeriodicalIF":4.4,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033229","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 rare stop-gain SNP mutation in BrGL2 causes aborted trichome development in Chinese cabbage (Brassica rapa L. ssp. pekinensis).","authors":"Biyuan Li, Xiaoya Ding, Zhichen Yue, Yanting Zhao, Juanli Lei, Yunxiang Zang, Qizan Hu, Peng Tao","doi":"10.1007/s00122-025-04905-z","DOIUrl":"https://doi.org/10.1007/s00122-025-04905-z","url":null,"abstract":"<p><strong>Key message: </strong>A rare stop-gain SNP mutation in BrGL2 confers short hair phenotype of Chinese cabbage via bulked-segregant analysis sequencing, fine-mapping and gene silencing analysis. Trichomes negatively affect the quality of Chinese cabbage, a leafy vegetable crop in the family Brassicaceae. The short hair trait is caused by abnormal trichome development. In this study, the BraA07g025490.3C gene was identified as a candidate gene for the short hair trait in Chinese cabbage by BSA-seq and fine-mapping analyses. It was subsequently named BrGL2 because of its strong homology to AtGL2 (At1g79840). Sequence analysis indicated that a C to G single-nucleotide polymorphism (SNP) mutation in the sixth exon of BrGL2 produced a premature stop codon in the HCW (short hair) line, resulting in a loss-of-function mutation of BrGL2. This stop-gain SNP mutation was found exclusively in the HCW line, and not in 524 diverse B. rapa accessions. Further analysis by virus-induced gene silencing showed that the knock-down of BrGL2 in HN19-G lines (wild-type hair) reduced the size of leaf trichomes. BrGL2 affected trichome development probably by impacting the expression of downstream transcription factor genes and cell wall-related genes, as determined by comparative transcriptome analyses of wild type and short hair lines. On the basis of the identification and verification of the key stop-gain SNP mutation in BrGL2 resulting in aborted trichome development in Chinese cabbage, we propose a model for trichome development.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"112"},"PeriodicalIF":4.4,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050167","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":"Prediction of biomass sorghum hybrids using environmental feature-enriched genomic combining ability models in tropical environments.","authors":"Pedro C O Ribeiro, Reka Howard, Diego Jarquin, Isadora C M Oliveira, Saulo Chaves, Pedro C S Carneiro, Vander F Souza, Robert E Schaffert, Cynthia M B Damasceno, Rafael A C Parrella, Kaio Olimpio G Dias, Maria M Pastina","doi":"10.1007/s00122-025-04895-y","DOIUrl":"https://doi.org/10.1007/s00122-025-04895-y","url":null,"abstract":"<p><strong>Key message: </strong>Incorporating environmental features improved the predictive ability of genomic prediction models under multi-environment trials in tropical conditions. Gathering environmental and genomic information can benefit the breeding of sorghum hybrids by overcoming complications imposed by the genotype-by-environment interaction (GEI). In this study, we explored the value of combining environmental features (EFs) and genomic data to enhance predictions for biomass sorghum hybrid breeding, addressing GEI complexities. We also investigated if considering specific time windows for EFs improves the prediction. We used a historical dataset from a tropical biomass sorghum breeding program featuring 253 genotypes across 64 trials. Initially, a first-stage analysis was performed to obtain the adjusted means (EBLUEs) and scrutinize the impact of 29 EFs (geographic, climatic, and soil-related EFs) on GEI. Subsequently, in the second-stage analysis, we used data from 221 hybrids that had both parents genotyped to evaluate the predictive ability and assertiveness of 12 models with different effects. The most relevant EFs included soil organic carbon, insolation on a horizontal surface, longitude, temperature at dew point, and nitrogen content. Across three cross-validation scenarios (CV1, CV0, and CV00), the most effective model encompassed main combining ability effects, GEI, and G <math><mi>ω</mi></math> I (genotype-by-specific environmental effects interaction), utilizing an environmental kinship matrix ( <math><mi>Ω</mi></math> ) derived from mean EF values. Only in CV2, a model with a similar structure but utilizing <math><mi>Ω</mi></math> from specific time windows outperformed others. Our findings highlight the potential of integrating environmental and genomic data to refine predictive models for optimizing biomass sorghum hybrid breeding strategies.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"113"},"PeriodicalIF":4.4,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144013957","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 structure of Ethiopian finger millet landraces and genome-wide association mapping for agronomic and nutritional traits.","authors":"Adane Gebreyohannes, Hussein Shimelis, Davis M Gimode, Prasad Grandham, Vinod Kumar Valluri, Habte Nida, Susan M Moenga, Chris O Ojiewo, Benjamin Kilian, Damaris A Odeny","doi":"10.1007/s00122-025-04892-1","DOIUrl":"https://doi.org/10.1007/s00122-025-04892-1","url":null,"abstract":"<p><p>Finger millet (Eleusine coracana subsp. coracana) (2n = 4x = 36) remains one of the most important millets in East Africa (EA), where it was most likely domesticated along the highlands of Ethiopia and Uganda. The goal of the current study was to understand the population structure of the Ethiopian finger millet landraces and identify quantitative trait nucleotides (QTNs) and haplotypes associated with agronomic and nutritional traits. In a field evaluation across three environments, 448 genotypes were assessed for days to flowering (DTF), days to maturity (DTM), thousand seed weight (TSW), grain yield (GY), stay-green score (STG), and drought score (DrtSc). The harvested grain was analyzed for Fe and Zn contents. A subset of 391 genotypes was skim-sequenced, generating 24,112 high-quality SNPs that were employed for population structure, association mapping, and haplotype analysis. Seventy marker-trait associations were detected including 15 major QTNs with more than 30% phenotypic variance explained (PVE) for all traits except STG and GY. Pleiotropic major QTNs were identified for DTM/DTF and Fe/Zn on chromosomes 9B and 2B, respectively. Haplotype analysis of major QTNs identified 54 significant haplotype blocks and 2 additional haplotypes for a multidrug ABC transporter gene family like protein on chromosome 4A that was associated with PTH. Favorable haplotypes from pleiotropic DTM/DTF and Fe/Zn QTNs were present in 13 and 12 genotypes respectively, majority from Tigray region. Two genotypes from Tigray and one from Amhara harbored favorable haplotypes for DTM/DTF and Fe/Zn. These findings provide invaluable insights for targeted breeding to enhance finger millet resilience, nutritional profile, and yield.</p>","PeriodicalId":22955,"journal":{"name":"Theoretical and Applied Genetics","volume":"138 6","pages":"111"},"PeriodicalIF":4.4,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12062187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144000799","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}