Molecular Breeding最新文献

{"title":"Elucidating the genetic architecture of yield components in pyramidale wheat (<i>Triticum turgidum</i> L.): a comparative approach using QTL analysis and genomic selection.","authors":"Tiantian Chen, Kazusa Nishimura, Kazuki Murata, Takanori Yoshikawa, Kyoka Nagasaka, Takahiro Maki, Ko Motoki, Yu Kinoshita, Yu Iwahashi, Hiromo Inoue, Tetsuya Nakazaki, Ryohei Nakano","doi":"10.1007/s11032-026-01728-8","DOIUrl":"10.1007/s11032-026-01728-8","url":null,"abstract":"<p><p>Wheat grain yield is determined by three primary components, one of which is grain number per spike (GPS; or spike fertility). GPS is further determined by spikelet number per spike (StPS) and grain number per spikelet (GPSt). TN28, a pyramidale wheat accession, produces up to five grains per spikelet, substantially exceeding the number in typical cultivars. To elucidate the genetic architecture underlying TN28's superior traits and determine the optimal breeding strategy for trait introgression, we evaluated yield-related traits in a biparental F₂ population derived from TN28 × Langdon across three environments over two years using quantitative trait locus (QTL) mapping and genomic selection (GS). QTL analysis using two mapping approaches detected no stable QTLs other than known flowering genes, indicating that TN28's yield-related traits cannot be reliably introgressed via single- or few-marker selection. Conversely, GS using five prediction models demonstrated potential for accumulating favorable minor-effect alleles. The ridge regression model exhibited optimal performance for GPSt-related traits, with the top 20% of individuals selected on the basis of genomic estimated breeding values (GEBVs) achieving approximately 9% higher grain number per spikelet at the basal section (GPStB) and 7% higher grain number per spike (GPS) relative to the population mean. These results support that QTL mapping is effective for traits controlled by a single major-effect gene, whereas GS offers a more powerful strategy for traits controlled by multiple minor-effect genes. This study suggests that TN28's superior yield-related traits may arise from the cumulative contribution of numerous minor-effect genes and establishes GS as the preferred tool for their improvement in breeding programs.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01728-8.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"108"},"PeriodicalIF":3.6,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13672774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149216471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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":"DNA injection through coleoptile; a choice to overcome species barrier and bring about rapid expansion of gene pool in rice.","authors":"Un-Hyang Ho, Yong-Il Choe, Sam-Rang Song, Kang Kim, Kwang Ri, Kuk-Myong Yo, Myong-Ryong Kim","doi":"10.1007/s11032-026-01729-7","DOIUrl":"10.1007/s11032-026-01729-7","url":null,"abstract":"<p><p>Selection and breeding of rice varieties depend on genetic diversity contained in the primary and secondary gene pools. So far, researches on introduction of total DNA by means of pollen tube pathway method, ovary injection, seed sink method, ion beam mediated transformation method so as to contribute to expansion of gene pool have been reported in rice. In this study, we injected millet DNA into primary leaf-drawn coleoptile surrounding shoot apical meristem so that we could introduce foreign DNA more easily and not to disturb growth of rice. In the following generations, we selected strain MR-4 exhibiting shortened growth period and more tillers. Although MR-4 exhibited short growth period than DNA recipient, Sohaechal 16, its yield was not significantly different from DNA recipient apparently due to more tillers. RM marker analysis indicates apparently homozygous integration of donor millet DNA in MR-4 genome. Total DNA introduction through rice coleoptile could overcome species barrier and expand gene pool rapidly, thus contributing to the development of rice germplasms with increased abiotic stress tolerance and higher yield.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"107"},"PeriodicalIF":3.6,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13661873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149182808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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":"Genome-wide association of flowering phenology stages in olive trees (<i>Olea europaea</i> L.): new insights from BLUPs and genotype × environment responses.","authors":"Othmane Lamoumni, Omar Abou-Saaid, Hayat Zaher, Adnane El Yaacoubi, Gaetan Droc, Gautier Sarah, Abdelilah Meddich, Abdelmajid Moukhli, Philippe Cubry, Cherkaoui El Modafar, Ahmed El Bakkali","doi":"10.1007/s11032-026-01731-z","DOIUrl":"https://doi.org/10.1007/s11032-026-01731-z","url":null,"abstract":"<p><p>Flowering is a key developmental stage determining reproductive success and yield in olive trees, integrating complex genetic regulation and environmental factors mainly temperatures. Given its environment-dependency, olive flowering phenology is increasingly challenged by ongoing global warming in the Mediterranean region. Therefore, understanding its genetic architecture is essential for developing efficient and climate-resilient breeding programs. Here, we investigated flowering phenology related-traits using a multi-model genome-wide association study (GWAS) framework. Phenological traits, representing first-observation dates of developmental stages for 257 olive Mediterranean varieties, along with more than 555 K high-quality variants, were analyzed. For each trait, Best Linear Unbiased Predictors (BLUPs), Finlay-Wilkinson slopes, and single-year data were examined using both single-locus and multi-loci models. Additionally, a multivariate GWAS was conducted for the traits. Our results revealed high inter-genotype variation and significant genotype-by-environment interactions, with heterogenous responsiveness to environmental changes. The integration of multiple GWAS models provided complementary insights into the genetic architecture of flowering phenology, highlighting both shared and model-specific associations. We identified both stage-specific and pleiotropic associations. Analyses of plasticity slopes identified additional distinct association patterns from BLUP-based results, suggesting a partially independent genetic basis of flowering phenology plasticity in olive trees. Our findings provide a comprehensive genomic dissection of olive flowering phenology and emphasize its complex architecture, involving pleiotropic, stage-specific and plasticity-related mechanisms.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01731-z.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"106"},"PeriodicalIF":3.6,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13658645/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149182918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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":"Genome-wide association study of grain hardness and novel <i>Puroindoline</i> alleles in bread wheat.","authors":"Chao Fu, Xiangxu Ren, Yuping Song, Mengyao Li, Li Yin, Hailiang Mao","doi":"10.1007/s11032-026-01727-9","DOIUrl":"https://doi.org/10.1007/s11032-026-01727-9","url":null,"abstract":"<p><p>Grain hardness is a critical quality trait that determines the processing properties and commercial value of wheat, playing an essential role in both food security and the high-quality development of the wheat industry. In this study, we used an association panel of 233 wheat accessions to measure the grain hardness index (HI) across four different environments. Based on the re-sequencing data, we performed a genome-wide association study (GWAS) to identify the genetic loci associated with wheat grain hardness. We detected two environmentally stable QTLs named <i>QHa.hzau-5D</i> and <i>QHa.hzau-6B.1</i>, which explained 11.27%-18.75% and 11.44%-15.54% of the phenotypic variation, respectively. <i>QHa.hzau-5D</i> co-localized with the known grain <i>hardness</i> locus (<i>Ha</i>), confirming that <i>Ha</i> locus plays a central role in regulating grain hardness. Sequence variability analysis of <i>Pina</i> and <i>Pinb</i> genes in the tested population revealed seven alleles for each gene, forming 12 distinct haplotypes. Among them, the haplotypes <i>Pina-D1a</i>/<i>Pinb-D1b</i> (<i>n</i> = 99) and <i>Pina-D1a</i>/<i>Pinb-D1a</i> (<i>n</i> = 80) were the most prevalent. A novel <i>PIN</i> allele with double-deletion allelic variation was detected in the cultivar Kenda4. The novel haplotype was characterized by an approximately 27-kb fragment deletion at the <i>Ha</i> locus. Additionally, we successfully developed five kompetitive allele-specific PCR (KASP) markers for four <i>PIN</i> allelic variations, including <i>Pina-D1n</i>, <i>Pinb-D1ac</i> (two SNPs), <i>Pinb-D1d</i>, and <i>Pinb-D1u</i>. Within the <i>QHa.hzau-6B.1</i> interval, two grain-hardness-associated SNPs (SNP-49222665 and SNP-49239367) were identified in genes <i>TraesCS6B02G247300</i> and <i>TraesCS6B02G247700</i>. Based on expression profiling and gene annotation, these two genes were proposed as key candidate genes to regulate wheat grain hardness. Furthermore, SNP-49222665 and SNP-49239367 were converted into a CAPS marker and a KASP marker, respectively, for subsequent genotyping. This study provides new insights into the molecular regulatory mechanism of wheat grain hardness and offers a novel theoretical basis and practical molecular markers for wheat quality breeding.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01727-9.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"105"},"PeriodicalIF":3.6,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13658664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149182929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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":"Introgression line libraries in melon (<i>Cucumis melo</i> L.): development, genetic insights, and applications in trait dissection and crop improvement.","authors":"Cristina Esteras, Marta Pujol, Juan Pablo Fernández-Trujillo, Maria José Gonzalo, Ana Monserrat Martín-Hernández, Ana María Pérez-de-Castro, Belén Picó, Jordi Garcia-Mas, Antonio José Monforte","doi":"10.1007/s11032-026-01725-x","DOIUrl":"10.1007/s11032-026-01725-x","url":null,"abstract":"<p><p>Introgression lines (ILs) are powerful genetic resources for dissecting the architecture of complex traits in crops. This review summarizes the development and characterization of six IL libraries and two additional ILs in melon (<i>Cucumis melo</i> L.), generated from diverse donor genotypes, including wild accessions, landraces, traditional and elite cultivars, introgressed into Mediterranean elite backgrounds, such as 'Piel de Sapo' and 'Védrantais.' Together, these libraries capture a wide representation of melon genetic diversity and have revealed numerous stable quantitative trait loci (QTLs) for key agronomic traits, including fruit shape, weight, color, firmness, soluble solids content, volatile composition, climacteric ripening, and resistance to Cucumber Mosaic Virus (CMV). Notably, large-effect QTLs were recurrently identified across independent IL libraries. This suggests that targeted improvement of complex traits may be achieved by manipulating a limited number of loci. Notably, several ILs displayed transgressive phenotypes relative to their donor parents. These results highlight their ability to uncover cryptic genetic variants relevant to modern breeding. Beyond QTL discovery, ILs have facilitated fine mapping and gene identification, leading to the cloning of genes such as <i>CmOFP13</i> (fruit shape), <i>CmNAC-NOR</i>, <i>CmERF024</i> (ripening), and <i>CmVPS41</i> (CMV resistance). Overall, this review highlights the value of ILs as tools for both breeding and fundamental genetic research and outlines future directions, including integrating transcriptomics and metabolomics approaches, developing ILs for abiotic stress tolerance, and extending IL resources to oriental melon germplasm, thereby enhancing their utility for global melon improvement.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01725-x.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"104"},"PeriodicalIF":3.6,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13642879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149137643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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":"QTL mapping of starch, protein, and fatty acid traits reveals pleiotropic loci governing rice eating quality in a recombinant inbred lines population.","authors":"MinQi Li, Lu Wang, GuanJun Gao, Yuqing He","doi":"10.1007/s11032-026-01726-w","DOIUrl":"10.1007/s11032-026-01726-w","url":null,"abstract":"<p><p>Rice grain quality is a complex trait governed by multiple genetic factors. In this study, a high-density genetic map was constructed using a recombinant inbred line (RIL) population derived from a cross between two <i>indica</i> rice varieties, DL208 and ZS97, based on genotyping-by-sequencing. Three categories of grain quality traits, starch composition, storage protein content, and fatty acid composition, were systematically evaluated across two environments (Wuhan and Hainan). A total of 168 QTLs were identified, of which 30 were stably detected across both environments with concordant effect directions. These stable QTLs were further integrated with 6 ECQ-specific QTLs to yield 36 high-confidence QTLs for downstream analysis. Eleven QTL clusters with overlapping genomic regions were identified, suggesting pleiotropic regulation of multiple quality traits. The most prominent cluster on chromosome 6 (0-2.17 Mb) co-localized with the <i>Wx</i> gene and coordinately regulated amylose content, amylopectin content, and eating quality. Backcross introgression line (BIL) validation confirmed the genetic effects of six pleiotropic QTL clusters through pairwise phenotypic comparison. These findings provide a genetic framework for marker-assisted selection and quality improvement in <i>indica</i> rice breeding.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01726-w.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"103"},"PeriodicalIF":3.6,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13638889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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":"Fine mapping of QTL and identification of candidate genes responsible for tuberous stem formation in Kohlrabi (<i>Brassica oleracea</i> var. <i>gongylodes</i> L.).","authors":"Md Nuruzzaman, Masato Sato, Motoki Shimizu, Daniel John Shea, Hiroyasu Kitashiba, Eigo Fukai, Keiichi Okazaki","doi":"10.1007/s11032-026-01717-x","DOIUrl":"https://doi.org/10.1007/s11032-026-01717-x","url":null,"abstract":"<p><p>Tuberous stem is a key determinant of yield and quality in kohlrabi, and it is a prime target of artificial selection for breeding and domestication. To dissect the genetic basis of stem tuberization, a previously identified quantitative trait locus, <i>REnBo2</i> on chromosome C03, was fine mapped to an 87.5-kb interval using recombinant populations from three successive backcross generations derived from double haploid lines of kohlrabi and broccoli. The fine-mapped interval contained three genes: <i>BolC03g081960.2 J</i> (encoding <i>CIPK6</i>), <i>BolC03g081970.2 J</i> (<i>FAD6</i>) and <i>BolC03g081980.2 J</i> (<i>WRKY32</i>). Integrated analysis of gene annotations, allelic variations, expression profiles, and previously generated transcriptome and endogenous phytohormone datasets identified <i>CIPK6</i> as the most promising candidate underlying <i>REnBo2</i>, whereas <i>WRKY32</i> remains a potential secondary candidate requiring further functional characterization. <i>CIPK6</i> exhibited allelic variation and significantly lower expression in kohlrabi stems during tuber initiation and development. Functional validation in Arabidopsis further supported the role of <i>CIPK6</i>, as the <i>atcipk6</i> knockdown mutant displayed swollen hypocotyls along with impaired root development. Heterologous expression of the broccoli <i>CIPK6</i> allele retrieve the non-swollen hypocotyl morphotype with a developed root system similar to the wild-type plants, whereas the kohlrabi <i>CIPK6</i> allele failed to restore the wild-type phenotypes despite high transgene expression, indicating allele-specific functional divergence. Collectively, our results identify <i>CIPK6</i> as a prominent candidate gene regulating stem tuberization in kohlrabi and provide a new insight into the auxin-associated molecular mechanisms controlling storage stem development in Brassica and related species.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01717-x.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"102"},"PeriodicalIF":3.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13631219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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":"Correction to: A BLH12-KN1 transcriptional module regulates embryo size in maize.","authors":"Tao Yun, Xiaoxia Du, Wenkang Chen, Xiaowei Li, Xuan Zhang, Min Wang, Jianghua Guo, Sixuan Xu, Pengfei Yin, Huaijun Tang, Jiansheng Li, Yingni Xiao, Xiaohong Yang","doi":"10.1007/s11032-026-01723-z","DOIUrl":"https://doi.org/10.1007/s11032-026-01723-z","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1007/s11032-026-01716-y.].</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"99"},"PeriodicalIF":3.6,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13627497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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":"GWAS-based identification of QTLs and candidate genes associated with seed oil content and oleic acid content in <i>Brassica napus</i> L.","authors":"Kaijie Ye, Liang Ran, Qiuting Wei, Nengwen Yin, Huiyan Zhao, Ti Zhang, Huafang Wan, Taocui Huang, Hai Du, Cunmin Qu, Haijiang Liu, Daixiang Xu","doi":"10.1007/s11032-026-01712-2","DOIUrl":"https://doi.org/10.1007/s11032-026-01712-2","url":null,"abstract":"<p><p>Oilseed rape (<i>Brassica napus</i> L.) is one of the world's most important oil crops. Seed oil content (SOC) and oleic acid content (C18:1) are major determinants of rapeseed oil quality. Identifying genomic loci and candidate genes associated with these traits is therefore important for improving the efficiency of molecular breeding. In this study, a recombinant inbred line (RIL) population comprising 188 <i>B. napus</i> lines was evaluated across three growing seasons, and SOC and C18:1 were measured. A genome-wide association study (GWAS) was performed using a mixed linear model (MLM) and more than 12,000 high-quality single-nucleotide polymorphisms (SNPs). Six and eight quantitative trait loci (QTLs) associated with SOC and C18:1, respectively, were detected. Based on the functional annotations and sequence variation of genes within these QTL intervals, five previously reported candidate genes were prioritized: <i>BnaC01.LPAT5</i>, <i>BnaA06.ABCA2</i>, <i>BnaA07.PIN1</i>, <i>BnaC08.GEM</i>, and <i>BnaA03.MYB102</i>. In addition, a consistently detected SNP cluster associated with multiple seed lipid-related datasets was detected on chromosome A09. By integrating genomic position, functional annotation, parental sequence variation, qRT-PCR expression data, and haplotype-phenotype associations, six genes within the A09 QTL region were newly prioritized as potential candidates associated with seed lipid accumulation. These genes exhibited significant differences in transcript abundance between the developing seeds of the two parental cultivars, GH06 and ZY821, at 20 days after flowering (DAF). Although these convergent lines of evidence support the prioritization of the six genes, their causal effects remain to be established through further functional validation. Overall, the QTLs and potentially favorable haplotypes identified in this study provide useful genetic resources for improving rapeseed oil quality, while the prioritized candidate genes provide targets for future functional studies and molecular breeding in <i>B. napus</i>.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01712-2.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"100"},"PeriodicalIF":3.6,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13627567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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":"Natural epigenetic mutation of <i>MLH3</i> affects seed-setting in rice.","authors":"Yongguang Li, Shihao Zhang, Minrui Chen, Yunjian Mei, Hongyang Ma, Qi Zhao, Wenhui Ding, Mingli Zhou, Yanqian Xiong, Yuanwu Min, Juan Yang, Jing Zhang, Linjie Yan, Yunyue Huang, Yun Chen, Biao Zhang, Zipei Fan, Wanqing Li, Shijia Liu, Liangming Chen, Xi Liu, Ling Jiang, Yulong Ren, Yunlu Tian, Zhigang Zhao, Xiaowen Yu, Jianmin Wan","doi":"10.1007/s11032-026-01724-y","DOIUrl":"https://doi.org/10.1007/s11032-026-01724-y","url":null,"abstract":"<p><p>Seed-setting rate is a major determinant of grain yield and depends on the normal development of both male and female gametophytes. Although considerable progress has been made in understanding the genetic regulation of female fertility in rice, few naturally occurring epialleles associated with this process have been identified. Here, we identified a naturally occurring recessive epiallele in rice (<i>Oryza sativa</i>), designated <i>Epi-mlh3</i>, that causes a severe reduction in seed-setting rate owing to female gametophyte abortion. <i>Epi-mlh3</i> exhibits no detectable DNA sequence variation but displays pronounced CG hypomethylation within the gene body of <i>OsMLH3</i>, accompanied by a marked reduction in full-length <i>OsMLH3</i> transcripts and premature transcriptional termination. Bisulfite sequencing identified a 443-bp gene-body region containing nine differentially methylated CG sites associated with reduced <i>OsMLH3</i> expression. CRISPR/Cas9-mediated knockout of <i>OsMLH3</i> faithfully recapitulated the major phenotypes of <i>Epi-mlh3</i>, including reduced seed-setting rate, embryo sac abortion, and meiotic chromosome defects. Cytological and molecular analyses further demonstrated that reduced <i>OsMLH3</i> expression was associated with impaired meiotic chromosome behavior and decreased chiasma frequency, consistent with impaired MutLγ-mediated crossover formation during meiosis. Collectively, our findings provide evidence that gene-body CG methylation is associated with stable <i>OsMLH3</i> transcription and identify <i>Epi-mlh3</i> as a naturally occurring functional epiallele that expands current understanding of the epigenetic regulation of female fertility in rice.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01724-y.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 10","pages":"101"},"PeriodicalIF":3.6,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13627576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}