Molecular Breeding最新文献

{"title":"QTL mapping and genomic prediction of resistance to apple blotch (<i>Diplocarpon coronariae</i>).","authors":"Michaela Jung, Bettina Hänni, Hélène Muranty, Andrea Patocchi","doi":"10.1007/s11032-026-01666-5","DOIUrl":"https://doi.org/10.1007/s11032-026-01666-5","url":null,"abstract":"<p><p>Apple blotch (AB) is an emerging disease in apple production, primarily causing premature defoliation. The rise of orchard management practices reducing fungicide use has coincided with an increase in AB incidence in Europe. Breeding for resistance to AB became important for long-term disease management. Depending on the genetic complexity of the trait, breeding can be supported using either marker-assisted or genomic selection. However, no such tools are currently available for AB. To address this issue, we established two biparental mapping populations, 'Topaz' × 'Granny Smith' and 'Topaz' × 'Parkapfel', and a diversity panel of 122 genotypes, all evaluated for their resistance to AB under natural field conditions across three growing seasons. Quantitative trait locus (QTL) mapping identified five associated loci on chromosomes 3, 5, 6, 10, and 11, each explaining a maximum of 12% of phenotypic variance, indicating a polygenic architecture of AB resistance. Strong seasonal effects were observed in disease development, and they were either removed (G model) or explicitly modeled (G + G×E model) using genomic prediction approaches. The average predictive ability reached 0.47 for the G model and 0.38 for the G + G×E model. While the detected QTLs have small individual effects that constrain their use in marker-assisted selection, the moderate predictive ability of genomic prediction models demonstrates the potential of genomic selection for accelerating resistance breeding. These findings provide the first genomic tools to support breeding for resistance to AB and illustrate the utility of genome-wide approaches in managing complex traits.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01666-5.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 5","pages":"44"},"PeriodicalIF":3.0,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13135599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840165","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":"Hongyou 789: a moderately compact, sulfonylurea-resistant rapeseed variety for high-density cultivation and mechanized seed production.","authors":"Chengming Sun, Xiaoying Zhou, Chunyun Wang, Feng Chen, Wei Zhang, Qi Peng, Yue Shen, Jianqin Gao, Xiaodong Wang, Maolong Hu, Jiefu Zhang, Jian Wu, Sanxiong Fu","doi":"10.1007/s11032-026-01668-3","DOIUrl":"https://doi.org/10.1007/s11032-026-01668-3","url":null,"abstract":"","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 5","pages":"43"},"PeriodicalIF":3.0,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13135016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817688","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":"Identification of loci and candidate genes related to SPAD via SNP- and InDel-GWAS.","authors":"Yajun Zhao, Dezhou Hu, Xiaoyong Li, Lixun Zhu, Zhiri Xu, Wei Zhao, Xu Guan, Deyue Yu","doi":"10.1007/s11032-026-01662-9","DOIUrl":"https://doi.org/10.1007/s11032-026-01662-9","url":null,"abstract":"<p><p>Chlorophyll is an essential component for capturing light energy to drive photosynthesis, and its content is crucial for leaf photosynthetic capacity and crop yield. SPAD, as a chlorophyll content-related parameter, has been widely applied. In this study, GWAS was performed on SPAD at the R2 stage of 219 accessions using 5,410,112 SNPs and 634,106 InDels, identifying 511 SNPs, 67 InDels and a candidate gene <i>GmPMI1</i> associated with SPAD. <i>GmPMI1</i> divided the natural population into three haplotypes, with Hap2 exhibiting higher SPAD values. The SNP in its promoter region (Chr08-3973347) may account for this phenomenon. This gene is regulated by the MYB transcription factor Glyma.05g013000 and functions in the ABA signaling pathway. Its effect on SPAD is likely mediated through the regulation of chloroplast movement rather than chlorophyll content. While most researchers consider \"optimizing photosynthesis by regulating chlorophyll content to improve crop yield\" as a breeding objective, maximizing photosynthetic potential under different environmental conditions by modulating chloroplast movement provides an alternative viable strategy for yield enhancement.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01662-9.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 5","pages":"42"},"PeriodicalIF":3.0,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13125562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817627","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":"From research to application: evaluation of literature-based and newly identified GWAS and GP-derived loci for anthracnose resistance in white lupin, across validation panels and environments.","authors":"András Patyi, Michael Schneider, Christine Arncken, Michał Książkiewicz, Monika M Messmer, Grit Schwertfirm, Mariateresa Lazzaro","doi":"10.1007/s11032-026-01661-w","DOIUrl":"https://doi.org/10.1007/s11032-026-01661-w","url":null,"abstract":"<p><p>Resistance to anthracnose disease, caused by <i>Colletotrichum lupini</i>, in white lupin is polygenic and rare in global germplasm, making breeding for resistance challenging. Several studies have identified genomic regions associated with resistance, but reported QTLs rarely overlap. Overall, anthracnose-associated loci have not yet been appropriately exploited in breeding due to the lack of validation, especially in unrelated material. We assessed three literature-based SNP-markers associated to a previously described QTL, as well as six originating from two published GWAS studies. In addition, by re-analysing two published datasets, we newly (i) identified five SNP-markers through a genome-wide association study (GWAS) and (ii) assembled a genomic prediction (GP) model based on a set of 42 SNP-markers. All SNP-markers were transformed to PCR-based assays to facilitate cost-efficient application in breeding and tested in a diversity panel and two breeding panels, phenotyped in field and/or controlled conditions. We validated the association to anthracnose resistance for the previously reported QTL on chromosome <i>Lalb_Chr10</i>, tagging a source of resistance in the resistant cultivar 'Frieda'. Two markers showed significant associations (<i>p</i> < 0.05) with anthracnose resistance in at least two panels, and an additional seven markers were significant in one. The GP model had a prediction accuracy of 0.84 (± 0.13) in the training panel, but is not applicable as such in the unrelated validation panels. However, re-training the GP model with the respective validation panel data showed clear prediction improvement buffering the limitation of environmental context and narrower genepools applied in a breeding programme.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01661-w.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 5","pages":"41"},"PeriodicalIF":3.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776388","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":"Marker-assisted introgression of brown planthopper resistance and herbicide tolerance for integrated pest management in direct seeded rice.","authors":"Pritiranjan Sahoo, Motilal Behera, Lambodar Behera, Sushmita Munda, Sutapa Sarkar, Mayabini Jena, Kutubuddin A Molla, Anilkumar Chandrappa, Prakash Chandra Rath, Debajyoti Roy, Nitiprasad N Jambhulkar, Amaresh Kumar Nayak, Guru-Pirasanna-Pandi Govindharaj, Meera Kumari Kar, Mridul Chakraborti","doi":"10.1007/s11032-026-01650-z","DOIUrl":"https://doi.org/10.1007/s11032-026-01650-z","url":null,"abstract":"<p><p>Brown planthopper (BPH) is a major pest of rice. Growing direct seeded rice (DSR) without constant standing water or intermittent draining reduces its population buildup. However, volunteer, wild and weedy rice create a major hurdle in adoption of DSR as conventional herbicides or manual weeding fail to control them. These invasive weeds from the same genus may attract BPH on the standing crops of resistant rice varieties besides supporting pest overwintering. Forty-eight accessions of 22 <i>Oryza</i> species along with trait-specific checks were screened for BPH-resistance and imazethapyr-tolerance. Only IRGC 88828 (<i>O. schweinfurthiana</i>) was BPH-resistant, and none were tolerant to imazethapyr indicating the scope of harnessing the complementary benefits through introgression of both the traits in a single genotype. Two epistatic BPH-resistance QTLs from a landrace Salkathi and novel <i>Aceto Hydroxy Acid Synthase</i> (<i>AHAS</i>) gene mutation conferring imazethapyr tolerance were separately introgressed in a popular rice variety Naveen. After blind multilocation trials, BPH resistant near isogenic lines (NILs) with <i>qBph4.3</i> + <i>qBph4.4</i> were notified for general cultivation in India. Introgression of <i>AHAS</i> gene through tightly linked marker RM6844 enabled efficient control of the weed complexes of rice through imazethapyr application. However, in comparison to Naveen, significant reduction of grain yield (5.28-15.84%) and head rice recovery (15.68-15.85%) were recorded in the NILs. While combining the two traits, recombinants between <i>AHAS</i> and RM6844 were identified, which circumvented the linkage drags. Cultivation of the dual improved NILs will enable integrated pest management besides reducing cultivation cost, grain admixtures, insecticide use and environmental footprint in rice cultivation.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01650-z.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 5","pages":"38"},"PeriodicalIF":3.0,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13096372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776402","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":"Huayouza 315, a novel rapeseed cultivar with high oleic acid content, superior resistance to clubroot, and high yield.","authors":"Qing Dong, Jingzhen Wang, Yu Duan, Zhihao Bian, Hanzi He, Qiufang Xiong, Yaru Shi, Wenjuan Hu, Zhiping Li, Zhigang Yao, Chuchuan Fan, Chunyu Zhang","doi":"10.1007/s11032-026-01664-7","DOIUrl":"https://doi.org/10.1007/s11032-026-01664-7","url":null,"abstract":"","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 5","pages":"40"},"PeriodicalIF":3.0,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13096393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776447","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-Seq and pyramiding of yield-related loci from wild rice (<i>Oryza rufipogon</i> Griff.) introgression lines under nutrient-deficient conditions.","authors":"Bright G Adu, Aizelle Y S Argete, Fakhrul I Monshi, Yoshihiro Ohmori, Akifumi Shimizu, Hiroaki Hayashi, Toru Fujiwara","doi":"10.1007/s11032-026-01651-y","DOIUrl":"https://doi.org/10.1007/s11032-026-01651-y","url":null,"abstract":"<p><p>Developing rice cultivars adapted to low-nutrient conditions is essential for sustainable production, and wild rice offers valuable genetic resources for improving stress resilience in cultivated varieties. In this study, we demonstrate that pyramiding yield-related quantitative trait loci (QTLs) derived from wild rice enhances panicle yield under nutrient-limited conditions. Two wild rice introgression lines, KRIL8 and KRIL37, each carrying a small <i>Oryza rufipogon</i> genomic segment in the <i>O. sativa</i> L. cv. Koshihikari background, exhibited significantly higher panicle weight than the recurrent parent (KH) under limiting nitrogen and/or NPK (nitrogen, phosphorus, potassium) conditions. Using next-generation sequencing-based QTL-seq analysis, QTLs associated with panicle weight were identified in KRIL8 (<i>qPW1</i>) and KRIL37 (<i>qPW6</i>). Selected F₃ pyramiding lines (PyL) developed through marker-assisted selection showed a 16-40% increase in panicle weight under no nitrogen (-N) conditions. Under nutrient-deficient (-NPK) conditions, the selected pyramiding line PyL14 showed a tendency towards higher brown rice yield (approximately 12%) compared with the best introgression line parent (KRIL8). Although the difference was not statistically significant, the trend shows a positive interaction between the pyramided QTLs. Candidate genes harboring nonsynonymous SNPs with high SNP indices were identified, and cultivar-specific expression patterns were observed for these genes under low ammonium conditions, including genes associated with yield-related traits and nutrient transport. These results identify PyL14 as a promising genetic resource with the potential to improve rice yield under nutrient-deficient conditions.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01651-y.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 5","pages":"39"},"PeriodicalIF":3.0,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13096384/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776397","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 variation in the promoter of <i>ZmMIR528b</i> mediates maize stem lodging resistance by regulating ZmmiR528 expression.","authors":"Dengke Shi, Wenshuai Lv, Yu Guo, Pengshuai Yan, Qingguo Du, Wen-Xue Li","doi":"10.1007/s11032-026-01658-5","DOIUrl":"10.1007/s11032-026-01658-5","url":null,"abstract":"<p><p>Stem lodging poses a major challenge to modern maize production by significantly reducing yield, impairing grain quality, and complicating mechanical harvest. Our previous work identified ZmmiR528 as a key post-transcriptional regulator of lignin biosynthesis and lodging resistance, highlighting its potential as a breeding target. However, strategies to leverage this gene in breeding programs have remained unexplored. In this study, we characterized stem lodging resistance in a diverse panel of 263 maize accessions under field conditions and performed sequencing of the <i>ZmMIR528a</i> and <i>ZmMIR528b</i> loci. An association analysis identified a single-nucleotide polymorphism (SNP) in the <i>ZmMIR528b</i> promoter that was significantly correlated with the stem lodging resistance index. Accessions carrying the <i>Pro</i>-C allele at this locus demonstrated a significantly higher stem lodging resistance index and greater stem lignin content than those with the <i>Pro</i>-T allele. Luciferase assays indicated that the <i>Pro</i>-C haplotype conferred lower transcriptional activity than the Pro-T haplotype. Consistent with this, stem-loop RT-qPCR revealed that mature ZmmiR528 abundance was significantly lower in accessions harboring the <i>Pro</i>-C allele. We subsequently developed a cleaved amplified polymorphic sequence (CAPS) marker based on this SNP and validated its efficacy in a panel of ten diverse inbred lines. Collectively, our findings identify a novel functional promoter allele that enhances lodging resistance by repressing ZmmiR528 expression, thereby providing a validated molecular tool for breeding lodging-resistant maize.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01658-5.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"37"},"PeriodicalIF":3.0,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13083467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147723381","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":"A mutation in <i>OsPPDK</i> impairs pyruvate phosphate dikinase activity, leading to floury endosperm in rice.","authors":"Umair Hassan, Yushi Zhang, Jingyao Yang, Hanghong Yu, Mohamed Ali Eweda, Xiaoli Jin","doi":"10.1007/s11032-026-01659-4","DOIUrl":"https://doi.org/10.1007/s11032-026-01659-4","url":null,"abstract":"<p><p>Rice (<i>Oryza sativa</i> L.) is a crucial global food source, whose appearance quality affects its market value. In this study, a mutant, designated <i>fe5</i>, was generated from the Japonica cultivar Nipponbare via ethyl methane sulfonate (EMS) mutagenesis, which present floury endosperm compared to the wild type (WT). By map-based cloning, loc <i>OsFE5</i> was located within a 103 kb region on the long arm of chromosome 5. Through whole-genome resequencing and Sanger sequencing between the WT and <i>fe5</i> mutant, we confirmed that there was a T to C mutation in LOC_Os05g33570, leading to the change in amino acid from serine (S) to proline (P). The examination of grain quality metrics reveals a substantial reduction in amylose content in <i>fe5</i> relative to the WT. The most crucial variation in the solubility of <i>fe5</i> was noted at a 4 M urea concentration, reflecting alterations in the amylopectin structure of <i>fe5</i> relative to the WT. Additionally, the gel consistency was elevated in <i>fe5</i> in contrast to the WT. Our research yields novel genetic material, and the established molecular markers can be employed in marker-assisted breeding to improve endosperm characteristics in rice.</p><p><strong>Graphical abstract: </strong></p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01659-4.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"36"},"PeriodicalIF":3.0,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13079256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147699133","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":"<i>OsCTP1</i> negatively regulates seedling cold tolerance in rice.","authors":"Peng Liu, Xuan Huang, Yuqi Xia, Yanchun Cui, Donghai Mao","doi":"10.1007/s11032-026-01660-x","DOIUrl":"https://doi.org/10.1007/s11032-026-01660-x","url":null,"abstract":"<p><p>Cold stress poses a significant threat to rice production and grain quality. As a complex quantitative trait, cold tolerance is regulated by multiple genetic loci and environmental factors. Here, we identified <i>OsCTP1</i> (<i>LOC_Os11g15570</i>), a homolog of the <i>Arabidopsis</i> gene <i>AtSLP2</i>, as a negative regulator of seedling cold tolerance in rice. Subcellular localization and expression analyses showed that <i>OsCTP1</i> is localized to the endoplasmic reticulum (ER) and mitochondria (Mito), with its transcripts predominantly accumulated in roots, leaves, leaf sheaths, husks, and anthers. Transcriptomic and quantitative analyses further revealed that <i>OsCTP1</i> likely suppresses the <i>OsWRKY76/OsbHLH148‑OsDREB1B</i> signaling pathway, thereby negatively modulating cold tolerance. Additionally, phenotypic evaluation under exogenous abscisic acid (ABA) treatment suggests that <i>OsCTP1</i> may function in an ABA‑dependent manner, though the precise molecular mechanism warrants further investigation. In summary, <i>OsCTP1</i> represents both a valuable genetic resource for elucidating low‑temperature signaling networks and a promising candidate for molecular breeding aimed at improving cold tolerance in rice.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01660-x.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"35"},"PeriodicalIF":3.0,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13076701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147691104","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}