Molecular Breeding最新文献

{"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":"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":3.6,"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}

{"title":"Combining promoter and induced intron 1 mutations of <i>Vrn-A1a</i> does not accelerate flowering in wheat.","authors":"Beáta Strejčková, Zbyněk Milec, Tereza Šlajsová, Vojtěch Hudzieczek, Rocío Alarcón-Reverte, Caroline A Sparks, Ales Pecinka, Stephen Pearce, Jan Šafář","doi":"10.1007/s11032-026-01657-6","DOIUrl":"10.1007/s11032-026-01657-6","url":null,"abstract":"<p><p>In temperate cereals, vernalization regulates the transition from vegetative to reproductive growth in response to low temperatures. A central component of this pathway is <i>VERNALIZATION 1</i> (<i>VRN1</i>). In winter wheat cultivars, the recessive <i>vrn1</i> allele is transcriptionally activated by cold and promotes the transition to flowering. In contrast, spring cultivars carry dominant <i>VRN1</i> alleles expressed in a cold-independent manner. This is caused by mutations in the <i>cis</i>-regulatory elements in the promoter or in the \"critical region\" of intron 1. The widespread spring bread wheat allele <i>Vrn-A1a</i> carries a promoter mutation but retains a winter-like allele intron 1. Intriguingly, <i>Vrn-A1a</i> is partially responsive to cold, suggesting regulatory element(s) beyond the promoter mutation. Here, we investigated the effect of combined promoter and first intron mutations on <i>Vrn-A1a</i> expression and flowering time in bread wheat. We deleted a 901-bp segment of the <i>Vrn-A1a</i> so-called \"critical region\", thus generating a novel combination of the promoter and intron 1 mutations not found in natural germplasm. Plants carrying both mutations exhibited <i>Vrn-A1</i> transcript levels and flowering times comparable to those of the wild-type under both vernalizing and non-vernalizing conditions. Hence, partial cold responsiveness of <i>Vrn-A1a</i> is controlled by regulatory element(s) outside the removed intron 1 segment. Overall, our study advances the understanding of <i>VRN1</i> transcriptional regulation and highlights the complexity of vernalization control in wheat.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01657-6.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"33"},"PeriodicalIF":3.6,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13065874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147674924","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 identification of the ARR-B gene family and functional characterization of <i>OsRR41</i> as a positive regulator of salinity tolerance in rice.","authors":"Huashuai Cao, Shilin Ding, Kunjie Li, Longhui Zhang, Yuting Yi, Chenyang Li, Yingxin Qiu, Lvni Tan, Quanqiang Lei, Weijun Chen, Bin Li, Yixing Li, Shufeng Song, Yi Pan, Li Li","doi":"10.1007/s11032-026-01648-7","DOIUrl":"10.1007/s11032-026-01648-7","url":null,"abstract":"<p><p>Salinity stress constitutes a primary environmental constraint that severely limits rice productivity. In this study, we identified the B-type response regulator <i>OsRR41</i> as an indispensable positive regulator of salinity tolerance in rice. Utilizing CRISPR/Cas9 technology, we generated knockout the three independent mutant lines, which exhibited hypersensitivity to salt stress. Under salt stress conditions, these mutants displayed more pronounced growth retardation compared to wild-type plants, characterized by significantly reduced biomass, severe leaf chlorosis, and accelerated wilting. Physiologically, the loss of <i>OsRR41</i> resulted in an inability to maintain cellular homeostasis, leading to excessive accumulation of reactive oxygen species (ROS) causing oxidative damage, and a severely disrupted ionic balance manifested by elevated Na⁺/K⁺ ratios. Combined transcriptomic and metabolomic analyses indicated that the loss of <i>OsRR41</i> function leads to widespread disruption of stress-responsive gene expression networks and metabolic homeostasis. Our findings thus establish <i>OsRR41</i> as a pivotal regulatory node conferring salinity tolerance in rice by orchestrating essential physiological and metabolic defense responses under stress conditions.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01648-7.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"34"},"PeriodicalIF":3.6,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13065919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147674937","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":"The genetic saga of barley leaf rust: evolution, resistance, and breeding innovations.","authors":"Madhu Patial, Santosh Kumar Bishnoi, Prem Lal Kashyap, Rahul Chandora, Om Prakash Gangwar","doi":"10.1007/s11032-026-01656-7","DOIUrl":"10.1007/s11032-026-01656-7","url":null,"abstract":"<p><p>Barley (<i>Hordeum vulgare</i> L.) plays a crucial role in global agriculture and food security, being the fourth most important cereal worldwide. Despite its significance, barley production faces threats, particularly from rust diseases, which can cause substantial yield losses, reaching 50-70% in susceptible varieties during epidemics. Additionally, changing climate patterns, including temperature fluctuations and unseasonal rainfall, contribute to the evolution of more virulent rust pathotypes, negatively impacting barley production. In response to these challenges, the development and deployment of rust-resistant barley cultivars have become imperative. The quest for rust resistance in barley has been a dynamic research area, initially relying on conventional breeding methods focused on phenotypic performance. Over time, various breeding methods such as pedigree breeding, backcrossing, single seed descent, recurrent selection, and doubled haploidy have been employed. However, the advent of molecular technologies has revolutionized the field, providing new avenues for discovering rust-resistant genes and developing improved barley varieties. Techniques like marker-assisted selection, quantitative trait loci (QTL) identification, cloning, etc. opened new avenues for discovering rust-resistant genes and developing improved barley varieties. These molecular approaches provide more precise and efficient means for identifying and introducing desirable traits. This review aims to provide a comprehensive understanding of these advanced breeding strategies, offering insights that can contribute for effective management of barley leaf rust management and ensure the sustained success of barley production in the face of evolving challenges.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"32"},"PeriodicalIF":3.6,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13038706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147609506","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":"Sesame improvement: traditional breeding to genomics-assisted breeding.","authors":"Sk Shoaibur Rahaman, Md Nahid Hasan, Jibon Chandro Roy, Md Rownokul Haque, A K M Zilani Rabbi, Khandker Shazia Afrin, Md Abdur Rahim","doi":"10.1007/s11032-026-01654-9","DOIUrl":"10.1007/s11032-026-01654-9","url":null,"abstract":"<p><p>Although sesame is an important oilseed crop, its production is significantly hindered by several factors, including capsule shattering and susceptibility to environmental stresses. To increase the sesame production, it is urged to develop high-yielding cultivars with shattering resistance and stress resilience. Traditional breeding alone is insufficient to develop such varieties, as it is less precise, time-consuming, and inappropriate for complex traits like yield, abiotic and biotic stress tolerance/resistance. To address these, genomics-assisted breeding (GAB) might be a valuable technique to assist conventional breeding, as it offers genomic tools such as molecular markers, genomic selection, genome sequencing, etc., to effectively identify, select, and combine useful alleles in sesame. When it is integrated with traditional breeding, developing sesame varieties with precise and fast selection for traits, including abiotic/biotic stress tolerance/resistance, and higher yield becomes possible. This review aims to explore the gaps (slow, inefficient, environment-dependent, etc.) in traditional breeding in sesame and simultaneously document the benefits of genomics-assisted breeding to overcome these barriers with recent advancements in sesame. Moreover, the major constraints of sesame improvements will be discussed, and later, a new possible combined model by integrating conventional and genomics-assisted breeding will be suggested to speed up the breeding cycle, with challenges and future outlook towards adopting a multi-omics approach, installing advanced technologies, interoperable applications, etc., to develop climate-resilient sesame varieties.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01654-9.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"31"},"PeriodicalIF":3.6,"publicationDate":"2026-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13035980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147593237","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 rapid, accurate and low-cost genomics-based seed quality control system for pigeonpea hybrids - a model for field crops.","authors":"Rachit K Saxena, Abhishek Bohra, K B Saxena, C V Sameer Kumar, Anupama J Hingane, Rajeev K Varshney","doi":"10.1007/s11032-026-01653-w","DOIUrl":"10.1007/s11032-026-01653-w","url":null,"abstract":"<p><p>Exploitation of hybrid vigour has led to a dramatic increase in yield and resistance performance in several crops. However, maintenance of genetic purity during large-scale production of hybrid seeds is a long-standing constraint in both public research organisations and the seed industry. This affects both the breeding efficiency as well as the supply of pure seed to growers. In a number of crop species, the seed production guidelines and procedures are ineffective in maintaining genetic purity of seed and were also found inadequate to meet the huge demand for quality seed. A new quality seed production scheme is proposed herewith that integrates the traditional seed production system and modern genetic marker technology. The DNA-marker-based assay is rapid, cost-effective, and can detect hidden genetic contamination of seed. We have also demonstrated the application of a seed testing model in pigeonpea hybrids. Our scheme is suitable not only for pigeonpea but in general for all crops.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01653-w.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"30"},"PeriodicalIF":3.6,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13031483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574548","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":"Multivariate colorimetric phenotyping reveals genetic loci associated with soybean seed coat pigmentation and epicatechin accumulation.","authors":"Eunsoo Lee, Sewon Park, Yeon Ju An, Jungmin Ha","doi":"10.1007/s11032-026-01655-8","DOIUrl":"10.1007/s11032-026-01655-8","url":null,"abstract":"<p><p>Seed coat pigmentation in soybean is controlled by complex genetic mechanisms involving structural and regulatory genes in the flavonoid biosynthetic pathway. Although brown seed coats are often associated with epicatechin (EC) accumulation, visual classification alone cannot reliably predict EC content. To quantitatively characterize seed coat coloration and its relationship with EC accumulation, we evaluated multivariate colorimetric traits (L*, a*, and b* values in the CIELAB color space) in 235 recombinant inbred lines (RILs) derived from Jinpung (yellow seed coat) and IT109098 (greenish-brown seed coat). Principal component analysis (PCA) of L*, a*, and b* values revealed that genotypes with detectable EC were confined to specific regions of the multivariate color space, indicating that EC accumulation is associated with coordinated color balance rather than overall pigmentation intensity. RILs with high EC content showed significantly lower L* (32.76 ± 2.49) and b* (13.18 ± 2.66) values and higher a* values (5.47 ± 1.31) than those with low EC content. Quantitative trait loci (QTL) mapping identified thirteen loci associated with L*, a*, b*, and principal component scores across chromosomes 01, 05, 06, 08, and 19 A major locus on chromosome 08 near the classical <i>I</i> locus explained a large proportion of phenotypic variance in pigmentation traits. In addition, loci on chromosomes 06 and 19 were associated with integrated color components, suggesting quantitative modulation of EC accumulation. Candidate genes within these regions included flavonoid 3'-hydroxylase and transcription factors such as <i>MYB117</i>, <i>MYB60</i>, and <i>TCP5</i>, supported by sequence variation and differential expression analyses. These findings demonstrate that multivariate colorimetric traits provide a useful phenotyping framework for dissecting seed coat pigmentation and EC accumulation and for pre-selecting high-EC soybean lines.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01655-8.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"28"},"PeriodicalIF":3.6,"publicationDate":"2026-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13022137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574542","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}