Molecular Breeding最新文献

{"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":"https://doi.org/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":3.0,"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":"https://doi.org/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":3.0,"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":"https://doi.org/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":3.0,"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":"https://doi.org/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":3.0,"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":"https://doi.org/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":3.0,"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":"https://doi.org/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":3.0,"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}

{"title":"Genome-wide association analysis of yield-related traits and identification of candidate genes in Sugarcane (<i>Saccharum spontaneum</i> L.).","authors":"Lijun Zhang, Meixing Xie, Ganfeng Zhuo, Zhen Wang, Xiping Yang","doi":"10.1007/s11032-026-01652-x","DOIUrl":"https://doi.org/10.1007/s11032-026-01652-x","url":null,"abstract":"<p><p>Sugarcane (<i>Saccharum</i> spp.) is the primary source of global sugar production, contributing for approximately 80% of the world's sucrose output. Despite its economic importance, the genetic basis underlying key agronomic traits in sugarcane remains largely uncharacterized. In this study, we conducted a genome-wide association study (GWAS) to investigate the genetic architecture of yield-related traits, including stalk length, stalk diameter, internode number, and single stalk weight, in a diverse panel of 251 wild sugarcane accessions (<i>S. spontaneum</i>). We identified 67 significant quantitative trait loci (QTLs) associated with yield using three GAPIT models (MLM, FarmCPU, and BLINK), of which 19 were stably detected. These QTLs explained 0.42%-57.96% of the phenotypic variation. Our results indicated that candidate genes in QTLs associated with single stalk weight were mainly enriched in metabolic pathways, including brassinosteroid biosynthesis and ubiquitin‑mediated proteolysis, whereas those for stalk length were enriched in pathways involved in cell wall biosynthesis. Additionally, candidate genes in QTLs associated with stalk diameter and internode number exhibited enrichment in functional categories related to arabinose kinase activity and nitrate transport, respectively. In summary, these findings not only elucidate the genetic bases of yield-related traits in sugarcane but also provide valuable genomic resources for molecular breeding, thereby accelerating varietal improvement and enhancing sugarcane yield.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01652-x.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 4","pages":"29"},"PeriodicalIF":3.0,"publicationDate":"2026-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13022120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574544","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 a novel fruit-length locus <i>Cpfl17.1</i> and development of near-isogenic lines by marker-assisted selection in <i>Cucurbita pepo</i> L.","authors":"Liuqing Sun, Yapei Sun, Xiyan Qiu, Wanlu Chen, Kiros Gebretsadik, Ying Duan, Qunfeng Lou, Changlin Wang, Kailiang Bo","doi":"10.1007/s11032-026-01646-9","DOIUrl":"10.1007/s11032-026-01646-9","url":null,"abstract":"<p><p>Pumpkin (<i>Cucurbita pepo</i> L.) is an economically important vegetable crop, and fruit size is a key agronomic trait determining its commercial value. Quantitative trait loci (QTLs) controlling fruit length (FL) have been widely studied in other cucurbit species, but few such studies have been reported in pumpkin. In this study, a short-fruited line Jin-GL was crossed with a long-fruited line Nei. The F₂ population displayed continuous fruit-length variation (5-25 cm). When classified using the F₁ mean FL (approximately 11 cm) as a threshold, the F₂ individuals showed a segregation of 191 short vs. 79 long (191:79; close to 3:1), supporting the presence of a major-effect locus. Then, we fine mapped the locus, designated <i>Cpfl17.1</i>, into a 21.6 kb interval. To construct the near-isogenic lines (NILs), three generations of backcrossing the F₁ to each parent were developed. The flanking markers InDel17-8 and InDel17-13 were used for foreground selection, and a total of 101 InDel markers was selected with good polymorphism between two parental lines for background selection which had relatively uniform distribution across 20 chromosomes. The proportion of recurrent parent genome (PRPG) of the NILs is larger than 98%. And the FL phenotypes showed significantly differ between the NILs and recurrent parent. Comparison with previously reported fruit-length QTLs showed no positional overlap with <i>Cpfl17.1</i>, suggesting that it may represent an independent locus. Our results demonstrate that <i>Cpfl17.1</i> is a new breeding target for marker-assisted selection, which will facilitate precise introgression of fruit shape-related alleles and accelerate the development of new varieties with improved fruit shape.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01646-9.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 3","pages":"26"},"PeriodicalIF":3.0,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12965950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147378056","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":"Accelerated development of rice near-isogenic lines based on rapid generation advance (RGA) and target capture sequencing (TCS).","authors":"Seung-Kyo Jeong, So-Myeong Lee, Jin-Kyung Cha, Hyeonjin Park, Sumin Jo, Ju-Won Kang, Ye Rin An, Woo-Jae Kim, Jong-Hee Lee, Youngho Kwon","doi":"10.1007/s11032-026-01647-8","DOIUrl":"https://doi.org/10.1007/s11032-026-01647-8","url":null,"abstract":"<p><p>Developing new crop cultivars with enhanced disease resistance, stress tolerance, and superior quality is urgently needed to address climate change and evolving agricultural demands. However, conventional breeding methods, particularly the development of near-isogenic lines (NILs), are notoriously time-consuming and labor-intensive. This study presents an innovative, integrated strategy to accelerate rice NIL development by combining a Rapid Generation Advance (RGA) system, Target Capture Sequencing (TCS), and a bulk DNA-based background selection approach applied at an advanced generation (BC₂F₆). Our strategy successfully established a NIL population within four years, a process traditionally requiring nearly a decade. The developed NILs exhibited a high recurrent parent genome (RPG) recovery rate, averaging 90.8% and reaching up to 97.2%. We validated the successful introgression of target genes, including <i>x</i> <i>a5</i> (bacterial blight resistance) and Pita-2 (blast resistance), through both phenotypic and genotypic analyses. Notably, our RGA system utilized natural short-day conditions, effectively overcoming photoperiod sensitivity constraints in late-maturing cultivars and enabling two generations per year. This integrated strategy provides a scalable and efficient framework that dramatically reduces the time, labor, and costs associated with conventional NIL development while ensuring high precision, offering significant potential to accelerate functional genomics and marker-assisted breeding programs in rice and other major crop species.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01647-8.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 3","pages":"25"},"PeriodicalIF":3.0,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12957748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147366081","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":"Dissecting the genetic basis of seed-iron content in Chickpea using a combinatorial approach of QTL-Seq and molecular haplotyping.","authors":"Gourav Singh, Anirban Chakraborty, Sangeeta Singh, Shubham Bhardwaj, Swarup K Parida, Sabhyata Bhatia","doi":"10.1007/s11032-026-01644-x","DOIUrl":"10.1007/s11032-026-01644-x","url":null,"abstract":"<p><p>In order to map the QTL(s) and genes regulating the complex seed-iron content (SFC) trait in chickpea, the quantitative trait locus (QTL)-seq approach was used. Whole genome re-sequencing of DNA bulks derived from a mapping population (ICC8261 × 1CC4958) contrasting for SFC led to the identification of three QTLs, [<i>CaqFe4.1</i> (0.10 Mb<i>)</i>, <i>CaqFe4.2</i> (0.54 Mb) and <i>CaqFe7.1</i> (0.83 Mb)] in chickpea. In-silico expression analysis of genes underlying the QTLs revealed their varied levels during stages of seed development. Moreover, estimation of G' values of the SNPs identified in the QTL region revealed a SNP that generated synonymous variant of the <i>MAIN-like-2</i> gene. Haplotype analysis of <i>MAIN</i>-<i>like-2</i> in a diverse panel of chickpea germplasm varying for SFC further exemplified its haplotypes that displayed strong association to this trait. Homology-based protein interaction analysis coupled with quantitative-real time PCR based-expression analysis revealed several co-expressing co-chaperone and heat shock proteins including P23-1, HSP 90.5 and HSP90.6, having well established roles in seed development as protein components of MAIN-like-2 proteins in chickpea. The functional loci as well as the molecular signatures defined in this study have potential to expedite marker assisted breeding of iron-rich chickpea varieties.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01644-x.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 3","pages":"24"},"PeriodicalIF":3.0,"publicationDate":"2026-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12950154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147344691","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}