Molecular Breeding最新文献

{"title":"Integrated GWAS and selective sweep analysis reveals the genetic basis of flower color variation and domestication in soybean.","authors":"Meng Wang, Bingqi Zhang, Wei Zhang, Fentuan Yang, Hongwei Xun","doi":"10.1007/s11032-026-01688-z","DOIUrl":"10.1007/s11032-026-01688-z","url":null,"abstract":"<p><p>Flower color is a crucial morphological trait and evolutionary marker in soybean (<i>Glycine max</i>). However, its complex genetic architecture and domestication history remain incompletely understood. Here, we performed a genome-wide association study (GWAS) on 741 soybean accessions, comprising 411 cultivated and 330 wild accessions, using three distinct statistical models (GLM, MLM, and FarmCPU) with over 7.95 million SNPs, integrated with selective sweep and transcriptomic analyses. We identified two significant quantitative trait loci (QTLs) governing floral pigmentation. The major locus, <i>qFC13</i>, explaining 48.63% of the phenotypic variance, corresponds to the classical <i>W1</i> gene (<i>GmW82.13G060100</i>, encoding F3'5'H). It exhibits strong signatures of a hard selective sweep, driving the domestication transition from the exclusively purple flowers of wild soybeans to dimorphic variations in cultivars. Additionally, a novel candidate (<i>GmW82.13G060300</i>) was also pinpointed within the <i>W1</i> locus as a potential regulator significantly involved in the terpenoid biosynthetic pathway. Furthermore, we uncovered a novel locus, <i>qFC19</i>, explaining 6.24% of the phenotypic variation and functioning as a quantitative modifier under soft selection. Haplotype and spatiotemporal expression profiling delineated key candidate genes within <i>qFC19</i>, distinct haplotypes of these genes exhibit pronounced stratification across different soybean species and flower color phenotypes, revealing divergent distribution patterns correlated with domestication and trait variation. Ultimately, the identification of these genes defines a unique genetic foundation for soybean flower color and uncovers a complex regulatory landscape. This work advances our understanding of secondary metabolism evolution and establishes new targets for marker-assisted crop breeding.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01688-z.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 7","pages":"66"},"PeriodicalIF":3.6,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13319293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148369118","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":"RenSeq-derived SNPs used in mapping resistance to <i>Phytophthora sojae</i> and three <i>Pythium</i> spp. in multiple soybean RIL populations.","authors":"Elizabeth M Clevinger, Ruslan Biyashev, Brian Hodge, Alison E Robertson, Leah K McHale, Anne E Dorrance, M A Saghai Maroof","doi":"10.1007/s11032-026-01686-1","DOIUrl":"10.1007/s11032-026-01686-1","url":null,"abstract":"<p><p><i>Phytophthora sojae</i> and <i>Pythium</i> spp. cause important root diseases of soybeans resulting in millions of dollars of loss for producers every year. Our previous studies on mapping <i>Rps</i> (Resistance to <i>Ph. sojae</i>) genes and quantitative disease resistance loci (QDRL) towards <i>Ph. sojae</i> and <i>Pythium</i> species, respectively, identified key regions for resistance to these diseases on chromosomes 3, 6, 7, 8, 13, 14 and 18. The development of <i>R</i> gene enrichment and sequencing (RenSeq) have allowed for the expedited discovery of new nucleotide-binding, leucine-rich repeat (NLR)-encoding genes. This study focused on exploring the co-localization of <i>Rps</i> loci or QDRL regions with single nucleotide polymorphism (SNP) markers derived from sequences identified from a RenSeq study of germplasm varying for resistance to <i>Ph. sojae</i> or <i>Pythium</i> species. Another aspect of this study was to saturate the QDRL regions on chromosomes 6, 8 and 14 for resistance to multiple <i>Pythium</i> species utilizing conventional molecular and SNP markers developed from RenSeq analysis. Nineteen RenSeq SNP markers were selected for evaluation in six RIL populations related to resistance to <i>Ph. sojae</i> and/or <i>Pythium</i> as allele-specific KASP markers. Most RenSeq SNP markers co-localized within the <i>Rps</i> loci or QDRL regions in these RIL populations. The development of RenSeq SNPs and their co-localization with <i>Rps</i> loci or QDRL regions indicate their potential use in designing resistance gene-specific markers and their application for marker-assisted selection in soybean resistance breeding programs.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01686-1.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 6","pages":"64"},"PeriodicalIF":3.6,"publicationDate":"2026-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13264645/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148258788","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":"Improving clubroot resistance of cabbage cultivar 'Xiyuan 4' by foreground marker assisted selection and whole-genome re-sequencing background assisted selection.","authors":"Xinmeng Han, Jiabing Wu, Qi Liu, Dayong Wei, Jun Si, Xuesong Ren, Zujun Tang, Lei Wu, Qinfei Li, Hongyuan Song","doi":"10.1007/s11032-026-01685-2","DOIUrl":"https://doi.org/10.1007/s11032-026-01685-2","url":null,"abstract":"<p><p>Cabbage is severely threatened by clubroot disease worldwide. To improve the clubroot resistance of cabbage, clubroot resistance from '9LQ18-5' was introgressed into the susceptible parent 'F416' of commercial cabbage variety 'Xiyuan 4'. During the backcrossing program, clubroot resistant individuals were selected by CCR1 and CCR2 markers, whereas the background of backcrossing progenies was detected by whole genome re-sequencing in BC₃F₁ individuals. Among them, 21 - 9 with the highest recurrent parent genomic recovery (83.93%) was identified, and a 47 kb interval (42,986,635 - 43,033,590 bp) on chromosome C07 was defined linking with clubroot resistance. Based on the whole genome re-sequencing, 49 indel markers were developed for background selection of the individuals carrying CCR1 and CCR2 markers in BC₄F₁. Progenies derived from line 21 - 9 were screened for developing BC₄F₂, which exhibited ~ 90% background recovery rate, high morphological similarity to the recurrent parent 'F416', and high resistance to clubroot upon artificial inoculation. Among eight hybrids between BC₄F₂ individuals and 'E2' (the other parent of 'Xiyuan 4'), 'CR64' displayed comparable agronomic traits to 'Xiyuan 4' alongside significantly high clubroot resistance in the field. These results demonstrated that new 'F416' line with clubroot resistance was developed, and it could be used for breeding 'Xiyuan 4R' variety with enhanced clubroot resistance in cabbage.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01685-2.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 6","pages":"63"},"PeriodicalIF":3.0,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13253904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148252340","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":"Nan-Nong 999: a new wheat cultivar combining FHB resistance and high yield developed through molecular design breeding.","authors":"Zibo Yang, Fengxin Mao, Yiduo Zhang, Yang Yang, Zhongxin Kong, Guoqiang Li, Zhengzhong Gu, Haiyan Jia, Zhengqiang Ma","doi":"10.1007/s11032-026-01683-4","DOIUrl":"https://doi.org/10.1007/s11032-026-01683-4","url":null,"abstract":"","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 6","pages":"62"},"PeriodicalIF":3.0,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13246977/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148218368","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":"Genomic selection for seed yield enhances flax breeding efficiency.","authors":"Frank M You, Chunfang Zheng, John Joseph Zagariah Daniel, Pingchuan Li, Kenneth Jackle, Megan House, Bunyamin Tar'an, Sylvie Cloutier","doi":"10.1007/s11032-026-01684-3","DOIUrl":"10.1007/s11032-026-01684-3","url":null,"abstract":"<p><p>Genomic selection (GS) is a promising strategy to improve breeding efficiency for complex traits such as seed yield by enabling early selection and reducing reliance on extensive field testing. However, practical deployment of GS remains challenging due to limited training populations sizes and reduced predictive ability when models are applied to true breeding germplasm. In this study, we evaluated GS for flax (<i>Linum usitatissimum</i> L.) seed yield under realistic breeding scenarios, with a focus on across-population prediction (APP) and breeding decision support rather than model benchmarking. Using historical germplasm collections and a newly developed breeding-oriented population as training sets, GS performance was assessed across multiple independent test populations representing contemporary breeding lines evaluated in replicated yield trials. APP predictive abilities ranged from <i>r</i> = 0.67 to 0.84 depending on population relatedness when training and test populations were genetically aligned, supporting routine breeding deployment. Training population composition emerged as a key determinant of prediction success, with breeding-oriented populations consistently outperforming broad germplasm collections for predicting true breeding lines. Check-based selection analyses showed that GS reliably reproduced phenotypic advancement decisions while eliminating 61-91% of low-performing lines, resulting in 48-78% reduction in field evaluation costs for a typical cohort of 300 lines. Marker subsampling analyses further indicated that moderate-density genotyping-by-sequencing panels (~ 2,500-3,000 SNPs) are sufficient to achieve stable predictive abilities. Overall, these results demonstrate that GS for seed yield in flax is ready for routine integration into breeding programs, offering a practical pathway to reduce costs, accelerate breeding cycles, and enhance selection efficiency.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01684-3.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 6","pages":"61"},"PeriodicalIF":3.6,"publicationDate":"2026-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13230323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148163667","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>OsBBX19</i> encoding a CCT domain-containing protein controls heading date in rice.","authors":"Qinqin Yang, Siliang Xu, Peng Xu, Ling Liu, Xiaoxia Wen, Guifang Ma, Tao Liu, Baobi Wang, Zhaozhong Wu, Mili Luo, Junming Zhou, Yingxin Zhang, Qunen Liu, Lianping Sun, Xiaodeng Zhan, Shihua Cheng","doi":"10.1007/s11032-026-01681-6","DOIUrl":"https://doi.org/10.1007/s11032-026-01681-6","url":null,"abstract":"<p><p>Heading date is a pivotal agronomic trait that governs regional adaptation and grain yield in rice (<i>Oryza sativa</i> L.). The CCT domain‑containing protein OsBBX19 (also known as OsCCT22) has been previously identified as a heading‑date regulator. In this study, we further report the molecular functional characterization of <i>OsBBX19</i>. Overexpression of <i>OsBBX19</i> delayed heading under both short-day conditions (SDs) and long-day conditions (LDs). GUS staining and RT-qPCR analyses revealed that <i>OsBBX19</i> was constitutively expressed across various organs, and that its overexpression significantly suppressed the expression of <i>Hd3a</i>, <i>RFT1</i>, and <i>Ehd1</i> while increasing <i>Ghd7</i> expression, suggesting that <i>OsBBX19</i> is associated with the <i>Ghd7</i>-<i>Ehd1</i>-<i>Hd3a</i>/<i>RFT1</i> flowering pathway. We also demonstrated that OsBBX19 physically interacts with CONSTANS-like protein interacting protein 1 (CPIP1). Haplotype analysis revealed significant <i>indica</i>-<i>japonica</i> differentiation of <i>OsBBX19</i>, and the frequency of Hap3 and Hap5 increased during the improvement process of <i>indica</i> rice. Collectively, our results provide additional insights into the molecular mechanism by which <i>OsBBX19</i> regulates heading date in rice, offering potential genetic resources for breeding optimization.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01681-6.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 6","pages":"60"},"PeriodicalIF":3.0,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13222157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148143930","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":"Pyramiding <i>nn1</i>6 and <i>rin1</i> alleles to balance plant height and node number at high latitudes.","authors":"Jialin Zhang, Yulin Wang, Jiemin Chen, Sijia Lu, Baohui Liu, Tong Su, Shichen Li","doi":"10.1007/s11032-026-01682-5","DOIUrl":"https://doi.org/10.1007/s11032-026-01682-5","url":null,"abstract":"<p><p>Breeding dwarf or semi-dwarf soybean varieties is an effective strategy to enhance lodging resistance and thereby increase yield potential. However, soybean plant height is co-determined by the number of nodes and internode length. Reducing plant height often leads to a decrease in node number, which subsequently reduces pod number and ultimately results in lower yield. Thus, balancing node number and internode length is of great significance for increasing soybean yield. Here, we identified a node number-regulating locus, <i>NUMBER of NODES 16</i> (<i>NN16</i>), encoded by <i>FLOWERING LOCUS T</i> (<i>FT5a</i>). Variations in the promoter and 3' untranslated region (3' UTR) of <i>nn16</i> downregulate its expression and increase node number. In addition, the <i>reduced internode 1</i> (<i>rin1</i>) gene that we previously reported shortens internode length but slightly reduces node number. To increase node number while shortening internode length, we constructed near-isogenic lines (NILs) carrying the genotypes <i>RIN1</i> ^<i>HH43</i> <i>/NN16</i>, <i>rin1/nn16</i>, <i>RIN1</i> ^<i>HH43</i> <i>/nn16</i>, and <i>rin1/NN16</i>. Among these NILs, the <i>rin1</i>/<i>nn16</i> genotype showed optimal plant height and the highest seed weight per plant. Collectively, our findings provide theoretical support and breeding resources for cultivating soybean cultivars with shortened internodes and increased node number, thereby further improving seed weight per plant.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01682-5.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 6","pages":"59"},"PeriodicalIF":3.0,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13221557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148138545","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":"High resolution mapping and development of diagnostic KASP markers for FHB resistance QTL on chromosome 1B in an elite soft red winter wheat cultivar 'Jamestown'.","authors":"Lovepreet Singh, Anmol Kajla, Prem Kumar Ganesan, Yanhong Dong, Gina Brown Guedira, Jared Smith, Vijay Tiwari, Nidhi Rawat","doi":"10.1007/s11032-026-01680-7","DOIUrl":"10.1007/s11032-026-01680-7","url":null,"abstract":"<p><p>Fusarium Head Blight (FHB) is a serious disease of wheat, causing yield and quality losses to the grain. Genetic resistance is one of the most important strategies to manage FHB. QTL from unadapted genetic backgrounds, such as wild relative species and exotic landraces, have been used in wheat breeding lines across the world. However, deployment of such sources poses problems associated with linkage drag, that impede their quick deployment in cultivars. Previously, we reported mapping of an FHB resistance QTL on chromosome 1B of an elite soft red winter wheat (SRW) cultivar Jamestown using Recombinant Inbred Lines (RIL) populations. In this work, we developed a high-resolution mapping population with 475 individuals by crossing resistant and susceptible RILs. Genome-specific KASP markers were developed and used to genotype the population. Phenotyping, followed by progeny testing of the recombinants, reduced the genetic interval to a 3 Mb region predicted to contain 17 high-confidence genes in the corresponding region in the Chinese Spring reference genome ver 1.0. The KASP marker flanking the 1B QTL region was validated on the SRW breeding germplasm of the Eastern US, which showed improved correlation over the previous markers used for MAS of this QTL. This work will facilitate breeding of 1B_FHB QTL from Jamestown to wheat varieties widely.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01680-7.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 6","pages":"57"},"PeriodicalIF":3.6,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13219567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148138566","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 signatures of selection and genetic diversity reveal the impact of modern breeding on Brazilian soybean.","authors":"Brizza Vargas, Newton Deniz Piovesan, Cleberson Ribeiro, Maximiller Dal-Bianco","doi":"10.1007/s11032-026-01679-0","DOIUrl":"10.1007/s11032-026-01679-0","url":null,"abstract":"<p><p>Soybean (Glycine max (L.) Merr.) breeding in Brazil has driven remarkable gains in yield and adaptation; however, intensive selection raises concerns regarding the erosion of genetic diversity in modern cultivars. Here, we conducted a genome-wide analysis of genetic diversity, population structure, linkage disequilibrium, and selection signatures in Brazilian soybean germplasm using high-density SNP genotyping. Ninety-five genotypes from the Soybean Breeding Program for Quality Traits at UFV, including commercial cultivars and advanced breeding lines from both in-house and external sources, representing different breeding periods were genotyped with the 180K Axiom® Soybean SNP array, and 61,712 high-quality SNPs were retained after quality control. Population structure analyses consistently identified two main genetic groups largely corresponding to older and modern cultivars, along with an admixed group. Modern cultivars exhibited reduced nucleotide diversity and lower Tajima's D values compared with older genotypes, while AMOVA, Fst, and Nei genetic distance estimates indicated moderate genetic differentiation between populations. Genome-wide linkage disequilibrium was extensive, with slow LD decay, reflecting the effects of self-pollination, domestication bottlenecks, and strong directional selection. BayeScan analysis detected 581 SNPs exhibiting signatures of positive directional selection (α > 0), indicating elevated genetic differentiation between groups, many of which overlapped with previously reported QTLs related to yield components, seed composition, and plant architecture. A pronounced selection hotspot on chromosome 19 showed near-complete haplotype differentiation between older and modern cultivars, highlighting a genomic region repeatedly targeted during recent breeding cycles. Together, these results demonstrate that contemporary soybean breeding in Brazil has reshaped genome-wide diversity by intensifying selection at key loci while maintaining a narrow genetic base, providing important insights for future breeding strategies aimed at sustaining long-term genetic gain.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01679-0.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 6","pages":"58"},"PeriodicalIF":3.6,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13219583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148138437","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":"Genetic dissection of apricot fruit skin color (<i>Prunus armeniaca</i> L.) using SNP and SSR molecular markers.","authors":"Germán Ortuño-Hernández, Lorenzo Bergonzoni, Stefano Tartarini, Mónica Moya-Andreo, Jesús López-Alcolea, David Ruiz, Pedro Martínez-Gómez, Luca Dondini, Juan Alfonso Salazar","doi":"10.1007/s11032-026-01674-5","DOIUrl":"10.1007/s11032-026-01674-5","url":null,"abstract":"<p><p>Fruit skin color is a key quality trait in apricot, strongly influencing consumer preference and market value. However, phenotypic evaluation of this trait is time-consuming and highly dependent on environmental conditions and harvest timing. This study aimed to develop reliable molecular markers associated with apricot skin color to support marker-assisted selection in breeding programs. A major skin color QTL located on chromosome 3 was explored, leading to the identification of an AP2/ERF domain-containing gene involved in carotenoid regulation. Within this gene, both SNP and SSR polymorphisms were characterized. High-resolution melting (HRM) analysis validated a highly significant SNP associated with fruit skin color in a segregating 'Goldrich' × 'Currot' population and in a panel of 57 apricot cultivars. The HRM-based SNP marker accurately discriminated between orange- and yellow-skinned fruits, reaching 100% efficiency in the segregating population and 89.5% in the cultivar set. In parallel, SSR markers developed within the AP2/ERF gene revealed allelic variation associated with skin color, with one SSR marker achieving an efficiency of 93.9%. Allelic and protein sequence reconstruction demonstrated that variation in polyalanine tract length and non-synonymous amino acid substitutions generate functional diversity in the AP2/ERF protein. Notably, this analysis indicated that a marker based on SNP4 (S3_22924316), which directly affects the protein sequence, may provide enhanced discriminatory power. comparable to that previously observed for the SSR-based marker. Overall, these results provide both mechanistic insight into apricot color regulation and practical molecular tools for efficient breeding.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11032-026-01674-5.</p>","PeriodicalId":18769,"journal":{"name":"Molecular Breeding","volume":"46 6","pages":"50"},"PeriodicalIF":3.6,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13197536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148016468","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}