Molecular Genetics and Genomics最新文献

{"title":"Unlocking genetic hotspots: GWAS reveals key nitrogen responsive genomic regions and key genes for root and yield traits in indica rice.","authors":"Ankur Poudel, Sachin Phogat, Jeet Roy, Manish Ranjan Saini, K M Shivaprasad, Jayanthi Madhavan, Viswanathan Chinnusamy, K K Vinod, Amitha Mithra Sevanthi, Pranab Kumar Mandal","doi":"10.1007/s00438-025-02249-3","DOIUrl":"https://doi.org/10.1007/s00438-025-02249-3","url":null,"abstract":"<p><p>Nitrogen (N) induced environmental pollution from rice cultivation has resulted in undesired environmental impacts. To minimize the impacts, improvement of inherent NUE is very crucial in rice as it has the lowest NUE among the cereals. Though many family based and association based QTL studies have been reported earlier on NUE in rice, the reports on indica rice and precise evaluation of root parameters till physiological maturity is lacking. This study reports the identification of candidate genes and QTLs through a genome-wide association study (GWAS) involving 96 diverse indica rice genotypes, grown under contrasting N regimes in hydroponics till maturity. Genotyping was carried out using 80 K Affymetrix chip containing 47,686 curated SNP markers. The differential response of ten different N-responsive traits indicated separate breeding program for each N-regime. The population structure analysis revealed two sub-populations with varying degrees of admixtures in the association panel. The linkage disequilibrium (LD) analysis revealed a LD block of 108.4 kb. GWAS using MLM, FarmCPU, and BLINK could identify 568 marker-trait associations (MTAs) across different traits and N-conditions. Out of 24 common MTAs identified, 13 were novel with 156 candidate genes in the genomic region spanning the LD blocks. Yield and root-related MTAs were found to be the most prominent. N-responsive genes were found to be associated with other abiotic stresses like drought and salinity, as seen from the available literature. Candidate genes (OsWAK15, OsNIN8, OsHCT2, Os02 g0612900, Os02 g0613100, and Os02 g0612700) showed a similar expression pattern under N-stress in both N use- efficient and inefficient genotypes, which can be potential targets for modulating gene expression for N stress tolerance. These MTAs and candidate genes can serve as key resources for enhancement of NUE in rice upon functional validation.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"53"},"PeriodicalIF":2.3,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring virulence characteristics of Klebsiella pneumoniae isolates recovered from a Greek hospital.","authors":"Lazaros A Gagaletsios, Andreas Tagkalegkas, Ibrahim Bitar, Costas C Papagiannitsis","doi":"10.1007/s00438-025-02258-2","DOIUrl":"https://doi.org/10.1007/s00438-025-02258-2","url":null,"abstract":"<p><p>The objective of this study was to characterize the virulence characteristics of a collection of Klebsiella pneumoniae isolates collected from different clinical sources. A collection of 60 non-repetitive K. pneumoniae isolates, was studied. In vitro, virulence was analyzed by testing the survival of bacteria in pooled human serum. Isolates were typed by MLST. The genomes of 23 K. pneumoniae isolates, representatives of different STs and virulence profiles, were completely sequenced using the Illumina platform. Of note, 26/60 of K. pneumoniae isolates were resistant to killing by complement. Serum-resistant isolates belonged to distinct STs. Analysis of WGS data with VFDB showed the presence of several virulence genes related various virulence functions. Specifically, serum-resistant isolates carried a higher number of ORFs, which were associated with serum resistance, compared to serum-sensitive isolates. Additionally, analysis of WGS data showed the presence of multiple plasmid replicons that could be involved with the spread and acquisition of resistance and virulence genes. In conclusion, analysis of virulence characteristics showed that an important percentage (31.6%) of K. pneumoniae isolates were in vitro virulent by exhibiting resistance to serum. Thus, the presence of several virulence factors, in combination with the presence of multidrug resistance, could challenge antimicrobial therapy of infections caused by such bacteria.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"52"},"PeriodicalIF":2.3,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polymorphic amino acid tract lengths in wine yeast coding microsatellites: different S. cerevisiae YPL009c and SCYOR267C alleles predict proteins with major primary sequence and structural alterations without apparent functional disruption.","authors":"María Laura Raymond Eder, Agustina Caffaratti, Alberto Luis Rosa","doi":"10.1007/s00438-025-02257-3","DOIUrl":"https://doi.org/10.1007/s00438-025-02257-3","url":null,"abstract":"<p><p>Yeast microsatellite loci consist of short tandem-repeated DNA sequences of variable length useful for strain differentiation, population genetics, and evolutionary biology. We have previously shown that, besides the variable number of their tandem-repeated motifs (TRM), allelic variants for some microsatellite loci of wine yeast species are also dependent on SNPs and/or indels flanking their TRM. In this work, we show that TRM for some microsatellite loci of the wine yeasts H. uvarum, S. cerevisiae, T. delbrueckii, B. bruxellensis, and M. guilliermondii are located within protein-coding sequences, most of them resulting in predicted polymorphic tracts of charged amino acid residues (i.e., E, Q, D, and N). In silico analyses predict that variations in the TRM lengths of S. cerevisiae microsatellites YPL009c and SCYOR267C, located within the coding sequences of the RQC2 and HRK1 genes, respectively, significantly disrupt the structure of the encoded proteins Rqc2 and Hrk1. Indigenous S. cerevisiae strains carrying TRM allelic variants that could potentially disrupt Rqc2 and Hrk1 function, do not exhibit the increased sensitivity to cycloheximide and acetic acid observed in ΔRQC2 and ΔHRK1 deletion strains, respectively. Interestingly, S. cerevisiae isolates carrying identical TRM alleles in either the RQC2 or HRK1 genes exhibit different growth behaviors in response to cycloheximide or acetic acid, suggesting that the genomic background contributes to the observed phenotypes. Taken together, our results suggest that coding microsatellites are common in wine yeast and may be located in regions of proteins that do not disrupt their function, and/or in proteins with a high degree of structural plasticity.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"51"},"PeriodicalIF":2.3,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144143011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The whole genome sequence of Cordyceps cicadae - an edible and potential medicinal fungus.","authors":"Yuwei Liu, Xueqian Li, Yiqi Meng, Yifan Wu, Yuting Jin, Xiaotong Ma, Wei Zhou, Yuchong Tan, Fu-Cheng Lin, Hongkai Wang","doi":"10.1007/s00438-025-02255-5","DOIUrl":"https://doi.org/10.1007/s00438-025-02255-5","url":null,"abstract":"<p><p>Cordyceps cicadae is an entomopathogenic fungus from the Cordyceps genus and a well-known edible mushroom with a long history of use in Asia. It contains many bioactive compounds beneficial to human health, giving it broad application prospects in medicine. In this study, we generated the complete genome sequence of C. cicadae strain 2-2 using a combination of Illumina, PacBio, and Hi-C sequencing technologies. This comprehensive genome sequence comprises 9 chromosomes, an N50 contig size of 4,798,690 bp, a GC content ratio of 52.65%, a total size of 34.60 Mb, and 8,019 predicted coding genes. Additionally, we conducted functional annotation of the genome, revealing that 63.2% of the genes were enriched in 50 GO terms and 87.8% in 387 KEGG pathways. We also identified 542 enzyme genes, noting that C. cicadae has a greater number of GHs compared to other fungi in the Cordyceps genus. Notably, NR database analysis revealed that 6,441 genes in C. cicadae are similar to those in Cordyceps fumosorosea, suggesting that C. cicadae may serve as a cost-effective alternative to this expensive traditional medicinal fungus. This study presents the first chromosome-level genome of the Cordyceps genus, providing a comprehensive analysis of the genetic composition and functions of C. cicadae and establishing a foundation for advancing research and development of Cordyceps fungi.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"50"},"PeriodicalIF":2.3,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HES1 in cancer: a key player in tumorigenesis and its prognostic significance.","authors":"Venkataraman Magesh, Ramya Sekar, Abdullah AlZahrani, Rajkapoor Balasubramanian, Salaheldin Abdelraouf Abdelsalam, Peramaiyan Rajendran","doi":"10.1007/s00438-025-02259-1","DOIUrl":"https://doi.org/10.1007/s00438-025-02259-1","url":null,"abstract":"<p><p>The dysregulation of transcriptional regulators is a critical feature in the progression of many malignancies. Hairy and enhancer of split homolog-1 (HES1), a member of the basic helix-loop-helix (bHLH) gene family, has emerged as a key player in tumorigenesis due to its regulatory roles in multiple cellular pathways. This review aims to systematically explore the relevance of HES1 in cancer development, emphasizing its activation through major signaling pathways such as Notch, Hedgehog, hypoxia, and Wnt, and its contribution to advanced tumor progression. Numerous studies have demonstrated that HES1 upregulates genes associated with stemness, proliferation, and metastasis, and its expression correlates with poor clinicopathological features, including enhanced tumor proliferation, self-renewal, migration, metastasis, and drug resistance. Furthermore, HES1 has been frequently identified as a downstream effector of critical oncogenic pathways, further consolidating its role in aggressive cancers. Based on current evidence, HES1 holds promise as both a prognostic biomarker and a potential therapeutic target in various lethal malignancies. A deeper understanding of HES1's molecular mechanisms could pave the way for the development of targeted interventions aimed at improving cancer outcomes.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"49"},"PeriodicalIF":2.3,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic associations unravel genomic regions/candidate genes of salt stress memory via enhancing antioxidant defense system in wheat.","authors":"Nora M Al Aboud, Fatmah Ahmed Safhi, Ahmad M Alqudah, Samar G Thabet","doi":"10.1007/s00438-025-02251-9","DOIUrl":"https://doi.org/10.1007/s00438-025-02251-9","url":null,"abstract":"<p><p>The concept of stress memory where plants \"remember\" previous exposure to stress and react more robustly upon subsequent exposures has gained traction in recent years. Therefore, this study successfully identifies key genetic loci and alleles that enhance stress memory in wheat, specifically focusing on germination parameters and antioxidant activities using a genome-wide association study (GWAS) under salt stress. Our study revealed that salt-stressed wheat genotypes showed highly significant increases in all germination traits and antioxidants compared to non-stressed wheat plants. For salt-stressed wheat genotypes, SOD showed highly significant positive correlations with DW, APX, and GR (r = 0.99***, 0.99***, 0.70***), respectively. These strong correlations suggest that SOD, along with APX and GR, plays a critical role in maintaining growth and enhancing antioxidant defense mechanisms in wheat under salinity stress conditions. Inside the linkage disequilibrium, 81 significant SNP markers were detected to be associated with our trait of interest. Furthermore, the study's exploration of several potential candidate genes involved in the \"stress memory\" effect provides a novel perspective on the adaptive responses of wheat to salinity stress. For instance, the gene TraesCS2B02G194200 is annotated as glycosyltransferase activity. Interestingly, glycosyltransferases play a critical role in mediating salt stress tolerance in cereal crops by modulating key metabolic pathways and enhancing the stability of cellular components. The presence of the G allele in this SNP was associated with higher antioxidant content in wheat genotypes compared to those carrying the A allele, indicating that selecting wheat genotypes with the G allele could enhance antioxidant defense, potentially leading to improved tolerance to salt stress. Identifying genes associated with this effect sheds light on the molecular mechanisms that enable plants to retain and pass on adaptive responses across generations and opens new avenues for targeted breeding and genetic engineering. These genes could serve as valuable targets for developing wheat varieties with enhanced salinity tolerance, providing a means to harness and enhance natural adaptive processes through crop improvement strategies.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"48"},"PeriodicalIF":2.3,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144027537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome sequence, CAZyme repertoire and sugar metabolic model of the phytopathogenic fungus Kretzschmaria zonata GFP 132.","authors":"Mariana Regina Almas do Carmo, Alessia Manassero, Rafaela Zandonade Ventorim, Mao Peng, Tulio Morgan, Kurt LaButti, Anna Lipzen, Steven Ahrendt, Igor V Grigoriev, Vivian Ng, Maxin Koriabine, Diane Bauer, Elodie Drula, Bernard Henrissat, Rafael Ferreira Alfenas, Ronald P de Vries, Gabriela Piccolo Maitan-Alfenas","doi":"10.1007/s00438-025-02253-7","DOIUrl":"https://doi.org/10.1007/s00438-025-02253-7","url":null,"abstract":"<p><p>Kretzschmaria zonata is an ascomycete fungus known as a significant plant pathogen that causes serious damage to teak plantations, but little is known about its genomic and metabolic features. Studies suggest this fungus is an interesting source of cell wall degrading enzymes. This study evaluated the genome and the diversity of genes encoding carbohydrate-active enzymes (CAZymes) of Kretzschmaria zonata GFP 132. The fungal ability to grow on different carbohydrates and its sugar metabolic network were also investigated. The findings were compared with other fungi, taxonomically close, phytopathogens or fungi known as good producers of plant cell wall degrading enzymes (CWDE). The assembled genome corresponding to 30.15 Mbp and 12,135 protein-coding genes, had approximately 5% of total protein-coding genes as putative CAZymes. In general, the closely related fungi, K. deusta, Hypoxylon submonticulosum, and Xylaria cf. heliscus exhibited a similar CAZymes profile. When compared with other phytopathogenic fungi, the variation in the CAZyme profile suggests that it does not accompany the similar species' lifestyle. Curiously, the repertoire of genes encoding CDWE was similar to Aspergillus niger, an Eurotiomycete, and different from Trichoderma reesei which is Sordariomycete like K. zonata. Based on genome, K. zonata possesses a complete sugar metabolic network, except for an absent gene in the galacturonic acid metabolic pathway. This is consistent with the inability of the fungus to grow in galacturonic acid as the sole carbon source. Finally, K. zonata was able to assimilate a wide range of mono and polysaccharides as carbon source, which opens perspectives for new studies to obtain new enzymes required to increase the efficiency of existing biotechnological industrial processes.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"47"},"PeriodicalIF":2.3,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144018435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of oxidative stress-related subgroups and signature genes for the prediction of prognosis and immune microenvironment in thyroid cancer.","authors":"Zhenwei Qiu, Jing Li, Mei Tian","doi":"10.1007/s00438-025-02252-8","DOIUrl":"https://doi.org/10.1007/s00438-025-02252-8","url":null,"abstract":"<p><p>Oxidative stress plays a crucial role in cancer progression and tumor immune microenvironment (TIME) modulation. However, its impact on thyroid cancer (THCA) subtypes and prognosis remains unclear. This study aimed to identify oxidative stress-related subgroups and construct a prognostic gene signature to enhance personalized treatment strategies in THCA. Using consensus clustering analysis, we categorized TCGA-THCA patients into two subgroups based on oxidative stress-related genes (OSRGs) expression. Cluster 1 had a poorer prognosis, higher BRAF mutation rates, and a suppressive TIME with fewer CD8 T cells. Kaplan-Meier survival analysis confirmed these findings. Six key OSRGs (BMI1, CDK5, IL1RN, PDP1, TP53, UCN) that significantly predicted THCA prognosis were identified. A risk model based on these genes accurately stratified patients into high and low-risk groups, with the high-risk group showing significantly worse outcomes. The model's predictive performance was validated by ROC analysis. Nomogram revealed that higher OSRG-related risk score indicated lower survival probability in THCA patients. In vitro validation confirmed the high expression of six OSRGs in THCA cells and tissues, with most being associated with the Wnt signaling pathway. Additionally, IL1RN knockdown significantly inhibited THCA cell malignant characteristics and reduced ROS generation. This study provided a novel oxidative stress-related classification system for THCA, highlighting key signature genes with prognostic and therapeutic relevance. These results may guide future research on oxidative stress-targeted therapies and immune modulation in THCA.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"46"},"PeriodicalIF":2.3,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12043743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical classification and molecular interpretation of germline pathogenic TP53 variations detected by multigene panel testing in patients with possible cancer predisposition.","authors":"Gizem Onder, Busra Unal, Ozkan Ozdemir, Ufuk Amanvermez, Merve Acıkel Elmas, Merve Gokbayrak, Cansu Ugurtas, Naci Cine, İrem Kalay, Ugur Ozbek, Ozden Hatirnaz Ng, Nihat Bugra Agaoglu","doi":"10.1007/s00438-025-02250-w","DOIUrl":"https://doi.org/10.1007/s00438-025-02250-w","url":null,"abstract":"<p><p>Advances in high-throughput sequencing have increased the detection of TP53 variations, many of which occur at low allelic fractions. Such variants may arise due to clonal hematopoiesis (CHIP) or constitutional mosaicism, complicating their clinical classification and management. Since guidelines recommend Li-Fraumeni syndrome (LFS)-like management for individuals carrying TP53 variations, accurately determining the origin of low variant allelic fraction (VAF) variants is essential for risk assessment and clinical decision-making. This study evaluates TP53 VAF in patients with suspected hereditary cancer predisposition, tested via multigene panels and emphasizes the importance of conducting a detailed investigation before making clinical decisions in patients with low-VAF. In retrospectively analyzed 1,520 cases, we identified 17 actionable TP53 variations in 16 cases (1%). All cases were female (mean cancer onset age of 45.9 years) and classified as attenuated LFS. Eleven of the variants had an allelic fraction of ≤ 20%. Patients over 60 years showed significantly lower VAF than those under 40 (p = 0.03). The TP53 variant was detected in only one ancillary sample, and her tumor sample was monoallelic, confirming the germline origin. For an accurate classification and successful management of cases with TP53 variations, defining the origin of variants, especially for low VAF, is imperative.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"45"},"PeriodicalIF":2.3,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic dissection of total protein content, phenolic content and seed quality traits in pigeonpea (Cajanus cajan) using 62K pigeonpea genic SNP chip.","authors":"Megha Ujinwal, Nisha Singh, Sapna Langyan, Nagendra Kumar Singh","doi":"10.1007/s00438-025-02235-9","DOIUrl":"https://doi.org/10.1007/s00438-025-02235-9","url":null,"abstract":"<p><p>Pigeonpea (Cajanus cajan L. Millsp.), South Asia's second most significant pulse crop and source of dietary protein, is facing production issues due to a lack of improved varieties with high nutritional and seed quality compositions, as well as environmental stress. Identification of genes/alleles governing the nutritional and seed quality traits is key for marker-assisted breeding for quality traits in pigeonpea. Hence, the present study was undertaken to unravel the complex genetic architecture of nutritional and seed quality traits in pigeonpea. We conducted a genome-wide association study (GWAS) to identify SNP markers associated with nutritional traits, namely total protein content (TPC), phenolics content, and seed quality traits, such as seed coat colour, length, width, size, shape, and weight using a 62K SNP genotyping chip array. We estimated TPC of a panel of 287 diverse pigeonpea genotypes using Kjeldahl method to identify 5 significant SNPs associated with TPC on chromosomes 6 and 11 (AX-165344137), encoding a putative disease resistance protein, and Chromosome 11 (AX-165358192), encoding a CBL-interacting serine/threonine-protein kinase. We identified five markers associated with the seed coat colour on Chromosomes 5 (AX-165369586), 2 (AX-165370277), and 8 (AX-165400346). Additionally, we identified 4, 6, 2, 3, 6, and 5 SNPs associated with phenolics content, seed length, seed shape, seed width, seed size, and seed weight, respectively. The study's findings are projected to bring considerable benefits to pigeonpea producers in marker-assisted breeding for the production of varieties with improved protein content and seed quality traits corresponded to consumer preferences, as well as promote improved health and nutrition. Therefore, GWAS provides strong support for exploring the genetic mechanisms underlying important pigeonpea qualities and improving breeding strategies.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":"300 1","pages":"44"},"PeriodicalIF":2.3,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144010233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}