Ecological Genetics and Genomics最新文献

{"title":"Complete genome sequences and comparative analysis of two nitrile biocatalysts Bacillus sp. WOD8 and Bacillus safensis WOIS2 isolated from solid waste leachates (SWL) at Olusosun and Oke-Afa Dumpsites, Lagos State, Nigeria","authors":"Adewale Kayode Ogunyemi ,&nbsp;Olanike Maria Buraimoh ,&nbsp;Wadzani Palnam Dauda ,&nbsp;Olufunmilayo Olukemi Akapo ,&nbsp;Bukola Caroline Ogunyemi ,&nbsp;Emmanuel Olukayode Olumuyiwa ,&nbsp;Simeon Kolawole Odetunde ,&nbsp;Olukemi Ajibola Tobun ,&nbsp;Titilola Aderonke Samuel ,&nbsp;Matthew Olusoji Ilori ,&nbsp;Olukayode Oladipo Amund","doi":"10.1016/j.egg.2025.100388","DOIUrl":"10.1016/j.egg.2025.100388","url":null,"abstract":"<div><div>Leachates from solid waste dumps represent a significant source of nitrile pollution. These leachates often consist of range of pollutants, including nitriles. Therefore, leachates act as hotspots for microorganisms that produce nitrilase, enzymes capable of degrading nitriles. We previously isolated two nitrile-metabolizing bacteria <em>Bacillus</em> sp. strain WOD8 and <em>Bacillus safensis</em> strain WOIS2, from solid waste leachates (SWL) at Olusosun and Oke-Afa dumpsites in Lagos State, Nigeria. These bacteria produce nitrilase, which acts as nitrile biocatalyst. Here, we report the whole genome sequences and comparative analysis of <em>Bacilllus</em> sp. WOD8 and <em>Bacillus safensis</em> WOIS2 with other <em>Bacillus</em> species. The whole genome sequences of two strains WOD8 and WOIS2, were de novo assembled from Illumina HiSeq 4000 paired-end sequence reads and annotated using the NCBI Prokaryotic Genome Annotation Pipeline. The genomes of strains WOD8 and WOIS2 produced 18,092,046 and 16,584,468 total reads, respectively, with genome coverages of 678 and 429X. The genomic sizes of strains WOD8 and WOIS2 were 5.2 × 10⁶ bp (5.2 Mb) and 3.7 × 10⁶ bp (3.7 Mb), respectively, with GC contents of 35.5 and 41.5 %. In addition, the strains had 5,543 and 3,875 total genes, as well as 5,266 and 3,753 protein coding sequences (CDSs). The genome shotgun project for two nitrile biocatalysts, strains WOD8 and WOIS2, has been deposited in GenBank with accession numbers JAYKZE000000000 and JAZAPO000000000. The study was conducted to address the nitrile pollution problem by providing whole genome sequencing analysis of two nitrile biocatalysts, <em>Bacillus</em> sp. WOD8 and <em>Bacillus safensis</em> WOIS2. Also, the study provides a better understanding of their bioremediation applications and their potential for bioprospecting to improve nitrile waste control and management in the near future. The findings align with Sustainable Development Goals, emphasizing a clean environment, human safety, and sustainable practices.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100388"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An integrated index-based and multivariate approach for evaluating drought resilience in the CIMCOG wheat","authors":"Mohammad Hasan Sadeghi ,&nbsp;Rasool Asghari Zakaria ,&nbsp;Seyed Abolghasem Mohammadi ,&nbsp;Omid Sofalian ,&nbsp;Saeid Aharizad","doi":"10.1016/j.egg.2025.100412","DOIUrl":"10.1016/j.egg.2025.100412","url":null,"abstract":"<div><div>Enhancing drought resilience in wheat is critical for global food security amidst increasing climate variability. We evaluated 60 diverse CIMCOG wheat genotypes under well-watered and water-deficient conditions at two semi-arid locations in Iran, measuring yield components and physiological traits (relative water content, chlorophyll stability). A multivariate analysis of 33 drought tolerance and stability indices identified the Mean Productivity Index (MPI), Stress Tolerance Index (STI), Geometric Mean Productivity (GMP), Mean Productivity (MP), Harmonic Mean (HM), Stress Resistance Score (SRS), and Yield Stability Index (YSI) as the most reliable metrics for selecting high-yielding, drought-adaptable genotypes. Principal component analysis (PCA) and fuzzy membership function values (MFV) validated top performers (genotypes 8, 15, 59, 33, 7, 25, 22, 19, 14, 3), which maintained productivity through sustained physiological performance. This integrated approach provides a robust framework for breeding climate-resilient wheat varieties for water-limited agroecosystems, with potential applications in semi-arid regions globally.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100412"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145266107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and characterization of Dof gene family in sesame","authors":"Md Nahid Hasan ,&nbsp;Khandker Shazia Afrin ,&nbsp;A.T.M. Majharul Mannan ,&nbsp;Tasmina Islam Simi ,&nbsp;Md Abdur Rahim","doi":"10.1016/j.egg.2025.100404","DOIUrl":"10.1016/j.egg.2025.100404","url":null,"abstract":"<div><div>The plant-specific TF family ‘Dof’ comprises a highly conserved ‘Dof domain’, which is the DNA binding domain with one ‘Zn²⁺’ finger. It plays a crucial role in plant responses to environmental stimuli affecting growth and development. The <em>Dof</em> genes have been analyzed in many plants, including <em>Arabidopsis</em>, but have not yet been well studied in sesame on a genome-wide scale. In the present study, we reported for the first time 32 <em>Dof</em> genes in sesame, which are located across 12 linkage groups (LGs). The <em>SiDof</em> genes comprised one to five exons and zero to four introns, which is comparable to <em>Dof</em> genes in other species. Of 32 <em>SiDof</em> genes, about 71.88 % were intronless. The <em>SiDof</em> genes were classified into six groups and exhibited evolutionary relationships with other species. Group III contained the highest number of <em>SiDof</em> genes (seven), while the lowest number was in group V (three). There was a robust protein-protein interaction between NAC071 and two Dof proteins, namely DOF5.3 and DOF5.6. Total 1668 ‘<em>cis</em>-regulatory elements’ were identified in the promoter of 32 <em>SiDof</em> genes. Among these, 733 were linked to the stress responses, 562 to the light responses, and 373 to the phytohormone response. The accessible transcriptome (‘RNA-seq’) data-based expression profiles have shown that <em>SiDof</em> genes might be associated with various abiotic stresses, including drought (<em>SiDof1</em>) and salinity (<em>SiDof32</em>) in sesame. Nonetheless, further investigation on the functionality analysis of candidate <em>SiDof</em> genes is required.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100404"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145050038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soybean genotype performance and seasonal stability in relay cropping with chili on coastal sandy soils","authors":"Rohimah H.S. Lestari ,&nbsp;Endang Sulistyaningsih ,&nbsp;Eka Tarwaca Susila Putra ,&nbsp;Benito Heru Purwanto","doi":"10.1016/j.egg.2025.100420","DOIUrl":"10.1016/j.egg.2025.100420","url":null,"abstract":"<div><div>Soybean production in Indonesia is constrained by land competition, yet coastal sandy soils planted with high-value chili offer a niche for soybean via relay cropping. We evaluated five varieties (Anjasmoro, Dena 1, Demas 1, Malika, Grobogan) in an irrigated soybean–chili relay at Samas, Indonesia, across two seasons in 2023 (CS1: January–May; CS2: July–October) using a randomized complete block design with three replications. Analysis of variance (ANOVA) and genotype-by-environment (GGE) biplots assessed genotype × environment interaction (GEI), and a Random Forest model with permutation importance identified agronomic predictors of seed weight per plant (SWP). Results showed that ANOVA detected significant GEI for SWP and several traits, and GGE grouped varieties as: (1) high-to-moderate yield with stability (Anjasmoro, Dena 1), (2) high yield with lower stability (Malika, Demas 1), and (3) low yield with relative stability (Grobogan). Random Forest ranked predictors as plant height &gt;100-seed weight &gt; pods per plant &gt; seeds per plant &gt; leaf area, indicating that canopy architecture and seed mass, supported by number components, underpin performance. Under the tested irrigated coastal-sand conditions (CS1–CS2 at one site-year), Anjasmoro was the most promising, whereas Dena 1 exhibited the greatest stability at moderate yield; broader recommendations require multi-location, multi-year validation.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100420"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the ligninolytic potential of soil bacteria isolated from Western Ghats, India","authors":"Supreet Kaur,&nbsp;Shazia Shareef,&nbsp;P. Hariprasad","doi":"10.1016/j.egg.2025.100423","DOIUrl":"10.1016/j.egg.2025.100423","url":null,"abstract":"<div><div>Lignin, a complex and recalcitrant component of plant biomass, remains a major bottleneck in agricultural waste valorization and bioprocessing, highlighting the importance of microbial degradation as a sustainable solution. In this study, 112 lignin-degrading bacterial strains were isolated from 24 diverse soil samples collected across the ecologically rich Western Ghats region of Karnataka, India. Their growth on lignin-containing substrates, including paddy straw, poplar wood, and Kraft lignin (KL) with or without nutrient supplementation, revealed substantial variability in ligninolytic potential. The isolates also exhibited lignin-mimicking dye decolorization activity against Azure B, Methylene Blue, Toluidine Blue O, Congo Red, and Remazol Brilliant Blue R, with efficiencies ranging from 0 % to 100 %. Notably, 24 strains showed superior KL degradation efficiency (50–60 %). GC-MS and LC-MS analyses confirmed lignin depolymerization, detecting low molecular weight aromatic intermediates and organic acids such as caffeic acid, sinapyl alcohol, coniferyl alcohol, cinnamic acid, eugenol, oxalic acid, benzoic acid, and butyric acid. The most efficient strains were identified as <em>Streptomyces griseorubens</em> CRDT-EB-21.6, <em>Ochrobactrum ciceri</em> CRDT-EB-22.2, <em>Streptomyces mangrovi</em> CRDT-EB-18.4, <em>Streptomyces</em> sp. CRDT-EB-19.7, and <em>Streptomyces</em> sp. CRDT-EB-21.12. Whole-genome sequencing of <em>S. griseorubens</em> CRDT-EB-21.6 revealed the presence of key genes associated with lignin degradation and aromatics assimilation pathways, including the β-ketoadipate, phenol catabolism, and gentisate routes, alongside glutathione peroxidase genes supporting extracellular peroxidase production. These data collectively emphasize that these lignolytic bacterial isolates from the Western Ghats are effective lignin degraders, possessing considerable potential for use in biorefineries, bioremediation, and sustainable biomass valorization.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100423"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The growth and biochemical traits including nutrient contents of fourteen commercial almond (Prunus sp.) genotypes affected by drought stress","authors":"Esmaeil Safavi Bakhtiari ,&nbsp;Mehrab Yadegari ,&nbsp;Asghar Mousavi ,&nbsp;Bijan Haghighati","doi":"10.1016/j.egg.2025.100410","DOIUrl":"10.1016/j.egg.2025.100410","url":null,"abstract":"<div><div>Due to its health and economic significance, almond (<em>Prunus</em> sp.) is largely grown in the arid and semi-arid areas. Drought stress affecting morphological and physiological characteristics of 14 young almond genotypes, during middle- and late--growth stages, was investigated in the field. The experiments (2020 and 2021) were split plot on the basis of randomized complete block design (RCBD) with three replicates investigating irrigation at 70 and 30 % of field moisture capacity (main factor) and 14 genotypes of almond vegetative rootstock (sub-factor) grafted on GN rootstock. Almond genotypes responses were different to drought stress. Although control treatment resulted in the highest height, stem diameter and leaf area of genotypes, drought stress significantly reduced growth of almond trees and increased leaf abscission. Considerable variations were observed among almond genotypes in terms of H₂O₂, and nutrient contents, during growing season in both years. Stressed Mamaei genotype with the least growth rate had the highest H₂O₂ content (19.99 μmol g⁻¹ FW). Plant nutrient uptake (excluding K and Fe) decreased in stressed genotypes. N content of GN genotype was the highest by control (3.54 %) and stress (2.52 %) treatments. Growth stage stress significantly affected plant growth and nutrient uptake. The highest Fe content was obtained in stressed GN genotype, and stressed Shahrood 13 and Shahrood 7 genotypes had the lowest Fe contents in both growth stages. Planting the most tolerant almond genotypes along with K fertilization may be one of the most effective methods to enhance almond growth and physiology in drought stressed conditions.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100410"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145266105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial abundance and diversity in rhizosphere and bulk soils of organic and conventional rice cultivation fields","authors":"Wubayehu Gebremedhin ,&nbsp;Tantriani ,&nbsp;Weiguo Cheng ,&nbsp;Keitaro Tawaraya","doi":"10.1016/j.egg.2025.100426","DOIUrl":"10.1016/j.egg.2025.100426","url":null,"abstract":"<div><div>The rhizosphere microbiome plays a critical role in plant growth, particularly under organic cultivation. However, the combined effects of rice agroecosystem (upland vs. lowland) and cultivation systems (organic vs. conventional) on rhizosphere bacterial communities remain poorly understood. In this study, we investigated bacterial abundance and diversity in rhizosphere and bulk soils under six treatments combining water regime and fertilizer input: organic lowland, organic upland, organic bulk soil, conventional lowland, conventional upland, and conventional bulk soil. Rice (Oryza <em>sativa</em> L.) was grown under controlled upland and lowland conditions using soils collected from organic and conventional fields. Amplicon sequencing of 16S rRNA genes revealed that organic upland significantly increased bacterial abundance, richness, and Shannon diversity at both phylum and genus levels compared to conventional upland. Similarly, organic lowland and organic bulk soil supported greater bacterial richness and diversity than their conventional counterparts (conventional lowland and conventional bulk soil, respectively). A total of 57 microbial phyla and 819 genera were identified, with Pseudomonadota and Actinomycetota dominating across samples. Notably, organic upland exhibited the highest genus-level bacterial richness and the largest number of unique operational taxonomic units, suggesting enhanced microbial niche differentiation. Principal component analysis further confirmed distinct community structuring between organic and conventional systems. These results demonstrate that organic cultivation fosters a more diverse and abundant rhizosphere bacterial community, highlighting its potential to increase microbial-driven soil health and ecosystem functioning in rice agroecosystems.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100426"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145519602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Missing mate pairs reported as poly-G reads can confound analyses of rare members of microbial assemblages","authors":"Amrit K. Dhillon ,&nbsp;Aspen Workman ,&nbsp;Larry A. Kuehn ,&nbsp;Bernadette Earley ,&nbsp;Sara Louise Cosby ,&nbsp;Amy J. Powell ,&nbsp;Tara G. McDaneld ,&nbsp;Gavin C. Conant","doi":"10.1016/j.egg.2025.100399","DOIUrl":"10.1016/j.egg.2025.100399","url":null,"abstract":"<div><div>Using sequence reads from shotgun metagenomic analyses in both cattle and sheep, we describe how failures in mate pairing on Illumina sequencing can interact with bioinformatics pipelines to give spurious patterns among rare components of a metagenomic sample. We identified several different shotgun metagenomic datasets from different animals and different laboratories where the two members of the read pair matched a viral database at very different frequencies. We traced this bias to a set of poly-G reads of high quality that resulted from failures in generating read pairs during library preparation. These results reinforce the need to remove poly-G-rich reads when quality filtering shotgun metagenomic data.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100399"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144920071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The complete mitochondrial genome of Androctonus mauritanicus (Arachnida: Scorpiones)","authors":"Douae EL Ghoubali ,&nbsp;Stacy Pirro ,&nbsp;Abdellah Idrissi Azami ,&nbsp;Chakib Nejjari ,&nbsp;Najib AL Idrissi ,&nbsp;Abderrazak Rfaki ,&nbsp;Rachid Eljaoudi ,&nbsp;Lahcen Belyamani ,&nbsp;Saaid Amzazi ,&nbsp;Salsabil Hamdi ,&nbsp;Hassan Ghazal","doi":"10.1016/j.egg.2025.100429","DOIUrl":"10.1016/j.egg.2025.100429","url":null,"abstract":"<div><div><em>Androctonus mauritanicus</em> is a significant species in the realm of venomous arthropods. Its native habitat in North Africa has led to its recognition as a large scorpion with highly potent venom, resulting in a critical number of fatalities among humans annually. The specimen used in this study was collected in Marrakech, Morocco, in 2019. To understand its genetic diversity, we sequenced, assembled, and annotated the mitochondrial genome of <em>A. mauritanicus</em> and compared it with those of other scorpions. The assembled mitochondrial genome resulted in 14886 base pairs of circular DNA with 32.37 % GC content. Genome annotation predicted 13 protein-coding genes, 21 transfer RNAs (with a notable absence of tRNA-Asp), and 2 ribosomal RNA genes. The nucleotide composition exhibits an AT bias of 67.7 %, with heterogeneity across codon positions. Phylogenetic analysis consistently shows <em>A. mauritanicus</em> is closely related to <em>Buthus occitanus</em> and <em>Androctonus australis</em>, with an evolutionary distance of 0.178 to <em>A. australis</em>. Selection pressure analysis using codon-based Z-tests indicates significant purifying selection across most mitochondrial protein-coding genes, with diminishing significance in more distantly related species, while positive selection was not statistically significant. This study improves our knowledge of scorpion biology, ecology and evolution and would further our ability to explore practical applications for medicine and species conservation.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100429"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145614389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the genetic basis of milk composition in cattle through pathway analysis and identification of key genes","authors":"Heydar Ghiasi ,&nbsp;Majid Khaldari ,&nbsp;Reza Taherkhani ,&nbsp;Navid Ghavi Hossein-Zadeh","doi":"10.1016/j.egg.2025.100424","DOIUrl":"10.1016/j.egg.2025.100424","url":null,"abstract":"<div><div>A total of 1724 genes reported to influence milk composition traits (MCT) in cattle were compiled from the Animal QTL Database (up to October 10, 2022) and used for pathway analysis and the identification of hub and common genes. MCT included the following traits: milk fat yield (MFY), milk protein yield (MPY), milk fat percentage (MFP), and milk protein percentage (MPP). These genes were primarily derived from studies in Holstein cattle but also included other dairy breeds. For each trait, a gene set was established, and the overlap among gene sets was examined. Using the R package SuperExactTest, we identified 130 genes shared across all four traits. Pathway analysis of these 130 genes using g:Profiler revealed 39 significant pathways. The most significant pathways (P &lt; 0.009) included the PI3K-Akt signaling pathway, Growth Hormone (GH) signaling, SHC-related events triggered by IGF1R, focal adhesion, basement membrane collagen trimer, collagen network, collagen type IV trimer, and network-forming collagen trimer. A gene network was subsequently constructed, and hub genes were identified using Cytoscape and cytoHubba. Ten hub genes (<em>IGF1R</em>, <em>IGF2</em>, <em>LEP</em>, <em>IGF1</em>, <em>PDGFRB</em>, <em>GH1</em>, <em>ERBB2</em>, <em>GHR</em>, <em>PTK2</em>, and <em>CDKN1A</em>) were highlighted as central regulators of milk composition traits. These findings provide insights into the shared genetic architecture of MCT across traits and suggest candidate genes for simultaneous genomic selection in dairy cattle.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100424"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}