Ecological Genetics and Genomics最新文献

{"title":"Multivariate analyses, heritability, and genotype environment interaction of dekoko (pisum sativum Var. abyssinicum) germplasms in tigray, northern Ethiopia","authors":"Gebru Equar Gebremichael ,&nbsp;Yemane Tsehaye Baryatsion ,&nbsp;Fetien Abay Abera ,&nbsp;Yemane G.Egziabher ,&nbsp;Desta Berhe Sbhatu ,&nbsp;Genet Atsbeha","doi":"10.1016/j.egg.2025.100374","DOIUrl":"10.1016/j.egg.2025.100374","url":null,"abstract":"<div><div>Dekoko <em>(Pisum sativum</em> var. abyssinicum) is native to Ethiopia and is known for its high nutritional value and unique flavor. Investigating the genetic variability, heritability, and genotype-environment interaction of Dekoko is essential for understanding its potential for crop improvement and adaptation to changing environmental conditions. Field-based phenotyping of 17 agro-morphological traits was used to assess the extent of genetic variability, heritability and genotype-environment interaction in 120 Dekoko germplasms. The experiment was laid at alpha lattice design with two replications, at Habes, Atsela, Bolonta, and H. burda experimental sites in two growing seasons. As a result, substantial genetic variation in phenological, vegetative, and yield-related traits was observed in the studied germplasms. High heritability was observed for days to 50 % emergence (86.69 %), seed length (85.70 %), seed width (76.67 %), and days to 50 % maturity (65.40 %). AMMI biplot models analysis revealed that the environment was the dominant factor (98.01 %), followed by genotypes (1.60 %) and genotype environment interaction (0.39). Genotypes G65, G46, and G73 exhibited stability, while G23, G33, G27, G62, G58, and G49 demonstrated adaptability across diverse environmental conditions. Additionally, GGE analysisbased on yield performance identified environmental classification and categorized Atsela_2019 Bolonta_2019, <em>Atsela_2020 and H. Burda_2020</em> as favorable environments for majority of the genotypes. The results indicate that certain genotypes maintain consistent performance across different locations, emphasizing the need to select appropriate varieties based on environmental conditions to optimize grain yield potential. These findings contribute to breeding programs focused on improving yield stability and adaptability in <em>P. sativum</em> var. abyssinicum.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"36 ","pages":"Article 100374"},"PeriodicalIF":0.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177688","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":"Butternut pumpkin-powdery mildew disease interaction as influenced by sowing type and date","authors":"Hilma Sabet ,&nbsp;Hossein Ali Asadi-Gharneh ,&nbsp;Mehdi Nasr-Esfahani","doi":"10.1016/j.egg.2025.100375","DOIUrl":"10.1016/j.egg.2025.100375","url":null,"abstract":"<div><div>Butternut pumpkin (<em>Cucurbita pepo</em> L.) is an economically important vegetable and summer crop. The seeds have high nutritional value due to their edible oil and protein content with a high medicinal value. Butternut pumpkin is attacked by several fungal diseases one of which is powdery mildew (PM) caused by <em>Podosphaera xanthii.</em> In this study, we analyzed the effect of sowing type and date on 14 local butternut pumpkin genotypes for resistance against powdery mildew. The two different sowing types were greenhouse vs. open field and the two sowing dates were first week of May vs. 3rd week of May 2021–22. The results showed that powdery mildew severity percentage (PMSP) was 42 % in the field #1 sown in the first week of May compared to the field #2 with 48 % severity sown two weeks later than the field #1 indicating 6 % increase in PMSP significantly. On the other hand, PMSP severity in the greenhouse was 55.2 % which was 8–13 % greater than those occurring in the field. There was also a wide variation in disease severity among the genotypes. The highest PMSP was recorded in” Orumiyeh1” (84.8 %) followed by “Maragheh3” (82 %), and the lowest ones were in “Maragheh1” (9.4 %) and “Shahreza” (6.1 %) genotypes. In conclusion, we found that the ideal conditions for cultivating butternut pumpkin with the least PMSP include sowing during the first week of May in field #1 and the use of resistant cultivars such as “Maragheh1” and “Shahreza” as a part of an integrated pest management program.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"36 ","pages":"Article 100375"},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168296","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":"De novo plastome assembly of Cymbopogon bhutanicus Noltie, an endemic lemon grass from Bhutan, with geospatial, comparative genomic, and phylogenetic insights","authors":"Mohan Singh Rana ,&nbsp;Nicolas Dierckxsens ,&nbsp;Pritesh Bhatt ,&nbsp;Bimal K. Chetri","doi":"10.1016/j.egg.2025.100372","DOIUrl":"10.1016/j.egg.2025.100372","url":null,"abstract":"<div><div><em>Cymbopogon bhutanicus</em> Noltie, an endemic Bhutanese Poaceae, is valued for its essential oils. While morphological taxonomy offers preliminary insights, molecular data enhances species delimitation. We performed <em>de novo</em> chloroplast genome assembly and used remote sensing to assess environmental influences on its distribution. Geospatial analysis of <em>C. bhutanicus</em> habitat (27.25952°N, 91.40823°E) within a 2km buffer zone utilized Sentinel-2 imagery (2018-2023). Mean Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), and Soil-Adjusted Vegetation Index (SAVI) values were 0.5974, 0.3356, and 0.3300, respectively. These values indicate robust vegetation health, while observed variations (e.g., NDVI standard deviation of 0.1780) highlight localized microhabitat heterogeneity influenced by topography and moisture gradients. Field observations aligned, confirming its preference for open, well-drained, sun-exposed slopes with minimal canopy. The assembled chloroplast genome (139,701 bp; 38.46 % GC) comprises an 81,663 bp LSC, 12,510 bp SSC, and two 22,764 bp IR regions. Annotation identified 129 genes (87 protein-coding, 34 tRNA, eight rRNA). Phylogenetic analysis confirmed a strong relationship with <em>C. citratus</em> and <em>C. flexuosus</em> (100 % bootstrap). This study enhances <em>C. bhutanicus</em> molecular identification, phylogeny, and ecological understanding, aiding conservation and sustainable use. This study enhances molecular identification, phylogenetic placement, and ecological understanding of <em>C. bhutanicus</em>, contributing to conservation efforts and sustainable utilization.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"36 ","pages":"Article 100372"},"PeriodicalIF":0.0,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155118","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":"Graphic analysis of genetic variation in morphological traits of garden cress (Lepidium sativum L.)","authors":"Mehdi Mohebodini ,&nbsp;Vahid Rahimi ,&nbsp;Naser Sabaghnia ,&nbsp;Mohsen Janmohammadi","doi":"10.1016/j.egg.2025.100368","DOIUrl":"10.1016/j.egg.2025.100368","url":null,"abstract":"<div><div>This study aimed to evaluate a range of morphological traits in 64 garden cress accessions, across Ardabil and Eyvanki, Iran. The experiment was conducted using a randomized block design with three replications. To facilitate the interpretation of the data, graphical analysis was performed using the genotype-by-trait (G × T) biplot model, which explained 73 % and 76 % of the variance in Ardabil and Eyvanki, respectively. The model employed symmetrical scaling of the first two components for both genotypes and traits. The analysis revealed a positive association between seed yield and the number of seeds in the main stem pods at both locations. Additionally, strong positive correlations were observed among key yield components, including lateral branches, total pods per plant, and seeds in the lateral branch pods. Genotypic performance varied across the two environments: in Ardabil, genotype 49 (LEP-108), followed by genotype 47 (LEP-106), exhibited superior performance for most traits. In Eyvanki, genotype 10, followed by genotypes 43 (LEP-76), 48 (LEP-107), and 62 (Tabriz), performed the best across nearly all measured traits. For increasing seed yield, genotype 10 (LEP-22 from Germany) and genotype 49 (LEP-108 from Armenia) were identified as the most promising candidates, so they will enter in multi environmental trails for exploring specific positive genotype by environment interaction and probably cultivar release process. Genotype 52 showed high biomass and moderate seed yield in both locations and may be a suitable candidate for cultivar release. However, all of the studied genotypes will conserve for using in next breeding programs aiming various targets.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"36 ","pages":"Article 100368"},"PeriodicalIF":0.0,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144138352","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":"Evaluation of genetic variability in neem (Azadirachta indica) germplasm for azadirachtin yield across peninsular and central India","authors":"K. Rajarajan,&nbsp;Shreishtha Singh,&nbsp;A. Arunachalam,&nbsp;A.K. Handa","doi":"10.1016/j.egg.2025.100371","DOIUrl":"10.1016/j.egg.2025.100371","url":null,"abstract":"<div><div>Azadirachtin, produced from neem, is a broad-spectrum, eco-friendly biopesticide properties. Enhancing neem genotypes for higher azadirachtin content can significantly improve the sustainability and efficiency of biopesticide production. This study evaluated 90 neem germplasms for seed morphological and biochemical traits to assess genetic variability and identify superior genotypes for azadirachtin improvement. A randomized block design (RBD) was employed for plantation. Traits such as seed length, seed breadth, seed kernel ratio, oil content, and azadirachtin concentration were measured. Substantial variation was observed across traits, indicating a broad genetic base. Seed length (10.17–17.10 mm), seed width (5.14–7.50 mm), and 100-seed weight (8.89–20.43 g) showed wide ranges. Seed kernel ratio ranged from 1.50 to 4.50, oil content from 11 % to 48 %, and azadirachtin concentration (AZC) from 148.85 to 2850.14 mg/kg, highlighting significant variability. The south-eastern (SE) population exhibited superior seed traits and AZC compared to others. Correlation analysis showed moderate positive associations between seed traits (length, width, and weight) and AZC, suggesting potential for indirect selection. Path analysis confirmed the direct contribution of seed width and weight to AZC. High heritability and genetic advance in AZC and oil content indicate additive gene action and suitability for selection. Principal component analysis identified seed length, width, and weight as primary contributors to variation (56.94 %). Five elite accessions (VKAF-75, VKAF-59, VKAF-58, VKAF-53, and VKAF-139) with high azadirachtin yield were identified, suitable for breeding. The findings offers the importance of seed traits and the potential of SE germplasms as donor parents for future breeding programs.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"36 ","pages":"Article 100371"},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144138353","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":"From wild to domesticated: exploring selection signatures caused by domestication in Carica papaya","authors":"Mónica I. Jiménez-Rojas ,&nbsp;Pedro J. Ruiz-Gil ,&nbsp;Mauricio Heredia-Pech ,&nbsp;Mariana Chávez-Pesqueira","doi":"10.1016/j.egg.2025.100367","DOIUrl":"10.1016/j.egg.2025.100367","url":null,"abstract":"<div><div>During plant domestication, artificial selection acts on traits to meet human needs, interacting with other evolutionary forces and shaping genetic diversity across the genome. However, its impact on perennial fruit crops like <em>Carica papaya</em> remains poorly understood. In this study, we investigated genomic regions under selection during papaya domestication using 2710 single nucleotide polymorphisms (SNPs) across 350 accessions—229 wild and 121 domesticated. Genetic structure was assessed through hierarchical clustering and three statistical methods (FST-based Fdist2, BayeScan, and XP-CLR) were applied to detect selection signatures. The results revealed two clearly differentiated genetic groups corresponding to wild and domesticated papaya. Eighteen loci showed strong evidence of selection, with six containing annotated genes linked to traits influenced by domestication. These genes were primarily associated with fruit traits, plant development, and fruit development. The findings align with expected patterns of selection under domestication, where traits beneficial for cultivation and yield are preferentially retained. This study not only advances the understanding of how domestication shapes the papaya genome but also identifies candidate genes that can serve as valuable targets for breeding programs. Moreover, the genetic differentiation observed reinforces the importance of conserving wild papaya populations as reservoirs of genetic diversity for future crop improvement.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"36 ","pages":"Article 100367"},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168292","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":"Functional metagenomics: A potential tool for mining of biomolecules from environmental samples","authors":"Vivek Kumar ,&nbsp;Anjali Singh ,&nbsp;Vijay Shankar Singh ,&nbsp;Rajan Chaurasia ,&nbsp;Mahesh Rao ,&nbsp;Pramod Kumar Sahu ,&nbsp;Durgesh Kumar Jaiswal","doi":"10.1016/j.egg.2025.100369","DOIUrl":"10.1016/j.egg.2025.100369","url":null,"abstract":"<div><div>Functional metagenomics is emerging as a transformative tool for discovering biomolecules from environmental samples, offering unprecedented insights into microbial diversity and functionality. This review explores the potential of functional metagenomics to uncover novel enzymes, antibiotics, and therapeutic compounds by analyzing environmental DNA (eDNA) without the constraints of traditional culture-based methods. The vast microbial biomass in diverse ecosystems, from soil to extreme habitats, harbors a wealth of genetic resources that can be harnessed for biotechnological applications. Researchers can use modern sequencing techniques and functional screening approaches to find and characterize genes with advantageous features, such as bioremediation capacities and industrially relevant enzymes. Despite challenges in DNA extraction and host expression systems, integrating functional metagenomics with multi-omics approaches promises to enhance our understanding of microbial interactions and facilitate the development of eco-friendly bioprocesses. This review underscores the importance of functional metagenomics in expanding our repertoire of biomolecules and highlights its potential to significantly impact biotechnology and environmental sustainability.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"36 ","pages":"Article 100369"},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144138982","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 first report of genetic polymorphisms of the equine growth hormone gene and its association with conformation and muscle-related traits in thoroughbred-Turkmen crossbred horses","authors":"D. Rakhsha ,&nbsp;M. Ahani-Azari ,&nbsp;M. Najafi ,&nbsp;A. Saedi","doi":"10.1016/j.egg.2025.100370","DOIUrl":"10.1016/j.egg.2025.100370","url":null,"abstract":"<div><div>The growth hormone (GH) gene is a significant for growth in livestock. The equine growth hormone gene is located on chromosome 11, comprising 5 exons and 4 introns. Numerous studies have explored genetic diversity among various horse breeds, yet limited research exists on Thoroughbred-Turkmen crossbred horses. The aim of the present study was to investigate the polymorphisms of exon 4 and 5 of the growth hormone gene and their associations with conformation and muscle-related traits in crossbred horses.</div><div>Blood samples from 96 horses underwent DNA extraction via a modified salting-out method. PCR-SSCP analysis indicated polymorphisms in exons 4 and 5 of the growth hormone gene. The band patterns A, B, and C frequencies for exon 4 were 36.45 %, 75 43.79 %, and 19.79 %, respectively. For exon 5, the band patterns A and B frequencies were 10.41 % and 89.58 %, respectively. The results of the sequencing analysis identified a novel single nucleotide polymorphism (SNP) (OP765334.1: 249(C/T)) located within exon 4, in addition to four other SNPs in exon 5, specifically OP765336.1: 118 T &gt; C, OP765336.1: 142 G &gt; A, OP765336.1: 175 T &gt; C, and OP765336.1: 238 C &gt; G, which collectively result in three missense SNPs leading to amino acid substitutions at positions 118, 142, and 175. These substitutions correspond to alterations in the amino acid sequences, notably aspartic acid (D), leucine (L), and alanine (A), respectively. The association analysis demonstrated a significant association between gender and various phenotypic measures, including neck midpoint circumference (NMC), forearm midpoint circumference (FMC), eye to eye width (EEW), muzzle circumference (MC), jaw width (JW), neck circumference at throat latch (NCTL), neck circumference at base (NCB) and fore cannon midpoint circumference (FCMC) with a statistical significance of P &lt; 0.05. Therefore, our findings indicate that body size is predominantly shaped by demographic characteristics, with age and gender exerting considerable influence on these phenotypic traits.</div><div>The investigation of genetic variants in the GH gene across various livestock species has revealed significant associations with growth traits, underscoring the need for further research with larger sample sizes. This is particularly important as the current studies indicate varying degrees of significance in the association between GH gene polymorphisms and growth metrics, suggesting that more comprehensive data could clarify these associations.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100370"},"PeriodicalIF":0.0,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144130944","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":"Exploring genetic variation and stripe rust resistance in ICARDA's spring bread wheat (Triticum aestivum L.) using GWAS in West Asia and North Africa (WANA) region","authors":"Alaa Youssef ,&nbsp;Mohamed El-soda ,&nbsp;Neama H. Osman ,&nbsp;Atef Shahin ,&nbsp;Zakaria El Gataa ,&nbsp;Aladin Hamweigh ,&nbsp;Sawsan Tawkaz ,&nbsp;Kumarse Nazari ,&nbsp;Khaled Al-Shamaa ,&nbsp;Wuletaw Tadesse","doi":"10.1016/j.egg.2025.100366","DOIUrl":"10.1016/j.egg.2025.100366","url":null,"abstract":"<div><div>Stripe rust, caused by <em>Puccinia striiformis f. sp. tritici,</em> poses a major threat to global wheat (Triticum aestivum) production. This study assessed stripe rust resistance in 154 spring bread wheat genotypes from ICARDA, tested across four locations: Izmir (Turkey), Merchouch (Morocco), Sakha, and Sids (Egypt). Disease severity was evaluated at the adult plant stage under natural infection using the coefficient of infection (CI). Genotyping was performed using 17,692 high-quality SNP markers, and genome-wide association studies (GWAS) identified significant marker-trait associations (MTAs) for resistance. The mixed linear model (MLM), accounting for population structure and relatedness, detected significant differences in genotype resistance across locations. Twenty elite genotypes, including G101, G117, and G125, exhibited high resistance across all sites. A total of 136 significant MTAs and 17 candidate genes were identified, with −log10(p) &gt; 3.0, primarily on chromosomes 2A, 3B, 4A, 5B, and 7A. Several MTAs aligned with known resistance genes, such as <em>Yr18</em> and <em>Yr57</em>, while others suggested novel loci. Key markers, including ‘<em>AX-109902001</em>’ (6A), ‘<em>AX-94992026</em>’ (7B), ‘<em>IAAV1650</em>’ (5A), and ‘<em>Excalibur_c37115_306</em>’ (3B), were significantly associated with resistance across locations. These findings enhance the understanding of the genetic architecture of stripe rust resistance and provide MTAs suitable for marker-assisted selection to pyramid resistance genes. The identified resistant genotypes hold potential for direct release or use as breeding parents in the WANA region, pending further adaptation trials assessing yield stability and agronomic performance.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100366"},"PeriodicalIF":0.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144072476","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":"A comprehensive genomic sequence analysis and characterization of plant specific Dof transcription factor gene family in Brassica oleracea var. capitata","authors":"Nurul Haque ,&nbsp;Arvind Agrawal ,&nbsp;Tuneer Khelkar ,&nbsp;Chitralekha Kodopi ,&nbsp;Samiksha Manjhi","doi":"10.1016/j.egg.2025.100365","DOIUrl":"10.1016/j.egg.2025.100365","url":null,"abstract":"<div><div>Dof proteins (\"DNA binding with one finger\") are plant-specific transcription factors involved in vital processes like development and stress response. A comprehensive bioinformatics analysis identified 59 <em>Dof</em> genes in the cabbage (<em>Brassica oleracea</em> var. capitata) genome, distributed unevenly across chromosomes and grouped into nine subfamilies (A, B1, B2, C1, C2.1, C2.2, C3, D1, and D2). Subfamilies varied in intron presence, with some lacking introns entirely. Chromosomes 3 and 7 contained the most <em>Dof</em> genes (10 each), and segmental duplication emerged as the primary driver of gene divergence. Cis-regulatory element analysis revealed that light-responsive elements were most abundant (28 %), followed by stress-related (19 %), development-related (17 %), and hormone-responsive elements (14 %). Gene expression profiling highlighted Bol<em>Dof</em>35 as a key regulator of stem, silique, seedling, and flower development, showing high activity in tissues like the stem, silk, bud, and callus. miRNA analysis revealed groups B1, C2.1, and C3 as the most targeted, while group D1 had minimal targeting. This study provides a valuable resource for cloning and functional research, enhancing understanding of <em>Dof</em> genes' roles in growth, stress responses, and regulatory mechanisms in cabbage.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100365"},"PeriodicalIF":0.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144107545","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}