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 Dof genes in the cabbage (Brassica oleracea 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 Dof 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 BolDof35 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 Dof genes' roles in growth, stress responses, and regulatory mechanisms in cabbage.
Dof蛋白（“单指结合DNA”）是植物特有的转录因子，参与发育和应激反应等重要过程。通过综合生物信息学分析，在甘蓝（Brassica oleracea var. capitata）基因组中鉴定出59个Dof基因，这些基因在染色体上分布不均匀，可分为A、B1、B2、C1、C2.1、C2.2、C3、D1和D2 9个亚家族。亚家族内含子的存在各不相同，有些亚家族完全不含内含子。染色体3和7含有最多的多夫基因（各10个），片段复制是基因分化的主要驱动因素。顺式调控元件分析显示，光响应元件最多（28%），其次是应激相关元件（19%）、发育相关元件（17%）和激素响应元件（14%）。基因表达谱显示BolDof35是茎、硅、幼苗和花发育的关键调控因子，在茎、丝、芽和愈伤组织中表现出高活性。miRNA分析显示B1、C2.1和C3组的靶向性最强，而D1组的靶向性最低。本研究为Dof基因的克隆和功能研究提供了宝贵的资源，有助于进一步了解Dof基因在白菜生长、胁迫反应中的作用及其调控机制。
{"title":"A comprehensive genomic sequence analysis and characterization of plant specific Dof transcription factor gene family in Brassica oleracea var. capitata","authors":"Nurul Haque , Arvind Agrawal , Tuneer Khelkar , Chitralekha Kodopi , 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":"2025-06-01","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}
Pub Date : 2025-06-01Epub Date: 2025-03-04DOI: 10.1016/j.egg.2025.100339
Emmanuel Yaw Owusu , Francis Kusi , Alexander Wireko Kena , Yussif Baba Kassim , Benjamin Annor , Frederick Justice Awuku , Patrick Attamah , Andrews Appiah , Salim Lamini , Felix Kuor , Richard Akromah
The objective of this study was to determine genetic potentials in extra-early maturing lines of cowpea. Sixteen early and extra-early maturing lines and their recurrent parents were evaluated at Nyankpala and Manga in the Guinea and Sudan savannah ecologies of Ghana, respectively during the rainy season of 2021 main cropping season. Data were collected on the key earliness-related traits, yield, and yield components. The results showed significant differences for genotypes (G) and locations (L). A hierarchical cluster on principal component analysis grouped the genotypes into super-early (≤55 days after sowing, DAS), extra-early (55–60, DAS) and early maturing (61–70, DAS). Within the extra-early maturing cluster, box plot analysis revealed that 75 % of the lines had high grain yield (≥2 t/ha) at Nyankpala, whilst 50 % of them had ≥1.8 t/ha at Manga. The study identified breeding lines which have key farmer preferred traits such as extra-early maturing, high grain yield, and large seed size. Five genotypes (SAC-20KTE-5, SAC-20KTE-3, SAC-20KTE-29, SAC-20KTE-6, and SAC-20KTE-7) were statistically higher than the parental lines, in terms of grain yield, number of days to maturity (≤60 DAS) and hundred seed weight (≥20 g). There was no trade-off for grain yield, biomass yield, and seed size in the selected early maturing lines. Potential lines identified from the study should be extensively evaluated at multi-locations and superior ones released to mitigate the effects of terminal drought and other stresses for cowpea production in the sub-region.
{"title":"Gains in genetic enhancement of early maturing advanced breeding lines of cowpea [Vigna unguiculata (L.) Walp]","authors":"Emmanuel Yaw Owusu , Francis Kusi , Alexander Wireko Kena , Yussif Baba Kassim , Benjamin Annor , Frederick Justice Awuku , Patrick Attamah , Andrews Appiah , Salim Lamini , Felix Kuor , Richard Akromah","doi":"10.1016/j.egg.2025.100339","DOIUrl":"10.1016/j.egg.2025.100339","url":null,"abstract":"<div><div>The objective of this study was to determine genetic potentials in extra-early maturing lines of cowpea. Sixteen early and extra-early maturing lines and their recurrent parents were evaluated at Nyankpala and Manga in the Guinea and Sudan savannah ecologies of Ghana, respectively during the rainy season of 2021 main cropping season. Data were collected on the key earliness-related traits, yield, and yield components. The results showed significant differences for genotypes (G) and locations (L). A hierarchical cluster on principal component analysis grouped the genotypes into super-early (≤55 days after sowing<em>,</em> DAS), extra-early (55–60, DAS) and early maturing (61–70, DAS). Within the extra-early maturing cluster, box plot analysis revealed that 75 % of the lines had high grain yield (≥2 t/ha) at Nyankpala, whilst 50 % of them had ≥1.8 t/ha at Manga. The study identified breeding lines which have key farmer preferred traits such as extra-early maturing, high grain yield, and large seed size. Five genotypes (SAC-20KTE-5, SAC-20KTE-3, SAC-20KTE-29, SAC-20KTE-6, and SAC-20KTE-7) were statistically higher than the parental lines, in terms of grain yield, number of days to maturity (≤60 DAS) and hundred seed weight (≥20 g). There was no trade-off for grain yield, biomass yield, and seed size in the selected early maturing lines. Potential lines identified from the study should be extensively evaluated at multi-locations and superior ones released to mitigate the effects of terminal drought and other stresses for cowpea production in the sub-region.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100339"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579727","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}
Stripe rust, caused by Puccinia striiformis f. sp. tritici, 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) > 3.0, primarily on chromosomes 2A, 3B, 4A, 5B, and 7A. Several MTAs aligned with known resistance genes, such as Yr18 and Yr57, while others suggested novel loci. Key markers, including ‘AX-109902001’ (6A), ‘AX-94992026’ (7B), ‘IAAV1650’ (5A), and ‘Excalibur_c37115_306’ (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.
{"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 , Mohamed El-soda , Neama H. Osman , Atef Shahin , Zakaria El Gataa , Aladin Hamweigh , Sawsan Tawkaz , Kumarse Nazari , Khaled Al-Shamaa , 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) > 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":"2025-06-01","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}
Pub Date : 2025-06-01Epub Date: 2025-05-22DOI: 10.1016/j.egg.2025.100370
D. Rakhsha , M. Ahani-Azari , M. Najafi , A. Saedi
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.
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 > C, OP765336.1: 142 G > A, OP765336.1: 175 T > C, and OP765336.1: 238 C > 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 < 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.
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.
生长激素（GH）基因对家畜的生长具有重要意义。马生长激素基因位于第11号染色体上，由5个外显子和4个内含子组成。许多研究探索了不同马品种之间的遗传多样性，但对纯种马-土库曼杂交马的研究有限。本研究的目的是研究生长激素基因外显子4和5的多态性及其与杂交马构象和肌肉相关性状的关系。96匹马的血液样本通过改良的盐析方法提取DNA。PCR-SSCP分析显示生长激素基因外显子4和5存在多态性。外显子4的A、B、C频带频率分别为36.45%、75 43.79%和19.79%。外显子5的A和B波段频率分别为10.41%和89.58%。测序分析结果表明，在第4外显子中发现了一个新的单核苷酸多态性（SNP） （OP765334.1: 249(C/T)），此外，在第5外显子中还发现了另外四个SNP，特别是OP765336.1: 118 T >；C, OP765336.1: 142 G >；A、OP765336.1: 175 T >；C，和OP765336.1: 238 C >；G，它们共同导致三个错义snp，导致118、142和175位的氨基酸替换。这些取代对应于氨基酸序列的改变，特别是天冬氨酸(D)、亮氨酸(L)和丙氨酸(A)。相关性分析显示，性别与颈中点围（NMC）、前臂中点围（FMC）、眼眼宽（EEW）、口口围（MC）、下颌宽（JW）、喉口围（NCTL）、颈底围（NCB）和前炮中点围（FCMC）等表型指标存在显著相关性，P <具有统计学意义；0.05. 因此，我们的研究结果表明，体型主要由人口统计学特征决定，年龄和性别对这些表型特征有相当大的影响。对不同家畜品种的生长激素基因遗传变异的调查显示，生长激素基因与生长性状存在显著关联，因此需要进一步开展更大样本量的研究。这一点尤其重要，因为目前的研究表明生长激素基因多态性与生长指标之间存在不同程度的相关性，这表明需要更全面的数据来阐明这些相关性。
{"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 , M. Ahani-Azari , M. Najafi , 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 > C, OP765336.1: 142 G > A, OP765336.1: 175 T > C, and OP765336.1: 238 C > 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 < 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":"2025-06-01","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}
This study examines the gut microbiome composition of Penaeus vannamei cultivated in low-saline (5 ppt) and saline (24 ppt) aquaculture ponds in Andhra Pradesh, India, using 16S rRNA (V3–V4 region) high-throughput sequencing. A total of 251,769 quality-filtered reads were obtained, identifying 466 distinct operational taxonomic units (OTUs). Alpha diversity metrics showed moderate variations between salinity groups, with saline conditions exhibiting increased OTU richness but fewer beneficial taxa. Proteobacteria were the dominant phylum in both environments; however, saline conditions favored halotolerant and potentially pathogenic genera such as Vibrio vulnificus and Shewanella, while low-saline conditions supported beneficial microbes like Lactobacillus murinus. Venn analysis revealed 308 shared OTUs, along with notable unique taxa in each environment. These findings highlight salinity as a significant factor influencing gut microbial structure, with implications for shrimp health and the sustainability of aquaculture practices. The study recommends microbiome-informed management strategies to enhance shrimp productivity in various environmental conditions.
本研究采用16S rRNA （V3-V4区）高通量测序技术，对印度安得拉邦低盐水（5 ppt）和盐水（24 ppt）养殖的凡纳滨对虾（Penaeus vannamei）肠道微生物组组成进行了研究。共获得251,769个高质量过滤的reads，鉴定出466个不同的operational taxonomic units （otu）。α多样性指标在不同盐度组间表现出中等程度的差异，盐度条件下OTU丰富度增加，但有益类群减少。变形菌门是两种环境下的优势门；然而，盐水环境有利于耐盐和潜在致病性属，如创伤弧菌和希瓦氏菌，而低盐水环境有利于有益微生物，如鼠乳杆菌。Venn分析显示，每个环境中共有308个otu，以及显著的独特分类群。这些发现强调了盐度是影响肠道微生物结构的重要因素，对虾的健康和水产养殖实践的可持续性具有影响。该研究建议采用微生物组信息管理策略，以提高虾在各种环境条件下的生产力。
{"title":"Comparative metagenomic analysis of core gut microbiome in white leg shrimp (Penaeus vannamei) cultivated in low-saline and saline farmland","authors":"Joseph Varatharajan , Elangovan Dilipan , Pitchiah Sivaperumal , Rajendran Rajaram","doi":"10.1016/j.egg.2025.100359","DOIUrl":"10.1016/j.egg.2025.100359","url":null,"abstract":"<div><div>This study examines the gut microbiome composition of <em>Penaeus vannamei</em> cultivated in low-saline (5 ppt) and saline (24 ppt) aquaculture ponds in Andhra Pradesh, India, using 16S rRNA (V3–V4 region) high-throughput sequencing. A total of 251,769 quality-filtered reads were obtained, identifying 466 distinct operational taxonomic units (OTUs). Alpha diversity metrics showed moderate variations between salinity groups, with saline conditions exhibiting increased OTU richness but fewer beneficial taxa. Proteobacteria were the dominant phylum in both environments; however, saline conditions favored halotolerant and potentially pathogenic genera such as <em>Vibrio vulnificus</em> and <em>Shewanella</em>, while low-saline conditions supported beneficial microbes like <em>Lactobacillus murinus</em>. Venn analysis revealed 308 shared OTUs, along with notable unique taxa in each environment. These findings highlight salinity as a significant factor influencing gut microbial structure, with implications for shrimp health and the sustainability of aquaculture practices. The study recommends microbiome-informed management strategies to enhance shrimp productivity in various environmental conditions.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100359"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143905889","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}
Pub Date : 2025-06-01Epub Date: 2025-03-19DOI: 10.1016/j.egg.2025.100344
Dinh Sy Nguyen , Le Nguyen Tieu Ngoc , Bich Thuy Vu , Phuong Thi Pham , Iuliia Pentekhina , Dinh Minh Tran
This work announced the whole genome resource of Brevibacillus formosus YSY-2.2, a chitin-degrading bacterium possessing antifungal activity and producing phytohormones previously isolated from Yok Don National Park, Vietnam, for the first time. The genome contained 6,191,946 bp with 47.3 % GC content, 5791 CDSs, 116 RNAs, 101 CAZymes, and 13 BGCs. It showed the highest values of both ANI (95.07 %) and dDDH (72.6 %) to those of B. formosus NF2 (CP018145). The genome sequence will provide useful information for further studies on the functional gene and application of B. formosus YSY-2.2.
{"title":"Genome resource of chitinolytic Brevibacillus formosus YSY-2.2","authors":"Dinh Sy Nguyen , Le Nguyen Tieu Ngoc , Bich Thuy Vu , Phuong Thi Pham , Iuliia Pentekhina , Dinh Minh Tran","doi":"10.1016/j.egg.2025.100344","DOIUrl":"10.1016/j.egg.2025.100344","url":null,"abstract":"<div><div>This work announced the whole genome resource of <em>Brevibacillus formosus</em> YSY-2.2, a chitin-degrading bacterium possessing antifungal activity and producing phytohormones previously isolated from Yok Don National Park, Vietnam, for the first time. The genome contained 6,191,946 bp with 47.3 % GC content, 5791 CDSs, 116 RNAs, 101 CAZymes, and 13 BGCs. It showed the highest values of both ANI (95.07 %) and dDDH (72.6 %) to those of <em>B. formosus</em> NF2 (CP018145). The genome sequence will provide useful information for further studies on the functional gene and application of <em>B. formosus</em> YSY-2.2.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100344"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143686720","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}
The genus Holigarna Buch.-Ham. ex Roxb. (Family: Anacardiaceae) contributes significantly to the Western Ghats forest flora, with seven species, five indigenous to the area. The genus is classified as taxonomically challenging owing to its diverse and complex floral features. In this context, we took the molecular phylogenetics of the genus Holigarna as the main objective of this study. Molecular tools are becoming more widely accepted as a useful tool in phylogenetic investigations of taxonomically challenging taxa. Molecular markers can depict the genetic link across plant groupings, and DNA-based molecular taxonomic techniques provide an accurate and quick way to differentiate specimens based on interspecies variance. The genetic profiles of five Holigarna species, Holigarna arnottiana Hook. f., Holigarna beddomei Hook. f., Holigarna ferruginea Marchand, Holigarna grahamii Wight, and Holigarna nigra Bourd. Phylogenetic results confirmed that the genus Holigarna is a monophyletic group with best-supporting bootstrap values and unresolved relationships and a polytomy within the group suggest rapid evolution or limited resolution from the current markers. The unresolved connections and polytomy within the group indicate either fast evolution or insufficient resolution from the existing markers. These results provide a foundation for further taxonomic and evolutionary research on Holigarna.
{"title":"Phylogenetic systematics of genus Holigarna Buch.-Ham. ex Roxb. An endemic tree plant species of Western Ghats","authors":"Kumbar Mudakappa Manjunath , Y.L. Krishnamurthy , K.S. Shreeharsha","doi":"10.1016/j.egg.2025.100348","DOIUrl":"10.1016/j.egg.2025.100348","url":null,"abstract":"<div><div>The genus <em>Holigarna</em> Buch.-Ham. ex Roxb. (Family: Anacardiaceae) contributes significantly to the Western Ghats forest flora, with seven species, five indigenous to the area. The genus is classified as taxonomically challenging owing to its diverse and complex floral features. In this context, we took the molecular phylogenetics of the genus <em>Holigarna</em> as the main objective of this study. Molecular tools are becoming more widely accepted as a useful tool in phylogenetic investigations of taxonomically challenging taxa. Molecular markers can depict the genetic link across plant groupings, and DNA-based molecular taxonomic techniques provide an accurate and quick way to differentiate specimens based on interspecies variance. The genetic profiles of five <em>Holigarna</em> species, <em>Holigarna arnottiana</em> Hook. f., <em>Holigarna beddomei</em> Hook. f., <em>Holigarna ferruginea</em> Marchand, <em>Holigarna grahamii</em> Wight, and <em>Holigarna nigra</em> Bourd. Phylogenetic results confirmed that the genus <em>Holigarna</em> is a monophyletic group with best-supporting bootstrap values and unresolved relationships and a polytomy within the group suggest rapid evolution or limited resolution from the current markers. The unresolved connections and polytomy within the group indicate either fast evolution or insufficient resolution from the existing markers. These results provide a foundation for further taxonomic and evolutionary research on <em>Holigarna</em>.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100348"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143823320","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}
Pub Date : 2025-06-01Epub Date: 2025-05-05DOI: 10.1016/j.egg.2025.100362
Aqib Zeb , Amir Sohail , Shengjia Tang , Zhonghua Sheng , Peisong Hu
The enhancement of grain yield and quality through conventional breeding is a time-consuming and challenging process. Therefore, CRISPR/Cas9 technology is increasingly utilize to improve the grain yield and quality in rice. Grain size and weight are critical agronomic traits that influence both grain yield and quality, primarily governed by two key genes; grain size 3 (GS3) and grain width 5 (GW5). In this study, we constructed knockouts of GS3 and GW5 in Zhongjiazao17 (YK17) using a CRISPR/Cas9-mediated multiplex genome editing method. The gs3-1 knockout produced slender grains with a significant increase in grain length and grain size. Similarly, the gw5-2 knockout exhibited and enhanced thousand-grain weight. Both gs3-1 and gw5-2 knockouts showed a significant decrease in the number of panicle per plant and panicle length compared to YK17. Notably, both gs3-1 and gw5-2 knockouts also demonstrated a significant reduction in panicle length and panicle number. The gs3-1 knockout reduced amylose content (AC) and the highest gel consistency (GC), while gw5-2 exhibited higher AC and reduced GC compared to YK17. Additionally, the gs3-1 knockout also showed a significant decrease in grain chalkiness percentage. Taken together these results demonstrate that GS3 and GW5 are valuable targets for breeding programs aimed at improving grain yield and quality through CRISPR/Cas9 gene editing of functional alleles.
{"title":"CRISPR/Cas9-mediated mutations of GS3 and GW5 positively regulate grain size and grain width in rice (Oryza sativa indica)","authors":"Aqib Zeb , Amir Sohail , Shengjia Tang , Zhonghua Sheng , Peisong Hu","doi":"10.1016/j.egg.2025.100362","DOIUrl":"10.1016/j.egg.2025.100362","url":null,"abstract":"<div><div>The enhancement of grain yield and quality through conventional breeding is a time-consuming and challenging process. Therefore, CRISPR/Cas9 technology is increasingly utilize to improve the grain yield and quality in rice. Grain size and weight are critical agronomic traits that influence both grain yield and quality, primarily governed by two key genes; <em>grain size 3</em> (<em>GS3</em>) and <em>grain width 5</em> (<em>GW5</em>). In this study, we constructed knockouts of <em>GS3</em> and <em>GW5</em> in Zhongjiazao17 (YK17) using a CRISPR/Cas9-mediated multiplex genome editing method. The <em>gs3-1</em> knockout produced slender grains with a significant increase in grain length and grain size. Similarly, the <em>gw5-2</em> knockout exhibited and enhanced thousand-grain weight. Both <em>gs3-1</em> and <em>gw5-2</em> knockouts showed a significant decrease in the number of panicle per plant and panicle length compared to YK17. Notably, both <em>gs3-1</em> and <em>gw5-2</em> knockouts also demonstrated a significant reduction in panicle length and panicle number. The <em>gs3-1</em> knockout reduced amylose content (AC) and the highest gel consistency (GC), while <em>gw5-2</em> exhibited higher AC and reduced GC compared to YK17. Additionally, the <em>gs3-1</em> knockout also showed a significant decrease in grain chalkiness percentage. Taken together these results demonstrate that <em>GS3</em> and <em>GW5</em> are valuable targets for breeding programs aimed at improving grain yield and quality through CRISPR/Cas9 gene editing of functional alleles.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100362"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143927682","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}
Yam (Dioscorea spp.) is an essential food crop particularly in Sub-Saharan Africa. As breeders struggle to meet the rising demand for high-yielding and quality yam, hybridising underutilised wild species presents a promising solution. This study therefore investigated the potentials of hybridising two wild yam species, Dioscorea abyssinica and Dioscorea praehensilis known for their resilience and genetic potential as ancestors of the cultivated West African yam, Dioscorea rotundata, using hand-pollination method. Hybridity was assessed with eight sub-sets of Kompetitive allele-specific markers, and the progenies were evaluated morphologically using standard descriptors. Markers detected heterozygosity in 65 (92.9 %) of 70 progenies, confirming successful hybridisation. Significant (p < 0.05) variation was observed in growth and yield traits, with TDabp2101048, TDabp2101010, and TDabp2101068 excelling in stem length (348.91 cm), internode length (23.36 cm), and vigour (5.85) respectively. The highest tuber length (42.91 cm), tuber weight (1.14 kg) and number of tubers (4) were produced by TDabp2101052, TDabp2101046 and TDabp2101054, respectively. Progenies showed comparable traits to D. rotundata, indicating high genetic compatibility. These findings suggest putative potential for selecting superior genotypes, improving yam breeding programs through genetic diversity, enhancing crop resilience and productivity.
{"title":"Molecular and agro-morphological evaluations of interspecific hybridisation in two wild yams (Dioscorea spp.) for genetic improvement","authors":"F.P. Oyedoyin , O.J. Olawuyi , P.A. Agre , Asrat Asfaw","doi":"10.1016/j.egg.2025.100345","DOIUrl":"10.1016/j.egg.2025.100345","url":null,"abstract":"<div><div>Yam (<em>Dioscorea</em> spp.) is an essential food crop particularly in Sub-Saharan Africa. As breeders struggle to meet the rising demand for high-yielding and quality yam, hybridising underutilised wild species presents a promising solution. This study therefore investigated the potentials of hybridising two wild yam species, <em>Dioscorea abyssinica</em> and <em>Dioscorea praehensilis</em> known for their resilience and genetic potential as ancestors of the cultivated West African yam, <em>Dioscorea rotundata</em>, using hand-pollination method. Hybridity was assessed with eight sub-sets of Kompetitive allele-specific markers, and the progenies were evaluated morphologically using standard descriptors. Markers detected heterozygosity in 65 (92.9 %) of 70 progenies, confirming successful hybridisation. Significant (p < 0.05) variation was observed in growth and yield traits, with TDabp2101048, TDabp2101010, and TDabp2101068 excelling in stem length (348.91 cm), internode length (23.36 cm), and vigour (5.85) respectively. The highest tuber length (42.91 cm), tuber weight (1.14 kg) and number of tubers (4) were produced by TDabp2101052, TDabp2101046 and TDabp2101054, respectively. Progenies showed comparable traits to <em>D. rotundata</em>, indicating high genetic compatibility. These findings suggest putative potential for selecting superior genotypes, improving yam breeding programs through genetic diversity, enhancing crop resilience and productivity.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100345"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143724529","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}
Pub Date : 2025-06-01Epub Date: 2025-04-24DOI: 10.1016/j.egg.2025.100356
Stalin Nithaniyal, Benniamin Asir, Kaushik Sarkar
Expert-verified curated collections of herbarium specimens are invaluable assets of plant biodiversity. Several historical specimens of rare and endangered taxa in herbaria face difficulty in identifying the morphology. The emerging DNA-based technology recovers genetic data from preserved herbarium are efficiently used for plant identification complementing taxonomy. Therefore, the current study utilized DNA barcodes from chloroplast (rbcL, trnH-psbA) and nuclear (ITS2) genomes to identify chronologically preserved specimens of endemic and threatened taxa. Fifteen herbarium accessions belonged to the 19th, 20th, and 21st centuries representing eight taxa studied as test samples by comparing with three control samples. Extraction of DNA from 16 to 140-year-old herbarium showed positive results using our standardised isolation protocol. The PCR amplification was successful using rbcL DNA barcode in all the samples but the trnH-psbA and ITS2 markers amplified only two species. The DNA sequence recovery from ∼100 old specimens yielded short fragments ranging between 100 bp and 150 bp. The DNA sequence was successfully recovered from the sixty and twenty-year-old herbarium specimens of Ischaemum santapaui and Lepidagathis lutea, respectively. The presence of mononucleotide repeats affected the sequence recoverability in trnH-psbA and ITS2 markers. Our results indicated that the increased rate of DNA degradation, fragmentation, and mixing of microbial DNA in the specimen during long-term storage significantly affected the PCR amplification in preserved herbarium specimens. This study highlighted the application of DNA barcoding in unmasking the trove of genetic diversity in the present and historical herbarium collections.
{"title":"Recovery of DNA signatures from historical herbarium specimens using chloroplast and nuclear barcodes","authors":"Stalin Nithaniyal, Benniamin Asir, Kaushik Sarkar","doi":"10.1016/j.egg.2025.100356","DOIUrl":"10.1016/j.egg.2025.100356","url":null,"abstract":"<div><div>Expert-verified curated collections of herbarium specimens are invaluable assets of plant biodiversity. Several historical specimens of rare and endangered taxa in herbaria face difficulty in identifying the morphology. The emerging DNA-based technology recovers genetic data from preserved herbarium are efficiently used for plant identification complementing taxonomy. Therefore, the current study utilized DNA barcodes from chloroplast (<em>rbcL</em>, <em>trn</em>H-<em>psb</em>A) and nuclear (ITS2) genomes to identify chronologically preserved specimens of endemic and threatened taxa. Fifteen herbarium accessions belonged to the 19th, 20th, and 21st centuries representing eight taxa studied as test samples by comparing with three control samples. Extraction of DNA from 16 to 140-year-old herbarium showed positive results using our standardised isolation protocol. The PCR amplification was successful using <em>rbcL</em> DNA barcode in all the samples but the <em>trn</em>H-<em>psb</em>A and ITS2 markers amplified only two species. The DNA sequence recovery from ∼100 old specimens yielded short fragments ranging between 100 bp and 150 bp. The DNA sequence was successfully recovered from the sixty and twenty-year-old herbarium specimens of <em>Ischaemum santapaui</em> and <em>Lepidagathis lutea,</em> respectively. The presence of mononucleotide repeats affected the sequence recoverability in <em>trn</em>H-<em>psb</em>A and ITS2 markers. Our results indicated that the increased rate of DNA degradation, fragmentation, and mixing of microbial DNA in the specimen during long-term storage significantly affected the PCR amplification in preserved herbarium specimens. This study highlighted the application of DNA barcoding in unmasking the trove of genetic diversity in the present and historical herbarium collections.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"35 ","pages":"Article 100356"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891787","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}
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