Ecological Genetics and Genomics最新文献_第2页

Characterization of heterozygosity-enriched regions and population structure in Indian cattle breeds 印度牛品种杂合性富集区及种群结构特征

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2025-12-27 DOI: 10.1016/j.egg.2025.100437

Aditi Yadav , Pallavi Rathi , S.P. Dixit , Indrajit Ganguly , Sanjeev Singh

Heterozygosity-rich regions (HRR) refer to genomic regions exhibiting increased heterozygosity, linked to influencing traits like immune response, survival, fertility, and other fitness-related characteristics. Analyzing HRR helps to identify areas of the genome with high genetic variation, thus providing deep insights into a population's genetic diversity and revealing specific genome segments where increased diversity is beneficial. In this study, heterozygosity rich regions were identified in 158 animals of eleven Indian cattle breeds (Bos indicus) using 777K BovineHD BeadChip. In total, 8127 heterozygous regions were identified. Among the breeds studied, the short-statured Ladakhi breed exhibited the highest number of heterozygous regions (1412), while the Sahiwal, a prominent dairy breed of the Indian subcontinent, exhibited the lowest (467). The Mean genome length of RoHet was maximum in the Ladakhi breed (44.09 Mb) and minimum in the Hariana breed (12.16 Mb). The highest number of RoHet was observed on chromosome 7 in the short statured Vechur breed spanning 9.2 % of the chromosome's length. In most breeds, the maximum average length of Runs of heterozygosity (ROHet) was found on the sixth chromosome, while the fifth chromosome harboured the highest number of ROHet. Functional classification of the 193 annotated genes identified in the heterozygous regions were involved in cellular processes, biological regulation, and metabolic process. Principal component analysis of ROHet regions to study the population structure revealed distinct clustering of short statured cattle breeds (Ladakhi and Vechur) from rest of the Indian breeds while the dairy and dual-purpose breeds clustered together.

杂合度丰富区域（HRR）是指杂合度增加的基因组区域，与影响免疫反应、生存、生育和其他健康相关特征等性状有关。分析HRR有助于确定基因组中具有高遗传变异的区域，从而深入了解种群的遗传多样性，并揭示增加多样性有益的特定基因组片段。本研究利用777K BovineHD BeadChip对11个印度牛品种（Bos indicus）的158头牛进行了杂合性富集区鉴定。共鉴定出8127个杂合区。拉达克品种RoHet的平均基因组长度最大（44.09 Mb），哈里亚纳品种最小（12.16 Mb）。在矮小的维库尔品种中，7号染色体上RoHet的数量最多，占染色体长度的9.2% %。在大多数品种中，最大平均长度的杂合性（ROHet）发现在第6染色体，而第5染色体拥有最多的ROHet数。在杂合区鉴定的193个注释基因的功能分类涉及细胞过程、生物调控和代谢过程。通过对ROHet地区种群结构的主成分分析发现，矮小牛品种（Ladakhi和Vechur）与其他印度品种明显聚集在一起，而乳制品和两用品种则聚集在一起。

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引用次数: 0

eDNA metabarcoding reveals halophilic and halotolerant bacterial assemblages in the salt flats of the northern Red Sea coast eDNA元条形码揭示了红海北部海岸盐滩的嗜盐和耐盐细菌组合

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2026-01-21 DOI: 10.1016/j.egg.2026.100448

Jayanath Gopi , Thadickal V. Joydas , Paravanparambil R. Jayachandran , Seerangan Manokaran , Sowmya P. Mohandas , Sajan C. Raju , Syed A. Hussain , Mohamed O. Abouelresh , Sudhanshu Dixit , Muhammed Rafeeq , Mohamed Asharaf , Karuppasamy P. Manikandan , Sharif Hala , Bruno Pulido

The salt flats (sabkhas in Arabic), located in NEOM, Saudi Arabia, along the northern Red Sea coast, are ecologically significant yet vulnerable arid ecosystems that harbor unique microbial biodiversity. These environments are increasingly exposed to varying salinity levels and anthropogenic pressures that may alter microbial community structure. Despite their recognized ecological significance, salt flats remain poorly studied in terms of bacterial diversity using molecular approaches. This study applied environmental DNA (eDNA) metabarcoding of 16 S rRNA gene to assess bacterial community diversity and composition across 30 sabkha soil samples from inland and coastal sites. High-throughput sequencing generated 285,900 high-quality reads, resulting in the identification of 363 operational taxonomic units (OTUs), spanning 219 genera, 49 families, 34 orders, and 8 phyla. The microbial community was dominated by halophilic and halotolerant taxa such as Halomonas, Caldalkalibacillus, Klebsiella, and Vibrio. The most abundant phyla identified were Pseudomonadota and Bacillota. Inland sabkhas contained fewer but highly specialized taxa, whereas coastal sabkhas supported more diverse assemblages, including marine-associated genera. Alpha and beta diversity metrics showed spatial variation, while multivariate analyses indicated soil texture as the key driver of community patterns. These findings represent the first molecular insight into bacterial communities of NEOM sabkhas, providing a baseline for long-term ecological monitoring. The findings support evidence-based conservation and sustainable development efforts and emphasize the utility of eDNA-based monitoring as a tool for guiding ecosystem management in the face of environmental change.

位于沙特阿拉伯NEOM的盐滩（阿拉伯语为sabkhas）沿着红海北部海岸，具有重要的生态意义，但脆弱的干旱生态系统却拥有独特的微生物生物多样性。这些环境越来越暴露于不同的盐度水平和可能改变微生物群落结构的人为压力之下。尽管盐滩具有公认的生态意义，但利用分子方法对其细菌多样性的研究仍然很少。本研究应用环境DNA （environmental DNA, eDNA）元条形码技术对16个 S rRNA基因进行了分析，分析了来自内陆和沿海地区30个sabkha土壤样品的细菌群落多样性和组成。高通量测序产生285,900个高质量reads，鉴定出363个操作分类单位（operational taxonomic units, otu），涵盖49科34目8门219属。微生物群落以嗜盐和耐盐类群为主，如嗜盐单胞菌、Caldalkalibacillus、Klebsiella和Vibrio。发现最多的门是假单胞菌门和杆菌门。内陆sabkhas包含较少但高度专门化的分类群，而沿海sabkhas支持更多样化的组合，包括海洋相关属。α和β多样性指标表现出空间差异，而多变量分析表明土壤质地是群落格局的关键驱动因素。这些发现代表了对NEOM sabkhas细菌群落的首次分子洞察，为长期生态监测提供了基线。这些发现支持了基于证据的保护和可持续发展努力，并强调了基于edna的监测作为面对环境变化指导生态系统管理的工具的效用。

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引用次数: 0

Generation mean analysis, genetic variability, advance, and heterosis for seed size traits in cowpea (Vigna unguiculata L. Walp.) 豇豆（Vigna unguiculata L. Walp.）种子大小性状的世代平均分析、遗传变异、进展及杂种优势

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2025-12-24 DOI: 10.1016/j.egg.2025.100435

Frederick Justice Awuku , Francis Kusi , John Saviour Eleblu , Isaac Asante , Kwadwo Ofori , Yosef Alemu Bekele , Patrick Attamah , Emmanuel Yaw Owusu , Gloria Mensah , Salim Lamini , Victoria Dedoe Larweh

A comprehensive understanding of gene action, heterosis, and genetic advance is essential for the effective improvement of cowpea traits. This study investigated the inheritance of seed size and related traits using four cowpea crosses: Wang Kae × SpM028, KT × SpM028, Bigbean × BR, and Agyenkwa × Padituya. Six generations (P₁, P₂, F₁, BC_1:1, BC_1:2, F₂) from each cross were evaluated in a randomised complete block design with three replications. Significant differences were observed across generations, indicating trait variability from one generation to another. The F₁ generation exhibited intermediate performance between parental means, highlighting additive allelic effects. Positive mid-parent heterosis was observed for all traits, indicating potential improvement through selection; however, some traits displayed negative heterobeltiosis. Generation mean analysis revealed significant means [m] and additive [a] effects, with additive × dominance [ad] epistatic interactions playing a key role. Traits such as seed volume showed solely additive × dominance effects, while hundred seed weight exhibited varying epistatic effects across the four crosses. Duplicate epistatic gene actions were prevalent, although complementary actions appeared in some traits. Positive dominance effects were identified for most traits, except for hundred seed weight in Wang Kae × SpM028, which showed negative dominance. Partial dominance was noted for large seed size and seed volume. High heritability and genetic advance suggested strong potential for trait improvement through selection. The genetic architecture of large-seed cowpea varieties from this study offers valuable opportunities for breeding programs aimed at enhancing seed size and related traits in cowpea.

全面了解基因作用、杂种优势和遗传进展对豇豆性状的有效改良至关重要。以王科 × SpM028、KT × SpM028、Bigbean × BR和Agyenkwa × Padituya 4个豇豆杂交组合为材料，研究了籽粒大小及相关性状的遗传特性。每个杂交的6代（P1、P2、F1、BC1:1、BC1:2、F2）采用3个重复的随机完全区组设计进行评估。代际间观察到显著差异，表明性状在代际之间存在差异。F1代表现为亲本之间的中间性状，突出了加性等位基因效应。所有性状中亲本杂种优势均为正，表明有通过选择改善的潜力；但部分性状表现为负杂种优势。代均值分析显示显著的均值[m]和加性[a]效应，其中加性 × 显性[和]上位相互作用起关键作用。种子体积等性状表现为单纯加性 × 显性效应，百粒重表现为不同的上位性效应。重复上位基因作用普遍存在，但在某些性状中存在互补作用。除百粒重王科 × SpM028为负显性外，其余性状均存在正显性效应。种子大小和种子体积大，为部分显性。高遗传率和遗传先进性表明，通过选择进行性状改良的潜力很大。本研究获得的大种子豇豆品种的遗传结构为提高豇豆种子大小和相关性状的育种计划提供了宝贵的机会。

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引用次数: 0

GC-biased codon usage and dinucleotide signatures reveal selection on Pi-ta blast resistance gene alleles in Oryza spp. gc偏态密码子使用和二核苷酸特征揭示了稻瘟病抗性基因Pi-ta等位基因的选择。

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2026-01-22 DOI: 10.1016/j.egg.2026.100449

Bhaskar Dowarah , Rafiul Amin Laskar , Anurag Kashyap , Bijoy Neog

The rice blast resistance gene Pi-ta is one of the most widely deployed nucleotide-binding leucine-rich repeat (NLR) loci in Oryza breeding programs, yet its synonymous and compositional evolution remains poorly understood. In this study, we analyzed 68 integrity-validated Pi-ta coding sequences (CDS) curated from 256 GenBank records to characterize codon usage bias (CUB) and dinucleotide composition across the genus Oryza. The gene exhibited moderate GC enrichment (49.36 ± 3.57 %), a strong preference for G/C-ending codons, and consistent third-position asymmetries (U > A and G > C). Neutrality analysis revealed a GC12–GC3 regression slope of 0.351, indicating that selective constraints, rather than neutral mutation pressure alone, predominantly shape codon usage at this locus. Dinucleotide profiling further identified universal depletion of TA and GT motifs and enrichment of CA and TG, defining a stable locus-specific compositional signature. Collectively, these results demonstrate that synonymous codon usage in Pi-ta is non-random and evolutionarily constrained, reflecting the combined effects of selection and nucleotide composition. By establishing a genus-wide, locus-specific synonymous profile for Pi-ta, this study provides a novel framework for codon optimization, allele validation, and precision engineering of resistance genes in rice improvement programs.

稻瘟病抗性基因Pi-ta是水稻育种中最广泛使用的核苷酸结合富亮氨酸重复（NLR）位点之一，但其同义性和组成进化尚不清楚。在这项研究中，我们分析了来自256个GenBank记录的68个经过完整性验证的Pi-ta编码序列（CDS），以表征整个水稻属的密码子使用偏差（CUB）和二核苷酸组成。该基因表现出适度的GC富集（49.36 ± 3.57 %），对G/C端密码子的强烈偏好，以及一致的第三位不对称（U >； a和G >； C）。中性分析显示GC12-GC3的回归斜率为0.351，表明选择性约束，而非中性突变压力，主要影响该位点的密码子使用。二核苷酸分析进一步确定了TA和GT基序的普遍缺失和CA和TG的富集，定义了一个稳定的位点特异性组成特征。总之，这些结果表明，同义密码子在Pi-ta中的使用是非随机的和进化约束的，反映了选择和核苷酸组成的综合作用。通过建立一个全属的、特异位点的Pi-ta同义基因图谱，本研究为水稻改良项目中的密码子优化、等位基因验证和抗性基因的精确工程提供了一个新的框架。

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引用次数: 0

Biological macromolecules in bioremediation: Exploring OMICs approaches for environmental cleanup 生物修复中的生物大分子：探索环境净化的组学方法

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2025-12-11 DOI: 10.1016/j.egg.2025.100434

Priti Duhan , Kumkum Verma , Charu Lata , Bhupesh Gupta , Poonam Bansal

Bioremediation is used for eliminating hazardous compounds from environment by using various microorganisms which attaining fame. Recently, the degradation of the environment has emerged as a significant threat to human life. The mechanism behind bioremediation and eco-friendly approach to mitigating environmental pollution depends on biological macromolecules including nucleic acids, proteins, carbohydrates and lipids. The integration of OMICs technologies like genomics, transcriptomics, proteomics and metabolomics has transformed the understanding of these macromolecules and their roles in pollutant degradation, microbial adaptation and ecosystem restoration. Further, bioinformatics approaches are emerging technologies for bioremediation process by taking data from diverse biological databases like database of structure and composition, enzymes, microorganism's degradation pathways, RNA and protein expression, organic compounds and comparative genome analysis to understand the degradation pathway supported by a specific microbe for exact waste product. Diverse bioinformatics tools are employed to analyze these sources for study bioremediation to develop more operative environmental cleaning techniques. This review explores the synergistic application of OMICs technologies to study biological macromolecules in bioremediation, highlighting their potential to optimize pollutant removal and enhance environmental cleanup efforts. By integrating molecular biology with environmental science, OMICs-driven approaches offer precise, effective and sustainable solutions for addressing complex contamination challenges and advancing global restoration efforts.

生物修复是利用各种微生物来消除环境中有害化合物的一种方法，已获得广泛的应用。最近，环境退化已成为对人类生活的重大威胁。生物修复和生态友好的方法减轻环境污染的机制取决于包括核酸、蛋白质、碳水化合物和脂类在内的生物大分子。基因组学、转录组学、蛋白质组学和代谢组学等组学技术的整合，改变了人们对这些大分子及其在污染物降解、微生物适应和生态系统恢复中的作用的理解。此外，生物信息学方法是一种新兴的生物修复技术，它从不同的生物数据库中获取数据，如结构和组成、酶、微生物降解途径、RNA和蛋白质表达、有机化合物和比较基因组分析等，以了解特定微生物对确切废物的降解途径。不同的生物信息学工具被用来分析这些来源，研究生物修复，以开发更有效的环境清洁技术。本文综述了组学技术在生物修复中的协同应用，强调了它们在优化污染物去除和加强环境清理方面的潜力。通过将分子生物学与环境科学相结合，omics驱动的方法为应对复杂的污染挑战和推进全球恢复工作提供了精确、有效和可持续的解决方案。

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引用次数: 0

Transcriptomic signatures and soil indicators reveal adaptive stress responses in Quercus oblongata under Pinus invasion in the Western Himalaya 西喜马拉雅地区松入侵下长叶栎的转录组学特征和土壤指标揭示了其适应性胁迫响应

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2026-01-12 DOI: 10.1016/j.egg.2026.100445

Md Asif Chowdhary, Hari Shankar Gadri, Sarbani Roy, Vikas Sharma, Pankaj Bhardwaj

Invasion of native oak (Quercus oblongata) forests by Pinus roxburghii is an emerging ecological concern in the Western Himalaya, with implications for biodiversity loss, soil degradation, and altered plant physiological responses. This study integrates transcriptomic analysis and soil chemistry to explore how Pinus invasion affects gene expression and soil conditions in pure and degraded oak forest stands. A total of 13 stress-responsive genes were quantified using transcript abundance data across six forest sites (three pure oak and three mixed Pinus-invaded). Correlation analysis revealed distinct expression patterns: genes such as CAX3, CBL10, and ECH2 showed strong negative associations with key soil parameters (e.g., nitrogen, pH, potassium), indicating upregulation under nutrient-poor, stressed conditions. Conversely, genes like MFL1, CPN20, ACA1, and ALA3 were positively correlated with healthier soil conditions, suggesting their role in supporting plant function in stable environments. Principal component analysis (PCA) further differentiated invaded and pure forests based on both gene expression and edaphic variables. These findings suggest that allelopathic stress and altered soil chemistry in Pinus invaded areas may drive specific molecular adaptations in native species. This approach identifies key genes as potential early biomarkers of forest degradation and offers a molecular insight into plant soil responses under Pinus invasion.

在西喜马拉雅地区，rosburghii松（Pinus roxburghii）入侵本地栎林（Quercus oblongata）是一个新兴的生态问题，可能导致生物多样性丧失、土壤退化和植物生理反应改变。本研究结合转录组学分析和土壤化学分析，探讨了松松入侵对纯栎林和退化栎林基因表达和土壤条件的影响。利用6个森林样地（3个纯栎和3个混松）的转录丰度数据，对13个应激响应基因进行了定量分析。相关分析揭示了不同的表达模式：CAX3、CBL10和ECH2等基因与关键土壤参数（如氮、pH、钾）呈强负相关，表明在营养不良、胁迫条件下表达上调。相反，MFL1、CPN20、ACA1和ALA3等基因与更健康的土壤条件正相关，表明它们在稳定环境中支持植物功能的作用。主成分分析（PCA）基于基因表达和土壤变量进一步区分入侵林和纯林。这些发现表明，化感胁迫和土壤化学的改变可能会驱动本土物种的特定分子适应。该方法确定了关键基因作为森林退化的潜在早期生物标志物，并为松松入侵下植物土壤反应提供了分子视角。

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引用次数: 0

Genetic erosion driven by inbreeding and introgressive hybridization in the endemic Manyara tilapia (Oreochromis amphimelas) from Tanzania's saline Rift Valley lakes 来自坦桑尼亚大裂谷盐碱湖的地方性曼雅拉罗非鱼（Oreochromis amphimelas）的近亲繁殖和渐进杂交导致的遗传侵蚀

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2026-02-05 DOI: 10.1016/j.egg.2026.100451

Hadija Hussein Said, Cyrus Rumisha

The endemic Manyara tilapia (Oreochromis amphimelas), confined to Tanzania's saline Rift Valley lakes (SRVLs), occurs in small, geographically isolated populations. This limited distribution, combined with recurrent droughts and intense fishing pressure, increases its vulnerability to inbreeding and genetic erosion. The introduction of non-native Nile tilapia (O. niloticus) into some SRVLs further risks introgressive hybridization. Despite these threats, information on the genetic status of Manyara tilapia in SRVLs remains scarce. In this study, we genotyped seven microsatellite loci in 123 individuals of both O. amphimelas and O. niloticus sampled from three SRVLs to test two hypotheses: (i) that O. amphimelas populations exhibit elevated inbreeding, and (ii) that introgressive hybridization has occurred between the two species. The results showed that O. amphimelas had lower genetic diversity and higher inbreeding (F_IS) across all sampled SRVLs than O. niloticus, which exhibited non-significant F_IS in all lakes except Lake Kitangiri. STRUCTURE and snapclust analyses identified two distinct genetic clusters corresponding to the two species in each lake, with most individuals clearly assigned to their respective clusters. However, several individuals in Lake Kitangiri exhibited intermediate ancestry proportions from both species, indicating ongoing hybridization. Because no populations of O. amphimelas exist outside the Tanzanian SRVLs to replenish genetic diversity, continued inbreeding and hybridization may progressively erode the species' evolutionary potential, ultimately leading to its extinction. We recommend preventing the further spread of O. niloticus into uninvaded SRVLs and safeguarding dry-season refugia by designating them as exclusion zones or implementing temporary fishing closures during the dry season.

地方性的Manyara罗非鱼（Oreochromis amphimelas）局限于坦桑尼亚的裂谷盐碱湖（SRVLs），发生在地理上孤立的小种群中。这种有限的分布，再加上经常性干旱和巨大的捕捞压力，增加了其近亲繁殖和遗传侵蚀的脆弱性。将非本土尼罗罗非鱼（O. niloticus）引入一些SRVLs进一步增加了渐进杂交的风险。尽管存在这些威胁，但关于SRVLs中曼雅拉罗非鱼遗传状况的信息仍然很少。在这项研究中，我们对从三个SRVLs中取样的123只O. amphimelas和O. niloticus的7个微卫星位点进行了基因分型，以验证两个假设：(i) O. amphimelas种群表现出较高的近交，（ii）两个物种之间发生了渐渗杂交。结果表明：水獭的遗传多样性较低，近交率较高；除基塔吉里湖外，其他湖泊水獭的近交率均不显著；结构和聚类分析确定了两个不同的遗传集群对应于每个湖泊的两个物种，大多数个体明确地分配到各自的集群。然而，Kitangiri湖的一些个体显示出来自两个物种的中间祖先比例，表明正在进行杂交。由于在坦桑尼亚srvl之外没有两栖动物种群来补充遗传多样性，持续的近亲繁殖和杂交可能会逐渐侵蚀该物种的进化潜力，最终导致其灭绝。我们建议防止niloticus进一步扩散到未入侵的SRVLs，并通过将其指定为禁区或在旱季实施临时休渔区来保护旱季避难所。

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引用次数: 0

Species-specific gut microbiomes in Anomala beetle larvae suggest predicted carbohydrate and xenobiotic processing capacities 异常甲虫幼虫的物种特异性肠道微生物组提示预测碳水化合物和异种生物处理能力

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2025-12-30 DOI: 10.1016/j.egg.2025.100439

R. Karthik , Henry Joseph Oduor Ogola , Ramganesh Selvarajan , Abhishek Walia , Suresh Kumar Mahala , R.S. Chandel

Soil-dwelling scarab beetle larvae rely on gut microbiomes for nutrient extraction from complex plant polymers and potentially for tolerating xenobiotic compounds, yet comparative functional insights across closely related species remain limited. Here, we characterized gut bacterial communities of four economically important cogeneric Anomala species (A. dorsalis, A. dimidiata, A. varicolor, and A. polita) using 16S rDNA amplicon sequencing and PICRUSt2 functional profiling. After quality filtering, 16,822–21,440 reads per species were analyzed, revealing distinct species-specific microbiome signatures. A. dorsalis exhibited the highest bacterial diversity (133 ASVs, Shannon = 3.83), followed by A. dimidiata and A. varicolor, while A. polita showed the lowest diversity (77 ASVs, Shannon = 3.04). All species were dominated by Bacillota_A (Firmicutes) (35.1–46.7 %), but taxonomic composition varied significantly. A. dorsalis, A. dimidiata, and A. varicolor were enriched in fermentative families (Lachnospiraceae, Anaerotignaceae: 10–14 %), whereas A. polita was characterized by Pseudomonadaceae (14.8 %) and minimal Lachnospiraceae (<0.9 %). Core microbiome analysis identified 23 shared genera accounting for 57.4 % relative abundance, alongside species-specific genera. Functional predictions revealed extensive carbohydrate-active enzyme (CAZyme) repertoires in all species, with A. dorsalis and A. dimidiata showing higher predicted abundances of cellulases (GH5/GH9; ∼1.8–2-fold) and xylanases (GH10/GH11; ∼1.5–1.9-fold) relative to A. polita. Predicted xenobiotic degradation pathways varied, with enrichment in glutathione S-transferases and peroxidases A. dimidiata (∼1.6–2.0-fold), and carboxylesterase genes (∼1.7-fold) in A. polita. These findings indicate that Anomala larvae employ distinct, ecology-linked microbial strategies balancing carbohydrate metabolism and detoxification, generating testable hypotheses for functional validation and microbiome-informed pest management.

居住在土壤中的圣甲虫幼虫依靠肠道微生物群从复杂的植物聚合物中提取营养物质，并可能耐受外源化合物，但在密切相关的物种之间的比较功能研究仍然有限。在这里，我们利用16S rDNA扩增子测序和PICRUSt2功能分析，对四种经济上重要的共属异常物种（A. dorsalis， A. dimidiata， A. varicolor和A. polita）的肠道细菌群落进行了表征。经过质量过滤，每个物种分析了16,822-21,440个reads，揭示了不同物种特异性的微生物组特征。dorsalis的细菌多样性最高（133种，Shannon = 3.83），其次是A. dimidiata和A. varicolor，而A. polita的细菌多样性最低（77种，Shannon = 3.04）。所有种均以Bacillota_A（厚壁门）为优势种（35.1 ~ 46.7 %），但分类组成差异较大。A. dorsalis， A. dimidiata和A. varicolor在发酵科（Lachnospiraceae, Anaerotignaceae: 10-14 %）中丰富，而A. polita以Pseudomonadaceae（14.8 %）和最少的Lachnospiraceae （<0.9 %）为特征。核心微生物组分析鉴定出23个共有属，相对丰度为57.4% %，以及物种特异性属。功能预测显示，所有物种都具有广泛的碳水化合物活性酶（CAZyme）谱，与A. dorsalis和A. dimidiata相比，其纤维素酶（GH5/GH9；约1.8 - 2倍）和木聚糖酶（GH10/GH11；约1.5 - 1.9倍）的预测丰度更高。预测的外源降解途径各不相同，在A. polita中富集谷胱甘肽s -转移酶和过氧化物酶A. dimidiata（约1.6 - 2.0倍）和羧酸酯酶基因（约1.7倍）。这些发现表明，异常幼虫采用独特的、与生态相关的微生物策略来平衡碳水化合物代谢和解毒，为功能验证和微生物组信息虫害管理提供了可测试的假设。

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引用次数: 0

Integrative assessment of pre-harvest sprouting resistance in Iranian wheat landraces and cultivars using PHS4A and TaPHS1 markers, seed color parameters, and α-amylase activity 利用PHS4A和TaPHS1标记、种子颜色参数和α-淀粉酶活性对伊朗小麦地方品种和栽培品种收获前发芽抗性进行综合评价

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2026-01-06 DOI: 10.1016/j.egg.2026.100441

Ehsan Rabieyan , Mohammad Reza Bihamta , Mohsen Esmaeilzadeh Moghaddam , Kobra Mokarian , Hadi Alipour , Valiollah Mohammadi

Pre-harvest sprouting (PHS) refers to a phenomenon, in which the physiologically mature seeds are germinated on the spike before or during the harvesting practice owing to high humidity or prolonged period of rainfall. Thus, the objectives of the research were 1) to assay the PHS resistance of Iranian wheat landraces and cultivars to select tolerance sources; 2) to evaluate the allelic variation of the PHS4A and TaPHS1 and their impacts on PHS resistance; 3) to explore the association between PHS and α-amylase, and colorimetric traits. To evaluate the PHS, a total of 298 bread wheat genotypes (208 native landraces and 90 Iranian cultivars) were cultured in two repeats in three crop seasons (2017–2020) under normal conditions. Then, pre-harvest sprouting, seed dormancy, alpha-amylase, and colorimetric traits were monitored. Based on correlation analysis, there were significant relationships between PHS-grain color (r = −0.39∗∗ and -0.32∗∗ in landraces and cultivars, respectively) and PHS-alpha-amylase activity (r = −0.91∗∗ and -0.88∗∗ in landraces and cultivars, respectively). Trait-linked molecular markers, PHS4A or TaPHS1, were found to be effective on the percentage of seed dormancy (SD); SD% in the AAAA and TTTT genotypes was 35.50 and 13.78 %, respectively. This study identified genotypes with high PHS-resistance, including landraces 622084, 622099, 622105, 622247, 622264, and 622272, together with CASGOGEN and FRONTANA cultivars. Overall, digital image analysis and alpha-amylase activity in this study offered the precise, high-throughput, and high-resolution monitoring of pre-harvest sprouting in wheat. This approach can be utilized to screen wheat germplasm in gene banks, permitting preselect genotypes with PHS-resistant potential for breeding.

采前发芽（PHS）是指在采收前或采收过程中，由于高湿度或长时间降雨，生理成熟的种子在穗上发芽的现象。因此，本研究的目的是：(1)测定伊朗小麦地方品种和品种对小灵通的抗性，以选择耐源；2)评估PHS4A和tapphs1等位基因变异及其对小灵通抗性的影响；3)探讨小灵通与α-淀粉酶及比色性状的关系。为了评价小PHS，在正常条件下，在3个作物季（2017-2020）进行2个重复培养，共培养298个面包小麦基因型（208个地方品种和90个伊朗品种）。然后，对采前发芽、种子休眠、α -淀粉酶和比色性状进行监测。相关分析表明，小麦籽粒颜色（地方品种和栽培品种的r值分别为- 0.39和-0.32∗∗）与小麦籽粒α -淀粉酶活性（地方品种和栽培品种的r值分别为- 0.91∗∗和-0.88∗∗）之间存在显著相关。发现性状连锁分子标记PHS4A或tapphs1对种子休眠率（SD）有效；AAAA和TTTT基因型的SD%分别为35.50和13.78 %。本研究鉴定出具有高ph - s抗性的基因型，包括地方品种622084、622099、622105、622247、622264和622272，以及CASGOGEN和FRONTANA。总的来说，本研究的数字图像分析和α -淀粉酶活性为小麦收获前发芽提供了精确、高通量和高分辨率的监测。该方法可用于筛选基因库中的小麦种质资源，允许预先选择具有phs抗性潜力的基因型进行育种。

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引用次数: 0

Advancing fisheries management in Saleh Bay, West Nusa Tenggara, Indonesia: Insights from DNA barcoding of orange-spotted grouper (Epinephelus coioides) 印尼西努沙登加拉萨利赫湾渔业管理的进步：来自橙斑石斑鱼（Epinephelus coioides） DNA条形码的见解

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-03-01 Epub Date: 2025-12-01 DOI: 10.1016/j.egg.2025.100432

Regi Darmawan , Budy Wiryawan , Ari Purbayanto , Irfan Yulianto , Asadatun Abdullah , Sonja Kleinertz

This study investigates the genetic diversity and population structure of the orange-spotted grouper (Epinephelus coioides) by analyzing 30 individuals collected from Saleh Bay (Indonesia), across multiple Indonesian regions (Pangandaran and Madura Island) and neighboring countries from GenBank, using mitochondrial DNA (COI) markers. The results showed that E. coioides exhibited 15 haplotypes across Indonesia and other countries, with a relatively high haplotypic diversity (Hd = 0.809). Based on the apparent genetic differentiation and gene flow among E. coioides populations in Indonesia and other countries indicates a low level. Also, In Indonesia, the populations of E. coioides in Saleh Bay (present study), Pangandaran, and Madura Island exhibit limited or low gene flow. Furthermore, the phylogenetic tree construction of population E. coioides in Indonesia revealed that all samples clustered into a single large clade and confirming their common species identity. Additionally, this study provides valuable of genetic diversity and genetic population structure insights that can serve as a scientific basis for informed and sustainable grouper fisheries management strategies in Saleh Bay. Due to the apparent geographical conditions and genetic isolation of the E. coioides population in Saleh Bay, the management of E. coioides in this region is conducted independently of that in other regions.

本研究利用线粒体DNA （COI）标记，分析了从印度尼西亚萨利赫湾（Saleh Bay）、印度尼西亚多个地区（Pangandaran和Madura岛）和GenBank邻国收集的30只橙斑石斑鱼（Epinephelus coioides）的遗传多样性和种群结构。结果表明，在印度尼西亚和其他国家共有15个大肠杆菌单倍型，具有较高的单倍型多样性（Hd = 0.809）。在印度尼西亚和其他国家的大叶蝉种群间，遗传分化和基因流动表明其水平较低。此外，在印度尼西亚的Saleh Bay（目前的研究）、Pangandaran和Madura岛的E. coioides种群表现出有限或低的基因流动。此外，通过构建印度尼西亚种群的系统发育树，发现所有样本都聚集在一个大进化枝上，证实了它们共同的物种身份。此外，本研究提供了有价值的遗传多样性和遗传种群结构的见解，可以为萨利赫湾石斑鱼渔业的知情和可持续管理策略提供科学依据。由于Saleh Bay的地理条件和种群的遗传隔离性，该地区的coioides管理独立于其他地区。

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引用次数: 0