Search Results (288)

Insect natural enemies are central agents in biological-control programs. Their pest-suppression performance depends not only on release strategy, but also on traits shaped by long-term laboratory rearing and selection. Conventional mass-rearing systems usually evaluate insect natural enemies using production-oriented indicators, such as survival, fecundity, emergence rate, sex ratio and production cost. However, continuous mass rearing can drive laboratory adaptation, genetic drift, inbreeding, shifts in host or prey use, and reduced field performance. In this review, we summarize key target traits for insect natural enemy improvement, including production efficiency, host or prey use, parasitism, predation, nonreproductive host killing, stress tolerance, pesticide compatibility, dispersal, retention and field efficacy. We further discuss how recurrent artificial selection, hybridization, population genetics, and genomics approaches can be integrated to improve insect natural enemies while maintaining genetic quality. Finally, we discuss the links among trait screening, selection design, quality control, storage and transport, and field-performance validation in the development and application of selected lines or improved strains. Overall, this review highlights practical directions for developing stable and field-proven natural enemy lines. Beyond agriculture, this perspective may also support ecological design in urban landscapes through natural enemy conservation and reduced pesticide use. Full article

The long-tailed goral (Naemorhedus caudatus) is facing severe habitat fragmentation along the Baekdudaegan Mountain Range, South Korea, due to expanding anthropogenic infrastructures and ASF fence installations. To evaluate the evolutionary impacts of these barriers, we assessed the genome-wide genetic diversity and structural connectivity of South Korean goral populations using a high-resolution triple-digest restriction site-associated DNA sequencing (3-RADseq) framework. Out of 36 biological samples collected across regional demes, 34 individuals were successfully genotyped, yielding an initial variant pool of 68,041 raw single nucleotide polymorphisms (SNPs) that filtered down to 9908 high-quality independent SNPs. Bayesian model clustering and principal coordinate analysis consistently identified K = 2 as the optimal number of genetic clusters, resolving a deep, distinct genetic split between the continuous Northern and Southern populations. This pronounced genetic structuring indicates severely restricted contemporary gene flow, heightening vulnerability to genetic drift and inbreeding depression within isolated terminal patches. Our genomic evidence suggests that single-protected-area approaches are insufficient; effective conservation priorities must focus on restoring landscape continuity and ecological corridors to revive historical migration pathways and preserve the adaptive potential of this endangered mountain ungulate. Full article

As a major tributary of the upper Yangtze River, the Chishui River possesses distinctive ecological frameworks and serves as a critical refuge for the aquatic germplasm resources of the Yangtze Basin. Acrossocheilus yunnanensis, a dominant native fish endemic to the river’s headwaters, contributes substantially to sustaining regional ecosystem functioning. Nevertheless, no population genetic research on this species has been documented in the headwater reaches of the Chishui River to date. Here, whole-genome resequencing was performed on 140 individuals from seven geographical populations of A. yunnanensis sampled from the headwaters of the Chishui River. A total of 242,504,293 high-quality single-nucleotide polymorphism (SNP) markers were identified, with an average sequencing depth of 10×. Population genetic analyses revealed observed heterozygosity (H_O) ranging from 0.290 to 0.340, expected heterozygosity (He) from 0.303 to 0.333, and nucleotide diversity (π) spanning 8.063 × 10⁻⁴ to 1.086 × 10⁻³. Genome-wide F_ROH values were generally low across the seven populations, and only several individuals within Population A exhibited clear signs of inbreeding risk. Pairwise differentiation results indicated that the Banbanqiao (A) was highly genetically divergent from the other six populations. Further genome-wide selective sweep analyses verified that A has evolved unique local adaptive signatures in pathways related to mechanosensory perception, neuromotor integration, anaerobic metabolic remodeling and protein homeostasis regulation. This study systematically characterizes the population genetic architecture and local adaptation mechanisms of headwater A. yunnanensis, providing pivotal genetic evidence for wild germplasm conservation and scientific aquatic ecosystem management across the watershed. Full article

The Arabian leopard (Panthera pardus nimr), native to the Arabian Peninsula, is critically endangered and faces acute threats from habitat fragmentation, low population size, and genetic erosion. As a continuation of our previous study on the complete mitochondrial genome of this subspecies, we now report the first nuclear genome assembly of P. p. nimr, generated from the same wild-born male individual sampled in the Oman. Using PacBio HiFi long-read sequencing, we produced 162.9 gigabases (Gb) of high-fidelity data and assembled a haplotype-aware draft genome with HiFiasm. The assembly spans approximately 2.43 Gb across 94 contigs, achieving a contig N50 of 62.4 Mb and zero gap content, with BUSCO completeness of 99.4%. Genome annotation predicted 23,459 protein-coding genes with annotation BUSCO completeness of 95.0%, and 84.1% of proteins were classified as consistent with the Panthera lineage by OMArk. Repetitive elements occupy 34.01% of the assembly, with retroelements dominating and L1/CIN4 LINEs (15.44%) and SINEs (9.61%) representing the two largest subclasses. Comparative simple sequence repeat (SSR) analysis across six Panthera genomes confirmed a conserved repeat motif architecture, with no lineage-specific expansions detected in P. p. nimr. This nuclear genome complements the mitochondrial reference and provides a foundational resource for future studies on genetic diversity, demographic history, inbreeding load, and conservation planning for the Arabian leopard and other Panthera lineages. Full article

The Arunachali mithun (Bos frontalis) is a semi-domesticated bovine of profound cultural and economic significance to the indigenous Arunachali tribal communities of Northeastern India, yet it remains among the least genomically characterised large ruminants, leaving its conservation status without an empirical genetic foundation. We performed whole-genome re-sequencing (~10× coverage) of 11 individuals and analysed 4,943,593 high-quality biallelic single nucleotide polymorphisms (SNPs) after stringent quality control. Genome-wide mean observed heterozygosity (H_o = 0.2854), expected heterozygosity (H_e = 0.3347), and nucleotide diversity (π = 7.16 × 10⁻⁴) revealed moderate genetic diversity, substantially lower than that of related commercial bovine species. A consistent heterozygosity deficit (H_o − H_e = −0.0493) and the convergence of four independent inbreeding coefficients around 0.143–0.147 indicated moderate inbreeding of predominantly reflecting an ancient origin, corroborated by runs of homozygosity (ROH) analysis in which 93.2% of 24,937 detected segments fell in the short length class (100–250 kb). Linkage disequilibrium decayed from r² ≈ 0.57 at <100 kb to a plateau of r² ≈ 0.33 beyond 4–5 Mb, consistent with a small effective population size (N_e) declining from approximately 101,850 (~2228 generations ago) to approximately 160 (~5 generations ago), with ab Ne of approximately 3865 at ~100 generations ago and 423 at ~10 generations ago. These findings establish a whole-genome-based genetic diversity baseline for the Arunachali mithun and provide actionable genomic evidence for conservation and managed breeding interventions. Full article

Cabbage (Brassica oleracea var. capitata), a member of the Brassicaceae family, is an important vegetable crop grown worldwide. Self-incompatibility (SI) in cabbage is a key trait that prevents self-fertilization and inbreeding, thereby maintaining genetic diversity within populations. Although several genes related to SI have been reported, its genetic control remains unclear. In this study, we developed an F₂ population from the highly self-compatible (SC) cabbage line 87-534 and the highly self-incompatible (SI) line 01-20, both of which exhibit the S5 haplotype. The segregation analysis of the F₂ population revealed the possible control of SI by a major gene with additional modifying genetic factors. Bulk segregant analysis sequencing (BSA-Seq) and RNA sequencing (RNA-Seq) were performed on SI and SC samples selected from the F₂ population. BSA-Seq revealed a candidate region on chromosome 7 (C07: 7.45 Mb to 8.93 Mb), including 32 differentially expressed genes (DEGs). RNA-Seq identified a total of 2400 DEGs between the two pools, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggested that plant hormone biosynthesis and signaling, plant immune response were significantly enriched and may be involved in SI. The combined analysis of BSA-Seq and RNA-Seq identified six candidate genes associated with SI, and their expression was confirmed using quantitative real-time PCR (qRT-PCR). Among them, Bol023956 encodes fructokinase, Bol023986 is involved in plant defense response, Bol024018 is related to pollen development, Bol024012 encodes a transport protein for phytohormones, Bol023943 encodes chorismate mutase 3, and Bol012515 is an important regulatory gene for chloroplast synthesis. These six genes, potentially linked to SI, should be targets for further validation. These findings provide insights into the molecular mechanisms of SI in cabbage and the selection of superior cabbage varieties. Full article

Chinese Simmental cattle are a high-quality breed developed through long-term crossbreeding and selection after their introduction into China and have become the main dual-purpose cattle population in the Xinjiang region. To deeply dissect the population structure, characteristics of the population structure, and the genetic basis of the twinning trait, this study focused on Xinjiang Chinese Simmental cattle as the main research subject. It integrated genomic data from global public databases to systematically conduct population structure analysis, genetic relationship analysis, and genome-wide selection signature analysis. Population genetic analysis revealed that the IBS matrix and G matrix indicated that some individuals from different geographical origins exhibited distant genetic relationships; the Xinjiang population showed the fastest LD decay, suggesting abundant genetic diversity; the inbreeding coefficient based on Runs of Homozygosity (ROH) across populations ranged from 0.036 to 0.063; principal component analysis and phylogenetic tree showed that some individuals from different geographical origins had certain genetic interconnections; admixture analysis indicated that K = 5 was the optimal model, with each population exhibiting clear genetic differentiation and admixture characteristics. Furthermore, by combining F_st and θπ analysis (comparing the Xinjiang population with other geographical populations), a total of 89 candidate genes associated with the twinning trait in Xinjiang Chinese Simmental cattle were screened, including CYP19A1, HORMAD1, GRB14, CADM2, CXCR4, and others that have been reported to be closely related to oogenesis and reproductive function. In summary, this study explores genome-wide genetic differences among Simmental cattle populations from different regions, deepens our understanding of their population structures, and offers new candidate genes and molecular markers for high-fecundity breeding in Simmental cattle. Full article

Accurate pedigree reconstruction is essential for genetic evaluation, inbreeding control, and family management in aquaculture breeding programs. In sturgeon, extremely high fecundity and communal rearing during early developmental stages often lead to the loss of family information, making reliable full-sib family assignment a critical challenge. In this study, we developed a machine learning-based framework for full-sib family assignment using simulated genotype datasets and whole-genome resequencing data from Russian sturgeon. Simulation analyses across five machine learning algorithms showed that training set size and marker density were the primary determinants of assignment accuracy. When at least 10 individuals per family were included in the training set, mean identification accuracy exceeded 99% across all evaluated scenarios, and exceeded 99.9% for all methods except XGBoost. In contrast, performance declined when the marker number was reduced to 200. At moderate marker densities (500–1000 markers), performance remained stable, with mean identification accuracy around 99% even when only 3–4 individuals per family were included in the training set. Validation using whole-genome resequencing data (sequencing depth ranging from 9.43× to 11.86×) from 582 individuals representing 19 full-sib families of Russian sturgeon confirmed the simulation findings, with several algorithms achieving assignment accuracies exceeding 99%. These results demonstrate that machine learning provides an accurate and robust approach for full-sib family assignment using genome-wide single nucleotide polymorphism (SNP) data. The proposed framework offers an effective solution for pedigree reconstruction and family identification in sturgeon breeding populations lacking reliable pedigree records. Full article

Indigenous pig breeds represent valuable reservoirs of genetic diversity but face increasing risks of genetic erosion due to uncontrolled crossbreeding with commercial lines. The Ashanti Dwarf Pig (ADP) of Ghana is an important local genetic resource well-adapted to tropical environments but poorly characterised at the genomic level. Using high-density SNP data from the ADPs and publicly available datasets from other African, European, and Asian pig populations, we examined genetic diversity, population structure, inbreeding, and selection signatures. After quality control, 59,124 SNPs across 875 individuals were retained. ADPs exhibited high polymorphism (~99%) and moderate heterozygosity but also elevated inbreeding (FIS = 0.15; FROH = 0.40), indicating recent inbreeding under free-range management. Population structure revealed that ADPs cluster closely with other African pigs and European breeds more than Chinese breeds. ADMIXTURE analysis, however, indicated recent introgression from both European and Chinese lines. Selection scans revealed candidate genes linked to metabolism-Zinc Finger Ran-Binding Protein 3 (ZRANB3), growth-Sortilin Related VPS10 Domain Containing Receptor 1 (SORCS1), reproduction–Sus Scrofa Chromosome 9 quantitative trait loci (SSC9 QTLs), and immunity-Tudor Domain-Containing Protein 3 and CKLF-like MARVEL transmembrane Domain Containing 7 (TDRD3, CMTM7), reflecting adaptation to tropical production systems. Our results provide a comprehensive genomic characterisation of the ADP within a global context, revealing both genetic richness and vulnerability to genetic erosion. These findings underscore the importance of structured breeding and conservation strategies in preserving this unique African genetic resource and supporting sustainable pig production under changing climatic conditions. Full article

Modern cattle comprise two major evolutionary lineages: intensively selected commercial breeds and locally adapted native populations. To investigate their genomic divergence, we performed a comparative population genomic analysis by integrating whole-genome resequencing (WGS) data from multiple representative native breeds and major European commercial breeds. Population genetic analyses showed clear phylogenetic separation between the two groups, with distinct patterns of genetic diversity. Chinese native cattle exhibited generally higher nucleotide diversity (π), lower inbreeding levels, and geographically structured admixed ancestry. Comparative analyses of selection signatures identified 886 candidate selected genes in European commercial breeds, which were primarily enriched in pathways related to production traits, including protein turnover, reproductive regulation, lipid metabolism, and neuro-regulation. In contrast, 50 candidate selected genes in Chinese native cattle were significantly enriched in nervous system functions, particularly ligand-gated ion channel activity and chloride transport (e.g., GRID2, GLRA2/4, GABRD), suggesting neural/ionic regulation may contribute to local adaptation alongside other polygenic mechanisms. Additionally, the two groups also differed in patterns of deleterious mutation load. These findings indicate partially distinct evolutionary trajectories between “production-optimized” and “environment-adapted” cattle and highlight the value of conserving the genetic diversity and adaptive alleles of Chinese native cattle. Full article

Background: Pine wilt disease (PWD), caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus), is a devastating forest disease. It has been reported in five provincial-level regions in Southwest China (Chongqing, Guizhou, Sichuan, Yunnan, and Tibet), threatening local pine forest ecosystems. Methods: To unravel the population genetic variation and population differentiation of PWN isolates in this region, we purified eighty-one isolates for whole-genome resequencing and bioinformatics analysis, identifying candidate genes associated with runs of homozygosity (ROH). Results: Population structure analysis clustered the 81 isolates into three distinct genetic groups (Groups 1, 2, and 3). Notably, Group 1 exhibited fewer and shorter ROH segments compared to Groups 2 and 3, indicating higher genetic diversity and a different inbreeding history. Functional annotation of genes overlapping ROH regions revealed that Group 1 contained a subset of the genes identified in Groups 2 and 3, primarily enriched in specific molecular function categories. Conclusions: The PWN populations in Southwest China exhibit genetic differentiation, forming three distinct groups. Group 1 shows a reduced ROH burden and lower inbreeding levels, whereas Groups 2 and 3 display more extensive ROH patterns that may reflect historical demographic processes or potential adaptive selection. The differential distribution of ROH-associated genes across groups suggests possible variation in historical demographic processes and could suggest possible directional selection. These findings contribute to understanding the population history and genomic characteristics of PWN in Southwest China, providing insights that could support disease management strategies. Full article

Inbreeding is a quantitative measure of autozygosity that underlies the assessment of genetic risks and the management of genetic progress in livestock populations. The development of methods for its estimation reflects a transition from probabilistic pedigree-based models to the direct analysis of genome structure. This review systematizes the evolution of approaches to inbreeding assessment—from the classical inbreeding coefficient F based on identity by descent (IBD) to marker-based, segment-based runs of homozygosity (ROH) and probabilistic homozygous-by-descent (HBD) models. It is shown that the coefficients F_ped, F_GRM, F_ROH, and F_HBD capture related but distinct aspects of autozygosity and are therefore not fully interchangeable. Particular attention is paid to the transition from integral indicators to spatially and temporally stratified analyses of autozygosity, enabling the differentiation between ancient and recent inbreeding. Methodological assumptions, limitations, and the sensitivity of various approaches to marker density, detection parameters, and population demographic structure are discussed. A comparative analysis of methods for calculating F_ROH and segment-based autozygosity is presented. The necessity of a comprehensive assessment of inbreeding and the standardization of analytical protocols for its application in modern breeding programs is substantiated. Full article

The guinea fowl (Numida meleagris), a thermo-tolerant and disease-resilient poultry species, holds great potential for sustainable poultry production in climate-vulnerable regions. The genomic aspects of this species remain largely understudied. The present study aims to delineate the patterns of domestication and understand the evolutionary dynamics of guinea fowl populations (wild and domestic) across three continents, utilizing whole-genome sequencing data from 122 genomes. The population structure analyses (ADMIXTURE, PCA, phylogeny, F_ST, LD, and MAF) revealed that Indian guinea fowl (CARI) shared close ancestry with Iranian (IRAD) and Chinese (CHID) domesticated populations while remaining distinct from wild lineages. The runs of homozygosity (ROH) identified 49,088 segments, with short fragments (ROHs) preponderant in Indian and domestic populations, reflecting historical inbreeding and effects of domestication cum selection. Copy number variation (CNV) analysis revealed 105,178 CNVs concatenated into 40,067 CNV regions (CNVRs) across 11 populations, establishing the first CNV atlas for guinea fowl at the global level. Gene annotation of overlapping ROH and CNVRs revealed 1080 common candidates across Asian guinea fowl populations, i.e., the Indian guinea fowl (CARI), IRAD, and CHID, including FOS, EPAS1, CD74, and CSF1R. These genes have earlier been associated with immune regulation, stress response, and thermal adaptation. Selection signature scans, integrating intra-population (iHS) and inter-population (XP-EHH) approaches, uncovered genes under positive selection linked to immune response (like BCL11B, IL18, and GPC3), thermo-tolerance (like TRPV4 and BAG3), lipid metabolism (like AACS and ELOVL4), and pigmentation (BCO2). These signatures highlight the molecular basis of resilience in guinea fowl and their potential to withstand climate-induced stresses. This study presents the first global CNV atlas for guinea fowl and provides the first comprehensive genomic characterization of the Indian domestic population, integrating ROH, CNV, and selection signature analyses. It offers a comprehensive assessment of guinea fowl genomes (wild and domesticated) across three continents, offering insights into domestication, evolutionary dynamics, and the genetic basis of their adaptation and resilience. Full article

Argali (Ovis ammon), the largest wild sheep in Asia, are of high conservation concern and remain taxonomically and genetically debated across parts of their range. We investigated population structure, relatedness, and inbreeding within Argali sampled in Kyrgyzstan using the Illumina Ovine High-Density SNP array, with an emphasis on dense within-population sampling rather than range-wide comparisons. After quality control, 72 individuals and 135,242 markers were retained for analysis. Principal component analysis revealed subtle genetic variation within the sampled population, but no clustering consistent with discrete subspecies. In particular, we found no genomic support for separating O. a. polii and O. a. karelini within Kyrgyzstan, suggesting that they represent a single genetic unit in this region. Estimates of identity by descent indicated a high average relatedness (0.35), consistent with harem-based breeding systems typical of wild sheep, while individual inbreeding coefficients averaged near zero, with some evidence of moderate inbreeding in a subset of animals. Together, these results characterize fine-scale genetic structure and kinship within Tian Shan Argali and provide a regional genomic baseline for conservation planning in Kyrgyzstan. Our findings highlight the importance of maintaining connectivity within and among managed populations while acknowledging that broader inference will require sampling across the core Pamir range and other parts of the species’ distribution. Full article

Accurate genealogical records are essential in livestock breeding for maintaining genetic diversity, preventing inbreeding, and mapping of economically important traits in beef production. This study aimed to assess parent–offspring relationships within South African Bonsmara and Nguni cattle populations using both traditional pedigree records and genomic data. Hair samples from 119 Nguni and 311 Bonsmara cattle were genotyped using the BovineSNP50 array, and these were imputed to Illumina BovineHD BeadChip using updated SNP coordinates from the assembly genome (ARC—UCSD 1.2). Quality control and data filtering were performed using PLINK v1.9, while relationship inference was conducted using KING v2.2.8 and PLINK v1.9 software for principal component analysis, IBD metrics and Mendelian error-based exclusion. Categories of relatedness through network relationship analysis revealed a predominance of half-sibling relationships in both breeds, with 2317 such relationships identified in Nguni and 1221 in Bonsmara. Inference of parent–offspring pairs showed discrepancies with the recorded pedigrees, with 49 inferred pairs compared to 47 recorded pairs in Nguni, and 62 inferred pairs compared to 75 pairs recorded in Bonsmara. Relationships based on IBD using PLINK with a ‘PI-HAT’ threshold greater than 0.45 revealed unique parent–offspring inferences that differed from those obtained using KING v2.2.8. Phylogenetic network analysis assigned each individual’s genomic origin independent of the pedigree records, supporting the efficiency of SNP data for genetic assignment. These results demonstrated that SNP-based pedigree verification can accurately identify parent–offspring and half-sibling relationships, providing a reliable foundation for recombination analysis and supporting precise trait mapping and informed selection in breeding programs. Full article