Whole-genome Resequencing Research Articles

Needle and Branch Trait Variation Analysis and Associated SNP Loci Mining in Larix olgensis.

Needles play key roles in photosynthesis and branch growth in Larix olgensis. However, genetic variation and SNP marker mining associated with needle and branch-related traits have not been reported yet. In this study, we examined 131 samples of unrelated genotypes from L. olgensis provenance trails. We investigated phenotypic data for seven needle and one branch-related traits before whole genome resequencing (WGRS) was employed to perform a genome-wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci that were significantly correlated with the studied traits. We identified a total of 243,090,868 SNP loci, and among them, we discovered a total of 161 SNP loci that were significantly associated with these traits using a general linear model (GLM). Based on the GWAS results, Kompetitive Allele-Specific PCR (KASP), designed based on the DNA of population samples, were used to validate the loci associated with L. olgensis phenotypes. In total, 20 KASP markers were selected from the 161 SNPs loci, and BSBM01000635.1_4693780, BSBM01000114.1_5114757, and BSBM01000114.1_5128586 were successfully amplified, were polymorphic, and were associated with the phenotypic variation. These developed KASP markers could be used for the genetic improvement of needle and branch-related traits in L. olgensis.

Construction of the First High-Density Genetic Linkage Map and QTL Mapping of Shikimic Acid Content in Liquidambar

High-quality genetic maps are effective tools for elucidating the genetic mechanisms of complex quantitative traits and facilitating marker-assisted breeding. Species within the genus Liquidambar (commonly called sweetgum), particularly Liquidambar styraciflua and Liquidambar formosana, are significant forest resources worldwide. These sweetgum trees have been extensively utilized in medical and cosmetic applications for centuries as they contain large amounts of valuable secondary metabolites. Among these, shikimic acid is a notable metabolite with significant pharmaceutical applications. Despite advances in conventional breeding and propagation techniques for sweetgum, the genetic basis and regulatory mechanisms of valuable traits remain largely unexplored. In this study, we constructed the first high-density genetic map for sweetgum using whole-genome resequencing (WGR) of 220 progeny individuals derived from a cross of L. styraciflua × L. formosana. The genetic map spanned a total distance of 1428.51 centimorgans (cM) with an average inter-marker distance of 0.33 cM, incorporating 4268 bin markers across 16 linkage groups. To identify the genetic loci controlling the shikimic acid content, quantitative trait locus (QTL) mapping was carried out based on the genetic map. Two QTLs located on linkage group (LG) 12 were detected, encompassing a total of 213 genes within the QTL interval. Some of these genes are closely related to secondary metabolism in plants, including YUCCA and DXS genes. This study presents the first high-quality genetic map of sweetgum and provides a preliminary QTL analysis for shikimic acid content. Our findings establish a foundational framework for the genetic improvement of sweetgum through marker-assisted breeding and offer valuable insights for further research in sweetgum genetics.

Alternative double strand break repair pathways shape the evolution of high recombination in the honey bee, Apis mellifera.

Social insects, particularly honey bees, have exceptionally high genomic frequencies of genetic recombination. This phenomenon and underlying mechanisms are poorly understood. To characterise the patterns of crossovers and gene conversion in the honey bee genome, a recombination map of 187 honey bee brothers was generated by whole-genome resequencing. Recombination events were heterogeneously distributed without many true hotspots. The tract lengths between phase shifts were bimodally distributed, indicating distinct crossover and gene conversion events. While crossovers predominantly occurred in G/C-rich regions and seemed to cause G/C enrichment, the gene conversions were found predominantly in A/T-rich regions. The nucleotide composition of sequences involved in gene conversions that were associated with or distant from crossovers corresponded to the differences between crossovers and gene conversions. These combined results suggest two types of DNA double-strand break repair during honey bee meiosis: non-canonical homologous recombination, leading to gene conversion and A/T enrichment of the genome, and the canonical homologous recombination based on completed double Holliday Junctions, which can result in gene conversion or crossover and is associated with G/C bias. This G/C bias may be selected for to balance the A/T-rich base composition of eusocial hymenopteran genomes. The lack of evidence for a preference of the canonical homologous recombination for double-strand break repair suggests that the high genomic recombination rate of honey bees is mainly the consequence of a high rate of double-strand breaks, which could in turn result from the life history of honey bees and their A/T-rich genome.

Whole-genome resequencing reveals melanin deposition candidate genes of Luning chicken

BackgroundMelanin in the black-bone chicken’s body is considered the material basis for its medicinal effects and is an economically important trait. Therefore, improving the melanin content is a crucial focus in the breeding process of black-bone chickens. Luning chickens are black-bone chickens, with black beaks, skin, and meat. To investigate the genetic diversity and molecular mechanisms of melanin deposition in Luning chickens, we conducted whole-genome resequencing to analyze their breeding history and identify candidate genes influencing their black phenotype, along with transcriptome sequencing of dorsal skin tissues of male Luning chickens.ResultsPopulation structure analysis revealed that Luning chickens tend to cluster independently and are closely related to Tibetan chickens. Runs of homozygosity analysis suggested potential inbreeding in the Luning chicken and Tibetan chicken population. By combining genetic differentiation index (Fst) and nucleotide diversity (θπ) ratios, we pinpointed selected regions associated with melanin deposition. Gene annotation identified 540 genes with the highest Fst value in LOC101750371 and LOC121108313, located on the 68.24–68.58 Mb interval of chromosome Z. Combining genomic and transcriptomic data, we identified ATP5E, EDN3, and LOC101750371 as candidate genes influencing skin color traits in black-bone chickens.ConclusionsThis study characterized the evolutionary history of Luning chickens and preliminarily excavated candidate genes influencing the genetic mechanism of pigmentation in black-bone chickens, providing valuable insights for the study of animal melanin deposition.

Milk Lipid Regulation in Dairy Goats: A Comprehensive Review.

The growth, development, and milk production traits of dairy goats, which are important sources of high-quality animal protein, are significantly influenced by a combination of genetic and environmental factors. It is imperative to identify key genetic loci that govern economically valuable traits in order to enhance breeding programs. Despite advancements in genomic technologies, there are still gaps in knowledge regarding the interplay between genetic factors and environmental influences, particularly in relation to the regulation of milk production and quality. Therefore, the aim of this paper was to synthesize advancements in the genetic and environmental factors affecting milk production and quality in dairy goats and identify key regulatory mechanisms. This review summarizes the recent progress on the identification of genes associated with milk production traits using whole-genome resequencing, the use of transcriptomic profiling to identify genes linked to milk production, the exploration of regulatory mechanisms of lipid metabolism in goat mammary epithelial cells, and the evaluation of the influence of nutritional factors on milk quality. A comprehensive understanding of these interactions is essential for enhancing breeding strategies and ensuring the sustainability of dairy goat farming. Future research should incorporate multi-omics approaches to unravel the intricate regulatory processes governing milk production and adapt practices to meet global demand while upholding economic and environmental sustainability.

Whole-Genome Resequencing Identifies SNPs in Sucrose Synthase and Sugar Transporter Genes Associated with Sweetness in Coconut.

Coconut (Cocos nucifera L.) is an important agricultural commodity with substantial economic and nutritional value, widely used for various products, including coconut water. The sweetness is an important quality trait of coconut water, which is influenced by genetic and environmental factors. In this study, we utilized next-generation sequencing to identify genetic variations in the coconut genome associated with the sweetness of coconut water. Whole-genome resequencing of 49 coconut accessions, including diverse germplasm and an F2 population of 81 individuals, revealed ~27 M SNPs and ~1.5 M InDels. Sugar content measured by °Bx was highly variable across all accessions tested, with dwarf varieties generally sweeter. A comprehensive analysis of the sugar profiles revealed that sucrose was the major sugar contributing to sweetness. Allele mining of the 148 genes involved in sugar metabolism and transport and genotype-phenotype association tests revealed two significant SNPs in the hexose carrier protein (Cnu01G018720) and sucrose synthase (Cnu09G011120) genes associated with the higher sugar content in both the germplasm and F2 populations. This research provides valuable insights into the genetic basis of coconut sweetness and offers molecular markers for breeding programs aimed at improving coconut water quality. The identified variants can improve the selection process in breeding high-quality sweet coconut varieties and thus support the economic sustainability of coconut cultivation.

Host genetics and gut microbiota synergistically regulate feed utilization in egg-type chickens

BackgroundFeed efficiency is a crucial economic trait in poultry industry. Both host genetics and gut microbiota influence feed efficiency. However, the associations between gut microbiota and host genetics, as well as their combined contributions to feed efficiency in laying hens during the late laying period, remain largely unclear.MethodsIn total, 686 laying hens were used for whole-genome resequencing and liver transcriptome sequencing. 16S rRNA gene sequencing was conducted on gut chyme (duodenum, jejunum, ileum, and cecum) and fecal samples from 705 individuals. Bioinformatic analysis was performed by integrating the genome, transcriptome, and microbiome to screen for key genetic variations, genes, and gut microbiota associated with feed efficiency.ResultsThe heritability of feed conversion ratio (FCR) and residual feed intake (RFI) was determined to be 0.28 and 0.48, respectively. The ileal and fecal microbiota accounted for 15% and 10% of the FCR variance, while the jejunal, cecal, and fecal microbiota accounted for 20%, 11%, and 10% of the RFI variance. Through SMR analysis based on summary data from liver eQTL mapping and GWAS, we further identified four protein-coding genes, SUCLA2, TNFSF13B, SERTM1, and MARVELD3, that influence feed efficiency in laying hens. The SUCLA2 and TNFSF13B genes were significantly associated with SNP 1:25664581 and SNP rs312433097, respectively. SERTM1 showed significant associations with rs730958360 and 1:33542680 and is a potential causal gene associated with the abundance of Corynebacteriaceae in feces. MARVELD3 was significantly associated with the 1:135348198 and was significantly correlated with the abundance of Enterococcus in ileum. Specifically, a lower abundance of Enterococcus in ileum and a higher abundance of Corynebacteriaceae in feces were associated with better feed efficiency.ConclusionsThis study confirms that both host genetics and gut microbiota can drive variations in feed efficiency. A small portion of the gut microbiota often interacts with host genes, collectively enhancing feed efficiency. Therefore, targeting both the gut microbiota and host genetic variation by supporting more efficient taxa and selective breeding could improve feed efficiency in laying hens during the late laying period.

Whole-genome re-sequencing reveals genetic structure and selection signals of different populations in Megalobrama amblycephala

Characterization of genetic variants is crucial for understanding the molecular mechanisms behind selected traits and enhancing the rate of genetic gain through artificial selection. This study explored the genetic diversity and population structure of blunt snout bream Megalobrama amblycephala, a key freshwater fish in Chinese aquaculture. We conducted whole-genome re-sequencing of individuals from six populations, comprising three natural and three genetically improved strains, to assess genetic diversity, population structure and the impacts of selective breeding. We identified 17,009,590 high-quality biallelic single nucleotide polymorphism (SNP) loci. Genetic diversity assessments revealed low levels of polymorphism across populations, with genetically improved strains showing moderate to high genetic differentiation from their source populations. The study also highlighted runs of homozygosity (ROH) and analyzed linkage disequilibrium (LD) decay, indicating minimal recent inbreeding and diverse recombination events among populations. Selective sweep analyses uncovered significant selection loci associated with growth and hypoxia tolerance traits. Enrichment analyses identified genes involved in olfactory signal transduction, immune response, and metabolism pathways, which are closely related to these selective traits. These findings offer insights into the genetic basis of critical traits in M. amblycephala, contributing to the conservation of germplasm resources and supporting ongoing selective breeding efforts.

Introgression drives adaptation to the plateau environment in a subterranean rodent

BackgroundIntrogression has repeatedly been shown to play an important role in the adaptation of species to extreme environments, yet how introgression enables rodents with specialized subterranean lifestyle to acclimatize to high altitudes is still unclear. Myospalacinae is a group of subterranean rodents, among which the high-altitude plateau zokors (Eospalax baileyi) and the low-altitude Gansu zokors (E. cansus) are sympatrically distributed in the grassland ecosystems of the Qinghai-Tibet Plateau (QTP). Together, they provide a model for the study of the role of introgression in the adaptation of low-altitude subterranean rodents to high altitudes.ResultsApplying low-coverage whole-genome resequencing and population genetics analyses, we identified evidence of adaptive introgression from plateau zokors into Gansu zokors, which likely facilitated the adaptation of the latter to the high-altitude environment of the QTP. We identified positively selected genes with functions related to energy metabolism, cardiovascular system development, calcium ion transport, and response to hypoxia which likely made critical contributions to adaptation to the plateau environment in both plateau zokors and high-altitude populations of Gansu zokors.ConclusionsIntrogression of genes associated with hypoxia adaptation from plateau zokors may have played a role in the adaptation of Gansu zokors to the plateau environment. Our study provides new insights into the understanding of adaptive evolution of species on the QTP and the importance of introgression in the adaptation of species to high-altitude environments.

Whole-genome resequencing and RNA-seq analysis implicates GPR75 as a potential genetic basis related to retarded growth in South China carp (Cyprinus carpio rubrofuscus)

The south China carp (Cyprinus carpio rubrofuscus) is an indigenous and important fish species, widely cultured in south China. However, part of individuals experienced retarded growth, the genetic basis of which has yet to be elucidated. In this study, whole-genome resequencing of 35 fast-growing and 35 retarded-growing south China carp were conducted to identify promising genes associated with retarded growth. Twelve candidate SNPs were detected and annotated to the Gpr75 gene, which has been reported to be related with body weight through regulating insulin homeostasis. RNA-seq analysis of muscle suggested that differentially expressed genes were significantly enriched in the insulin signaling pathway. Additionally, the fasting serum insulin level was significantly lower while the blood glucose level was significantly higher in the retarded-growing group. Our preliminary study provides insights into the genetic basis underlying the retarded growth and may facilitate further genetic improvement of south China carp.

Pan-genome analyses of 11 Fraxinus species provide insights into salt adaptation in ash trees

Ash trees (Fraxinus) exhibit rich genetic diversity and wide adaptation to various ecological environments, and several species are highly salt tolerant. Dissecting the genomic basis of salt adaptation in Fraxinus is vital for its resistance breeding. Here, we present 11 high-quality chromosome-level genome assemblies for Fraxinus species, which reveal two unequal subgenome compositions and two recent whole-genome triplication events in their evolutionary history. A Fraxinus pan-genome was constructed on the basis of structural variations and revealed that presence–absence variations (PAVs) of transmembrane transport genes have likely contributed to salt adaptation in Fraxinus. Through whole-genome resequencing of an F1 population from an interspecies cross of F. velutina ‘Lula 3’ (salt tolerant) with F. pennsylvanica ‘Lula 5’ (salt sensitive), we mapped salt-tolerance PAV-based quantitative trait loci (QTLs) and pinpointed two PAV-QTLs and candidate genes associated with Fraxinus salt tolerance. Mechanistically, FvbHLH85 enhances salt tolerance by mediating reactive oxygen species and Na+/K+ homeostasis, whereas FvSWEET5 enhances salt tolerance by mediating osmotic homeostasis. Collectively, these findings provide valuable genomic resources for Fraxinus salt-resistance breeding and the research community.

Genomic insights into oxalate content in spinach: A genome-wide association study and genomic prediction approach

Oxalate content in spinach is a key trait of interest due to its relevance to human health. Understanding the genetic basis of it can facilitate the development of spinach varieties with reduced oxalate levels. In pursuit of understanding the genetic determinants, a diverse panel comprising 288 spinach accessions underwent thorough phenotyping of oxalate content and were subjected to whole-genome resequencing, resulting in a comprehensive dataset encompassing 14 386 single-nucleotide polymorphisms (SNPs). Leveraging this dataset, we conducted a genome-wide association study (GWAS) to identify noteworthy SNPs associated with oxalate content. Furthermore, we employed genomic prediction (GP) via cross-prediction, utilizing five GP models, to assess genomic estimated breeding values (GEBVs) for oxalate content. The observed normal distribution and the wide range of oxalate content, exceeding 600.0 mg · 100 g−1, underscore the complex and quantitative nature of this trait, likely influenced by multiple genes. Additionally, our analysis revealed distinct stratification, delineating the population into four discernible subpopulations. Furthermore, GWAS analysis employing five models in GAPIT 3 and TASSEL 5 unveiled nine significant SNPs (four SNPs on chromosome 1 and five on chromosome 5) associated with oxalate content. These loci exhibited associations with six candidate genes, which might have potential contribution to oxalate content regulation. Remarkably, our GP models exhibited notable predictive abilities, yielding average accuracies of up to 0.51 for GEBV estimation. The integration of GWAS and GP approaches offers a holistic comprehension of the genetic underpinnings of oxalate content in spinach. These findings offered a promising avenue for the development of spinach cultivars and hybrids optimized for oxalate levels, promoting consumer health.

Mutation of a RING E3 ligase, OsDIRH2, enhances drought tolerance in rice with low stomata density.

Drought is a major environmental stress factor that negatively affects rice growth and yield. From a forward genetic perspective, we selected a drought-insensitive TILLING line (ditl4) from a gamma-ray-induced core mutant population (M10). Under drought conditions, ditl4 exhibited greater fresh weight, survival rate, chlorophyll, proline, and soluble sugar contents, and lower H2O2 and MDA levels than wild-type (WT). In addition, the activities of antioxidant enzymes, such as superoxide dismutase, catalase, and peroxidase, were higher in ditl4 than in the WT. In the relative water loss assay, dilt4 showed significantly decreased leaf curling and water loss compared to WT. Also, the ratio of "closed" stomata aperture was increased in ditl4 under drought stress, suggesting reduced transpiration to prevent water loss. The ditl4 mutant showed decreased stomatal conductance, transpiration, and CO2 assimilation and increased water use efficiency due to the low density of stomata. Whole-genome resequencing analysis of dilt4 identified a single nucleotide polymorphism (SNP) in OsDIRH2 (LOC_Os11g39640), annotated as a RING-H2 type E3 ligase, resulting in a premature stop codon. CRISPR/Cas9-mediated knock-out mutants (OsDIRH2a and OsDIRH2b) enhanced drought tolerance by lowering stomatal density compared to empty vector control plants. These findings suggested that ditl4 with low stomatal density would be useful as a genetic resource for a drought-tolerant breeding program to improve water-use efficiency.

Whole-Genome Resequencing Analysis of Hybrid White Goats to Identify Fertility-Related Genes

Whole-Genome Resequencing Analysis of Hybrid White Goats to Identify Fertility-Related Genes

Genomic Diversity as a Key Conservation Criterion: Proof-of-Concept From Mammalian Whole-Genome Resequencing Data.

Many international, national, state, and local organizations prioritize the ranking of threatened and endangered species to help direct conservation efforts. For example, the International Union for Conservation of Nature (IUCN) assesses the Green Status of species and publishes the influential Red List of threatened species. Unfortunately, such conservation yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, and with future evolutionary potential. To test whether populations of genome sequences could help improve conservation assessments, we estimated GD metrics from 82 publicly available mammalian datasets and examined their statistical association with attributes related to conservation. We also considered intrinsic biological factors, including trophic level and body mass, that could impact GD and quantified their relative influences. Our results identify key population GD metrics that are both reflective and predictive of IUCN conservation categories. Specifically, our analyses revealed that Watterson's theta (the population mutation rate) and autozygosity (a product of inbreeding) are associated with the current Red List categorization, likely because demographic declines that lead to "listing" decisions also reduce levels of standing genetic variation. We argue that by virtue of this relationship, conservation organizations like IUCN could leverage emerging genome sequence data to help categorize Red List threat rankings (especially in otherwise data-deficient species) and/or enhance Green Status assessments to establish a baseline for future population monitoring. Thus, our paper (1) outlines the theoretical and empirical justification for a new GD-based assessment criterion, (2) provides a bioinformatic pipeline for estimating GD from population genomic data, and (3) suggests an analytical framework that can be used to measure baseline GD while providing quantitative GD context for consideration by conservation authorities.

Development and characterization of 40 SNP markers of endangered species Cuora flavomarginata by whole-genome resequencing

Development and characterization of 40 SNP markers of endangered species Cuora flavomarginata by whole-genome resequencing

Contribution of homoeologous exchange to domestication of polyploid Brassica

BackgroundPolyploidy is widely recognized as a significant evolutionary force in the plant kingdom, contributing to the diversification of plants. One of the notable features of allopolyploidy is the occurrence of homoeologous exchange (HE) events between the subgenomes, causing changes in genomic composition, gene expression, and phenotypic variations. However, the role of HE in plant adaptation and domestication remains unclear.ResultsHere we analyze the whole-genome resequencing data from Brassica napus accessions representing the different morphotypes and ecotypes, to investigate the role of HE in domestication. Our findings demonstrate frequent occurrence of HEs in Brassica napus, with substantial HE patterns shared across populations, indicating their potential role in promoting crop domestication. HE events are asymmetric, with the A genome more frequently replacing C genome segments. These events show a preference for specific genomic regions and vary among populations. We also identify candidate genes in HE regions specific to certain populations, which likely contribute to flowering-time diversification across diverse morphotypes and ecotypes. In addition, we assemble a new genome of a swede accession, confirming the HE signals on the genome and their potential involvement in root tuber development. By analyzing HE in another allopolyploid species, Brassica juncea, we characterize a potential broader role of HE in allopolyploid crop domestication.ConclusionsOur results provide novel insights into the domestication of polyploid Brassica species and highlight homoeologous exchange as a crucial mechanism for generating variations that are selected for crop improvement in polyploid species.

The Biological Characteristics of Mycobacterium Phage Henu3 and the Fitness Cost Associated with Its Resistant Strains.

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is an infectious disease that seriously affects human life and health. Despite centuries of efforts to control it, in recent years, the emergence of multidrug-resistant bacterial pathogens of M. tuberculosis due to various factors has exacerbated the disease, posing a serious threat to global health. Therefore, a new method to control M. tuberculosis is urgently needed. Phages, viruses that specifically infect bacteria, have emerged as potential biocontrol agents for bacterial pathogens due to their host specificity. In this study, a mycobacterium phage, Henu3, was isolated from soil around a hospital. The particle morphology, biological characteristics, genomics and phylogeny of Henu3 were characterized. Additionally, to explore the balance between phage resistance and stress response, phage Henu3-resistant strains 0G10 and 2E1 were screened by sequence passage and bidirectional validation methods, which significantly improved the sensitivity of phage to antibiotics (cefotaxime and kanamycin). By whole-genome re-sequencing of strains 0G10 and 2E1, 12 genes involved in cell-wall synthesis, transporter-encoded genes, two-component regulatory proteins and transcriptional regulatory factor-encoded genes were found to have mutations. These results suggest that phage Henu3 has the potential to control M. tuberculosis pathogens, and phage Henu3 has the potential to be a new potential solution for the treatment of M. tuberculosis infection.

Genome wide detection of CNV and their association with body size in Danzhou chickens

Copy number variation (CNV) is a crucial component of genetic diversity in the genome, serving as the foundation for the genetic architecture and phenotypic variability of complex traits. In this study, we examined CNVs in the Danzhou (DZ) chicken, an indigenous breed exclusive to Hainan Province, China. By employing whole-genome resequencing data from 200 DZ chickens, we conducted a comprehensive genome-wide analysis of CNVs using CNVpytor and performed CNV-based genome-wide association studies (GWAS) on six body size traits, including body slope length (BSL), keel length (KeL), tibial length (TiL), tibial circumference (TiC), chest width (ChW), and chest depth (ChD) utilizing linear mixed model methods considering a genomic relationship matrix. We identified a total of 144,265 autosomal CNVs among the 200 individuals, comprising 67,818 deletions and 76,447 duplications. After merging these variants together, we obtained 4,824 distinct copy number variant regions, which accounted for approximately 20% of the chicken autosomal genome. Furthermore, we discovered several significantly associated CNV segments with body size traits located proximal to genes such as IHH, WNT6, WNT10A, LPR4, FZD2, WNT7B, and GNAS that have been extensively implicated in skeletal development and growth processes. These findings enhance our understanding of CNVs in chickens and their potential impact on body size traits by revealing candidate genes involved in the regulation of these traits. This establishes a solid framework for future studies and may prove particularly beneficial for exploring genetic structural variation in chickens.

A Whole-Genome Scan Revealed Genomic Features and Selection Footprints of Mengshan Cattle.

(1) Background: Mengshan cattle from the Yimeng mountainous region in China stand out as a unique genetic resource, known for their adaptive traits and environmental resilience. However, these cattle are currently endangered and comprehensive genomic characterization remains largely unexplored. This study aims to address this gap by investigating the genomic features and selection signals in Mengshan cattle. (2) Methods: Utilizing whole-genome resequencing data from 122 cattle, including 37 newly sequenced Mengshan cattle, we investigated population structure, genetic diversity, and selection signals. (3) Results: Our analyses revealed that current Mengshan cattle primarily exhibit European taurine cattle ancestry, with distinct genetic characteristics indicative of adaptive traits. We identified candidate genes associated with immune response, growth traits, meat quality, and neurodevelopment, shedding light on the genomic features underlying the unique attributes of Mengshan cattle. Enrichment analysis highlighted pathways related to insulin secretion, calcium signaling, and dopamine synapse, further elucidating the genetic basis of their phenotypic traits. (4) Conclusions: Our results provide valuable insights for further research and conservation efforts aimed at preserving this endangered genetic resource. This study enhances the understanding of population genetics and underscores the importance of genomic research in informing genetic resources and conservation initiatives for indigenous cattle breeds.