Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia

Genome-wide analysis of genetic diversity and selection signatures in Fuzhou cattle

The Fuzhou cattle breed, native to northeast China, is widely recognized for its adaptability, disease resistance, and docility. Despite being known for these qualities, its population has declined recently, and there is a significant lack of genomic studies on this species. We sequenced 21 samples from a primary breeding farm to determine the genetic structure, diversity, and selection signature to address this. Additionally, we combined 100 published genomic datasets from diverse geographical regions to characterize the genomic variation of Fuzhou cattle. There were 53 752 978 bi-allelic SNPs retained for downstream analysis. In population structure analysis, Fuzhou cattle show a predominantly East Asian taurine ancestry, with strong genetic affinities to Hanwoo and Yanbian cattle. Despite high nucleotide diversity within the Bos taurine lineage, genetic diversity analysis also revealed significant levels of inbreeding in Fuzhou cattle populations, indicating the need for conservation. Utilizing various methods such as θπ, iHS, FST, π-ratio, and XP-EHH, we identified genes associated with traits like growth, meat quality, energy metabolism, and immunity. Several genes related to cold adaptation were identified, including PLIN5, PLB1, and CPT2. These findings provide a basis for conservation strategies to safeguard the genetic resources of Fuzhou cattle.

Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India

Crossbreeding in India has been widely adopted to address low sustainability and poor productivity in non-descript cattle. This study analyzed Vrindavani (VRI) crossbred cattle and their parental populations (Holstein Friesian (HOL), Jersey (JER), Brown Swiss (BSW), Hariana (HAR) using SNP data to characterize locus-specific ancestry in VRI's genome along with admixture proportions and population stratification. Admixture analysis showed VRI have 67.3% HOL, 20.1% HAR, 8.5% JER, and 4% BSW ancestry. Locus-specific ancestry estimation identified regions with adaptive admixtures, which can be defined as admixed genomic regions favored by evolutionary forces and increased their frequencies, revealed 79.7% Bos taurus and 20.3% Bos indicus ancestry. Notably, regions on chromosome (chr) 2, 3, 4, 5, 7, 10, 12, 13, 14, 16, 17, 19, 20, 21, 22, 23, and 24 were associated with disease resistance contributed by indicine ancestry and chr 1, 6, 9, 11, 15, 18, 27, and 28 related to production which were contributed by taurine ancestry. The study concluded that increased taurine ancestry contributes to higher milk yield in VRI crosses, while indicine ancestry confers disease resistance and adaptability to tropical climates. This comprehensive genomic analysis suggests that while taurine inheritance enhances milk yield, a balance with indicine traits is essential for resilience. Understanding locus-specific ancestry patterns can aid in refining breeding strategies by selectively promoting beneficial alleles. Future advancements in genomic tools may enable controlled inheritance of desirable traits, maximizing heterosis in structured breeding programs for sustainable cattle production.

The CNV map construction and ROH analysis of Pinan cattle

Pinan cattle, as the progeny of crossbreeding improvement between Nanyang cattle and Piedmontese, have attracted attention for their excellent growth performance. In this study, we constructed a copy number variation map by whole genome resequencing of 132 Pinan cattle. In the genome of Pinan cattle, deletion-type copy number variants occupied a higher proportion and only 3.31% of CNVRs overlapped with exonic regions. It showed that Pinan cattle was clearly distinguishable from other breeds and Pinan cattle was closer to Nanyang cattle by population genetic structure analysis based on CNVRs. The degree of inbreeding in the Pinan cattle population was explored by ROH analysis, which showed that the degree of inbreeding in Pinan cattle was lower than that in European beef cattle, suggesting that the risk of inbreeding was low. Candidate genes related to muscle development (CADM3, CNTFR, DOCK3), reproductive traits (SCAPER), embryonic development (RERE) and immune traits (CD84) were identified by VST selection analysis, ROH islands and iHS selection analysis, which provided a new scientific basis for the genetic basis of the excellent traits in Pinan cattle.

Admixture and selection offer insights for the conservation and breeding of Guyuan cattle

BACKGROUND

The admixture between taurine and indicine cattle increases breed diversity and provides new genetic resources for human and natural selection. The climate of northwestern China is typified by cold and arid conditions, and cattle in this region are primarily taurine breeds. However, Guyuan cattle inhabit a transitional zone in northwestern China, typified by semi-arid and semi-humid climates. It is hypothesized that Guyuan cattle have a little of indicine ancestry. These results suggest that Guyuan cattle are a valuable genetic resource.

RESULTS

We established a conservation population of Guyuan cattle in their native habitat. We found that Guyuan cattle were an admixture between 78.09% East Asian taurine (EAT) and 20.26% East Asian indicine (EAI) ancestries. The admixture in Guyuan cattle was dated to 255 years ago. Notably, we identified Guyuan cattle as a unique genetic resource, representing a transitional breed between northern and central Chinese cattle with distinct admixture proportions. We revealed that the selection signals in Guyuan cattle with excess EAT ancestry were associated with reproduction, immunity, body length, cold climate adaptation, pigmentation, muscle development, residual feed intake, and fat deposition and that the selection signals in Guyuan cattle with excess EAI ancestry were associated with disease resistance. Remarkably, we discovered valuable single nucleotide polymorphisms (SNPs) in the promoter regions of the RBM39 and NEK6 genes, which may play key roles in regulating muscle development and disease resistance.

CONCLUSIONS

Our results suggest that Guyuan cattle are a newly identified genetic resource, and the native taurine and indicine ancestries in Guyuan cattle remain a valuable genetic resource of conservation and breeding.

Whole Genome Insights into Genetic Diversity, Introgression, and Adaptation of Hunan Cattle

Hunan Province, located in Central-South China, has a hot and humid climate, which has shaped the unique characteristics of its cattle. In this study, we analyzed the genomic diversity of 110 indigenous Hunan cattle using whole-genome sequencing and found that they have a mixed ancestry of indicine and taurine. By grouping the cattle based on their collection regions (western, central, southeastern, and southern Hunan), we used an unsupervised three-component Gaussian model to classify the runs of homozygosity (ROH) and calculated the genomic inbreeding coefficient based on runs of homozygosity (FROH) to assess inbreeding levels. The results showed that western Hunan cattle had the highest level of hybridization, while southern Hunan cattle had the lowest. Through selective sweep analysis, we identified candidate genes and pathways related to environmental adaptation and homeostasis. Notably, the SLC5A2 gene showed strong selection signals across all four regions and exhibited a distinct haplotype compared to other referenced cattle breeds. Additionally, we detected introgression from wild species into Hunan domestic cattle and analyzed their Y-chromosome haplotypes.

Genomic diversity of Cameroonian Gudali and Gudali-cross cattle

Information on population structure and diversity in cattle breeds is critical for understanding environmental adaptation, as well as optimal utilisation of genetic resources and breed improvement. In this study, we investigated at the genomic level the population structure, genetic diversity and admixture of the local Gudali breed and its crossbred with the Italian Simmental (Simgud) in three agroecological zones of Cameroon. A total of 717 Gudali and 139 Simgud were genotyped using the GeneSeek® Genomic ProfilerTM (GGP) Bovine 100K array and analyzed together with reference breed data from public databases. Principal component (PCA) and admixture analysis separated European Bos taurus from Asian Bos indicus, African Bos taurus and African Bos indicus breeds. These analyses showed that, except for recently admixed cattle, all African indigenous breeds are either pure African Bos taurus (N'dama) or admixtures of African Bos taurus and Bos indicus. Analysis revealed an ancient admixture from Asian origin in Gudali and a more recent and ongoing European introgression. Simgud is an unmanaged crossbreed expected to be primarily a 50% admixture of Gudali and Simmental. We show here that Simgud is, in actuality, composed of two genetic groups representing admixture of between ∼25% to ∼50% Simmental proportion. Diversity analysis revealed high average heterozygosity ([Formula: see text], [Formula: see text]) for the Gudali and ([Formula: see text] , [Formula: see text]) for Simgud respectively. Inbreeding measures based on the mean FIS coefficient were 0.03 for Gudali and 0.07 for Simgud. A general decline in effective population size was observed in Gudali from a large population (Ne=2475), 959 generations (4797 years ago), back to 13 generations (65 years) (Ne=1404) ago. These results were expected, given the breeding efforts that began in 1952 with the introduction of various exotic (imported taurine) breeds and the Gudali selection initiative. This has affected the effective population size of Gudali, despite the general increase in cattle population in the ranches over that period. These results highlight the need for a structured breeding program in Cameroon for improving productivity, while maintaining a large genetic base of the pure Gudali population.

Genomic Characterization of Crossbred-Driven Adaptation in the Endangered Yangba Cattle of China

This study unveils the unique origins, evolution, and genetic variations of the Yangba cattle, an endangered breed in China, through a comparative genomic analysis involving 202 individuals from 21 domestic and international breeds. Genetic component analysis revealed that the Yangba cattle comprise four ancestral lineages: Eurasian taurine (18%), East Asian taurine (26%), Chinese indicine (39%), and Indian indicine (17%). Their high genetic diversity and low inbreeding coefficient set them apart significantly from mainstream commercial breeds. Gene introgression analysis indicated that the influx of genetic material from East Asian taurine has enhanced the Yangba cattle's adaptability to environmental stress, while the introgression from Chinese indicine has endowed them with unique advantages in muscle development and tissue repair. A genome-wide selection scan identified strong positive selection signals for genes such as ABCC2, which is involved in immune regulation, and NCOA3, which plays a role in growth regulation, in the Yangba cattle. This study systematically elucidates, for the first time, the composite ancestral composition and mechanisms of adaptive evolution in Yangba cattle. These findings offer critical insights into the conservation and sustainable utilization of endangered cattle resources and underscore the importance of implementing effective breeding programs.

Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations

Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.

Genomic Insights into Vector-Pathogen Adaptation in Haemaphysalis longicornis and Rhipicephalus microplus

As crucial vectors that transmit pathogens to humans and livestock, ticks pose substantial global health threats and economic burdens. We analyzed 328 tick genomes to explore the population's genetic structure and the adaptive evolution of H. longicornis and R. microplus, two tick species with distinct life cycle characteristics. We observed distinct genetic structures in H. longicornis and R. microplus. Gene flow estimation revealed a closer genetic connection in R. microplus than H. longicornis, which was facilitated by geographical proximity. Notably, we identified a set of candidate genes associated with possible adaptations. Specifically, the immune-related gene DUOX and the iron transport gene ACO1 showed significant signals of natural selection in R. microplus. Similarly, H. longicornis exhibited selection in pyridoxal-phosphate-dependent enzyme genes associated with heme synthesis. Moreover, we observed significant correlations between the abundance of pathogens, such as Rickettsia and Francisella, and specific tick genotypes, which highlights the role of R. microplus in maintaining these pathogens and its adaptations that influence immune responses and iron metabolism, suggesting potential coevolution between vectors and pathogens. Our study highlights the vital genes involved in tick blood feeding and immunity, and it provides insights into the coevolution of ticks and tick-borne pathogens.

The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle

Cattle (Bos taurus) play an important role in the life of humans in the Iberian Peninsula not just as a food source but also in cultural events. When domestic cattle were first introduced to Iberia, wild aurochs (Bos primigenius) were still present, leaving ample opportunity for mating (whether intended by farmers or not). Using a temporal bioarchaeological dataset covering eight millennia, we trace gene flow between the two groups. Our results show frequent hybridisation during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry in domestic cattle remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (~20%) continues into modern Western European breeds including Iberian cattle selected for aggressiveness and fighting ability. This study illuminates the genomic impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.

Whole-genome sequencing reveals genetic architecture and selection signatures of Kazakh cattle

Local cattle breeds play a critical role in breeding programs due to their genetic adaptations to diverse environmental conditions. However, the genomic architecture of local cattle breeds in Kazakhstan remains largely unexplored. This study utilized whole-genome sequencing data from Kazakh cattle to elucidate their genetic composition, uncovering three primary ancestral components: European, Eurasian, and East Asian taurine. The East Asian taurine lineage likely represents the earliest genetic contribution to Kazakh cattle but was largely replaced by subsequent waves of cattle migrations across Eurasia, leaving only a minor genetic signature in the current cattle population. In contrast, Eurasian taurine ancestry predominated in the Alatau and Kazakh local breeds, while the European taurine component was most prevalent in Kazakh white-headed cattle, consistent with their documented breeding history. Kazakh cattle exhibited higher genetic diversity and lower inbreeding coefficients compared to European commercial breeds, reflecting reduced exposure to intense artificial selection. A strong selection signal was identified on chromosome 6 at a locus encompassing PDGFRA, KIT, and KDR, which may be associated with the white-headed pigmentation characteristic of Kazakh white-headed cattle. Additional genes under selection were linked to lipid metabolism ( IRS1, PRKG1, and ADCY8), meat production traits ( KCNMA1, PDGFRA, HIF1A, and ANTXR1), and dairy production ( ATP2B1, DHX15, FUK, NEGR1, CCDC91, COG4, and PTK2B). This study represents the first comprehensive analysis of nuclear genome data from local Kazakh cattle. It highlights the impact of historical cattle migrations across Eurasia on their genetic landscape and identifies key genomic regions under selection. These findings advance our understanding of the evolutionary history of cattle and offer valuable genetic resources for future breeding strategies.

Identification and differential expression analysis of microRNAs in the liver and spleen tissues of Yunnan Zebu and Holstein cattle

Extensive research has shown that miRNAs play a crucial role in regulating biological processes within organisms. This study analyzed miRNAs differentially expressed and potentially associated with immune function and tissue-specific expression in Yunnan Zebu and Holstein cattle. To achieve this, 20 liver and spleen tissue samples from the two cattle breeds were collected for high-throughput miRNA sequencing, with the liver tissue as a reference. The findings revealed that bta-miR-122 and bta-miR-143 are the most abundantly expressed known miRNAs in the liver and spleen tissues of Yunnan Zebu and Holstein cattle, respectively. Additionally, AC_000181.1_27195 and AC_000168.1_14386 emerged as the most highly expressed novel miRNAs in these tissues, exhibiting significant homology with human hsa-miR-3591-3p and hsa-miR-126-3p, respectively. Six differentially expressed miRNAs were selected for validation using stem-loop RT-qPCR, and the results were largely consistent with the high-throughput sequencing data. Functional enrichment analysis of the target genes of these known miRNAs revealed their association with critical metabolic and immune-related pathways in cattle, such as the insulin pathway, mTOR signaling, IFN-γ pathway, and signaling mechanisms mediated by IL5 and IL3. These results enriched the miRNA database for liver and spleen tissues of Yunnan Zebu and Holstein cattle.

Whole genome insights into genetic diversity, introgression, and adaptation of Yunnan indigenous cattle of Southwestern China

BACKGROUND

Yunnan Province, located in Southwestern China, the intricate geography, variable climate, and abundant vegetation of the region have collectively contributed to shaping the distinctive germplasm characteristics observed in Yunnan indigenous cattle through prolonged domestication. The different breeds of Yunnan cattle exhibit distinct advantageous characteristics and traits, which are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. However, a comprehensive genomic landscape of genetic resources has yet to be delineated.

RESULTS

Herein, we employed 140 whole-genome sequencing data from Yunnan indigenous cattle across eight breeds to elucidate their genetic diversity and population structure. Utilizing both uniparental and biparental markers, we elucidated the intricate genetic composition of Yunnan indigenous cattle, which is closely correlated with the geographic environment. A predominant East Asian indicine ancestry which gradually diminishes towards the north. The analysis revealed a high genetic diversity among populations and a low-to-moderate inbreeding coefficient, underscoring the rich genetic reservoir of Yunnan cattle breeds. Additionally, gene flow between Yunnan indicine and wild Bos species in and around Yunnan was verified, highlighting localized introgression from Yunnan Gayal as a critical factor in the successful adaptation of Yunnan indicine cattle to the local hot and humid environments.

CONCLUSIONS

Our findings established the SNPs database for facilitating resource conservation and selective breeding. Moreover, these valuable insights into the genomic diversity and adaptive history of Yunnan indigenous cattle breeds contribute significantly to our understanding of their evolutionary dynamics and offer a foundation for future genetic improvement and conservation strategies.

Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity characteristics in three Chinese cattle breeds

BACKGROUND

Cattle have evolved genetic adaptations to a diverse range of agroecological zones, such as plateaus and arid zones. However, little is known about its genetic basis of adaptation to harsh environments within a short period of time after domestication. Here, we analyzed whole-genome sequence data from three indigenous cattle breeds (Anxi, Qaidam and Zhangmu) in northwest China and five worldwide cattle breeds (Angus, Holstein, Jersey, Gir and N'Dama) to explore their genetic composition and identify selective sweeps in the Chinese cattle breeds.

RESULTS

Analyses of phylogenetic and population structure revealed that three indigenous cattle breeds share genomic components from Bos taurus and Bos indicus. A novel set of candidate genes was identified through comparative genomic analyses of cattle from contrasting environments based on SNP and copy number variation (CNV) data. These candidate genes are potentially associated with adaptive phenotypes, including high-altitude adaptability (e.g., ANGPT1, PPARGC1A, RORA), cold climate adaptation (e.g., TSHR, PRKG, OXCT1), and dryland adaptation (e.g., PLEKHA7, NFATC1, PLCB1).

CONCLUSIONS

This study unravels the unique adaptive diversity of three Chinese indigenous cattle breeds, providing a valuable resource for future research on sustainable livestock breeding strategies to response to climate change.

Genetic Comparison and Selection of Reproductive and Growth-Related Traits in Qinchuan Cattle and Two Belgian Cattle Breeds

This study investigates the genetic structure of Belgian Red (BR), Belgian Red and White (BWR), and Qinchuan (QinC) cattle, with a focus on identifying genes associated with reproductive functions, growth, and development. A total of 270 Belgian cattle (91 BR and 179 BWR) and 286 Qinchuan cattle were genotyped using the Illumina Bovine SNP 50K microarray. Data analysis was conducted using PLINK and Beagle 5.1 to estimate linkage disequilibrium (LD) and effective population size (Ne). Candidate SNP loci were identified by selecting the top 5% based on the weighted fixation index (Fst) and nucleotide diversity (θπ ratio), followed by gene annotation. The analysis revealed 160 candidate genes under selection between Qinchuan and Belgian Red cattle, and 98 candidate genes between Qinchuan and Belgian Red and White cattle. Key genes associated with reproductive functions, including NFKBIA, PTHLH, UGT2B10, TRPC4, and ALOX5AP, were identified. Additionally, genes involved in growth and muscle development were highlighted, particularly those influencing protein synthesis, fatty acid metabolism, and collagen synthesis. These findings provide valuable molecular markers for enhancing reproductive efficiency, growth, and meat production through genetic selection and selective breeding strategies.

Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus

BACKGROUND

India harbors the world's largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome.

RESULTS

Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics 'linked-read' technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb, comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 Mb was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs encompassing ~ 2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis. The protein-coding genes were found in various prominent quantitative trait locus (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance.

CONCLUSIONS

This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.

Selection Increases Mitonuclear DNA Discordance but Reconciles Incompatibility in African Cattle

Mitochondrial function relies on the coordinated interactions between genes in the mitochondrial DNA and nuclear genomes. Imperfect interactions following mitonuclear incompatibility may lead to reduced fitness. Mitochondrial DNA introgressions across species and populations are common and well documented. Various strategies may be expected to reconcile mitonuclear incompatibility in hybrids or admixed individuals. African admixed cattle (Bos taurus × B. indicus) show sex-biased admixture, with taurine (B. taurus) mitochondrial DNA and a nuclear genome predominantly of humped zebu (B. indicus). Here, we leveraged local ancestry inference approaches to identify the ancestry and distribution patterns of nuclear functional genes associated with the mitochondrial oxidative phosphorylation process in the genomes of African admixed cattle. We show that most of the nuclear genes involved in mitonuclear interactions are under selection and of humped zebu ancestry. Variations in mitochondrial DNA copy number may have contributed to the recovery of optimal mitochondrial function following admixture with the regulation of gene expression, alleviating or nullifying mitochondrial dysfunction. Interestingly, some nuclear mitochondrial genes with enrichment in taurine ancestry may have originated from ancient African aurochs (B. primigenius africanus) introgression. They may have contributed to the local adaptation of African cattle to pathogen burdens. Our study provides further support and new evidence showing that the successful settlement of cattle across the continent was a complex mechanism involving adaptive introgression, mitochondrial DNA copy number variation, regulation of gene expression, and selection of ancestral mitochondria-related genes.

Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of leucistic plumage of blue peafowl

INTRODUCTION

The blue peafowl (Pavo cristatus) and the green peafowl (Pavo muticus) have garnered significant public affection due to their stunning appearance, although the green peafowl is currently endangered. The causative mutation that causes the leucistic plumage of the blue peafowl (also called white peafowl) remains unknown.

RESULTS

In this study, we generated a chromosome-level reference genome of the blue peafowl with a contig N50 of 30.6 Mb, including the autosomes, Z and W sex chromosomes, and a complete mitochondria DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes, and 33 peafowl W chromosomes genomes provided the first substantial genetic evidence for recent hybridization between green peafowls and blue peafowls. We found 3 hybrid green peafowls in zoo samples rather than in the wild samples, with a blue peafowl genomic content of 16-34%. Maternal genetic analysis showed that 2 of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Some animal protection agencies release captive green peafowls in order to maintain the wild population of green peafowls. Therefore, to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to prevent the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in 4 zoo blue peafowl individuals. The introgressed genomic regions contain IGFBP1 and IGFBP3 genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G>A) in the EDNRB2 gene is the genetic causative mutation for leucistic plumage of blue peafowl, preventing melanocytes from being transported into plumage, thereby inhibiting melanin deposition.

CONCLUSION

Our research provides both theoretical and empirical support for the conservation of the endangered green peafowl. The high-quality genome and genomic data also provide a valuable resource for blue peafowl genomics-assisted breeding.

Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, since that time, substantial genomic differences have evolved between the two lineages. During the last two millennia, genetic exchange in Africa has resulted in a complex tapestry of taurine-indicine ancestry, with most cattle populations exhibiting varying levels of admixture. Similarly, there are several Southern European cattle populations that also show evidence for historical gene flow from indicine cattle, the highest levels of which are found in the Central Italian White breeds. Here we use two different software tools (MOSAIC and ELAI) for local ancestry inference (LAI) with genome-wide high- and low-density SNP array data sets in hybrid African and residually admixed Southern European cattle populations and obtained broadly similar results despite critical differences in the two LAI methodologies used. Our analyses identified genomic regions with elevated levels of retained or introgressed ancestry from the African taurine, European taurine, and Asian indicine lineages. Functional enrichment of genes underlying these ancestry peaks highlighted biological processes relating to immunobiology and olfaction, some of which may relate to differing susceptibilities to infectious diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. Notably, for retained African taurine ancestry in admixed trypanotolerant cattle we observed enrichment of genes associated with haemoglobin and oxygen transport. This may reflect positive selection of genomic variants that enhance control of severe anaemia, a debilitating feature of trypanosomiasis disease, which severely constrains cattle agriculture across much of sub-Saharan Africa.

Complete Genomic Landscape Reveals Hidden Evolutionary History and Selection Signature in Asian Water Buffaloes (Bubalus bubalis)

To identify the genetic determinants of domestication and productivity of Asian water buffaloes (Bubalus bubalis), 470 genomes of domesticated river and swamp buffaloes along with their putative ancestors, the wild water buffaloes (Bubalus arnee) are sequenced and integrated. The swamp buffaloes inherit the morphology of the wild buffaloes. In contrast, most river buffaloes are unique in their morphology, but their genomes cluster with the wild buffaloes. The levels of genomic diversity in Italian river and Indonesian swamp buffaloes decrease at opposite extremes of their distribution range. Purifying selection prevented the accumulation of harmful loss-of-function variants in the Indonesian buffaloes. Genes that evolved rapidly (e.g., GKAP1) following differential selections in the river and swamp buffaloes are involved in their reproduction. Genes related to milk production (e.g., CSN2) and coat color (e.g., MC1R) underwent strong selections in the dairy river buffaloes via soft and hard selective sweeps, respectively. The selective sweeps and single-cell RNA-seq data revealed the luminal cells as the key cell type in response to artificial selection for milk production of the dairy buffaloes. These findings show how artificial selection has been driving the evolutionary divergence and genetic differentiation in morphology and productivity of Asian water buffaloes.

Local Ancestry and Adaptive Introgression in Xiangnan Cattle

Exploring the genetic landscape of native cattle is an exciting avenue for elucidating nuanced patterns of genetic variation and adaptive dynamics. Xiangnan cattle, a native Chinese cattle breed mainly produced in Hunan Province, are well adapted to the high temperature and humidity of the local environment and exhibit strong disease resistance. Herein, we employed whole-genome sequences of 16 Xiangnan cattle complemented by published genome data from 81 cattle. Our findings revealed that Xiangnan cattle are pure East Asian indicine cattle with high genetic diversity and low inbreeding. By annotating the selection signals obtained by the CLR, θπ, FST, and XP-EHH methods, genes associated with immunity (ITGB3, CD55, OTUD1, and PRLH) and heat tolerance (COX4I2, DNAJC18, DNAJC1, EIF2AK4, and ASIC2) were identified. In addition, the considerable introgression from banteng and gaur also contributed to the rapid adaptation of Xiangnan cattle to the environment of Southern China. These results will provide a basis for the further conservation and exploitation of Xiangnan cattle genetic resources.

Recent selection and introgression facilitated high-altitude adaptation in cattle

During the past 3000 years, cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia, ultraviolet (UV) radiation, and extreme cold. The genetic mechanism underlying this rapid adaptation is not yet well understood. Here, we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations, including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m. Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries. We found that recently selected genes in Tibetan cattle were related to body size (HMGA2 and NCAPG) and energy expenditure (DUOXA2). We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes, covering 0.64%-3.26% of their genomes, which included introgressed genes responsible for hypoxia response (EGLN1), cold adaptation (LRP11), DNA damage repair (LATS1), and UV radiation resistance (GNPAT). We observed that introgressed yak alleles were associated with noncoding variants, including those in present EGLN1. In Tibetan cattle, three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1, suggesting that these genomic variants enhance hypoxia tolerance. Taken together, our results indicated complex adaptation processes in Tibetan cattle, where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.

Evolution and legacy of East Asian aurochs

Aurochs (Bos primigenius), once widely distributed in Afro-Eurasia, became extinct in the early 1600 s. However, their phylogeography and relative contributions to domestic cattle remain unknown. In this study, we analyzed 16 genomes of ancient aurochs and three mitogenomes of ancient bison (Bison priscus) excavated in East Asia, dating from 43,000 to 3,590 years ago. These newly generated data with previously published genomic information on aurochs as well as ancient/extant domestic cattle worldwide through genome analysis. Our findings revealed significant genetic divergence between East Asian aurochs and their European, Near Eastern, and African counterparts on the basis of both mitochondrial and nuclear genomic data. Furthermore, we identified evidence of gene flow from East Asian aurochs into ancient and present-day taurine cattle, suggesting their potential role in facilitating the environmental adaptation of domestic cattle.

The evolution of contemporary livestock species: Insights from mitochondrial genome

The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.

Insights into Adaption and Growth Evolution: Genome-Wide Copy Number Variation Analysis in Chinese Hainan Yellow Cattle Using Whole-Genome Re-Sequencing Data

Copy number variation (CNV) serves as a crucial source of genomic variation and significantly aids in the mining of genomic information in cattle. This study aims to analyze re-sequencing data from Chinese Hainan yellow cattle, to uncover breed CNV information, and to elucidate the resources of population genetic variation. We conducted whole-genome sequencing on 30 Chinese Hainan yellow cattle, thus generating 814.50 Gb of raw data. CNVs were called using CNVnator software, and subsequent filtering with Plink and HandyCNV yielded 197,434 high-quality CNVs and 5852 CNV regions (CNVRs). Notably, the proportion of deleted sequences (81.98%) exceeded that of duplicated sequences (18.02%), with the lengths of CNVs predominantly ranging between 20 and 500 Kb This distribution demonstrated a decrease in CNVR count with increasing fragment length. Furthermore, an analysis of the population genetic structure using CNVR databases from Chinese, Indian, and European commercial cattle breeds revealed differences between Chinese Bos indicus and Indian Bos indicus. Significant differences were also observed between Hainan yellow cattle and European commercial breeds. We conducted gene annotation for both Hainan yellow cattle and European commercial cattle, as well as for Chinese Bos indicus and Indian Bos indicus, identifying 206 genes that are expressed in both Chinese and Indian Bos indicus. These findings may provide valuable references for future research on Bos indicus. Additionally, selection signatures analysis based on Hainan yellow cattle and three European commercial cattle breeds identified putative pathways related to heat tolerance, disease resistance, fat metabolism, environmental adaptation, candidate genes associated with reproduction and the development of sperm and oocytes (CABS1, DLD, FSHR, HSD17B2, KDM2A), environmental adaptation (CNGB3, FAM161A, DIAPH3, EYA4, AAK1, ERBB4, ERC2), oxidative stress anti-inflammatory response (COMMD1, OXR1), disease resistance (CNTN5, HRH4, NAALADL2), and meat quality (EHHADH, RHOD, GFPT1, SULT1B1). This study provides a comprehensive exploration of CNVs at the molecular level in Chinese Hainan yellow cattle, offering theoretical support for future breeding and selection programs aimed at enhancing qualities of this breed.

Temperature adaptation patterns in Chinese cattle revealed by TRPM2 gene mutation analysis

Cattle are sensitive to temperature fluctuations but adapt well to inclement weather conditions. When environmental temperatures exceed specific thresholds, heat stress becomes a critical concern for cattle. The TRPM2 gene, which resides on cattle chromosome 1 encodes a TRP channel protein, holding a unique capacity to sense temperature changes and facilitate rapid response to avoid heat stress. Here, we utilized the Bovine Genome Variation Database (BGVD) (http://animal.omics.pro/code/index.php/BosVar), and identified a missense mutation site, c.805A > G: p. Met269Val (rs527146862), within the TRPM2 gene. To elucidate the functional assessment of this mutation in temperature adaptation attributes of Chinese cattle, we genotyped 407 samples from 20 distinct breeds representing diverse climatic zones across China. The association analysis incorporates three temperature parameters and revealed compelling insights in terms of allele frequency. Interestingly, the prevalence of the wild-type allele A was notably higher among northern cattle breeds and this trend diminished gradually as observed in southern cattle populations. Conversely, the mutant-type allele G demonstrated a contrasting trend. Moreover, southern cattle exhibited markedly higher frequencies of GG and GA genotypes (P < 0.01). The presence of heterozygous and homozygous mutations appears to confer an enhanced capacity for adaptation to elevated temperatures. These results provide unequivocal correlation evidence between TRPM2 genotypes (AA, GA, GG) and environmental temperature parameters and comprehend the genetic mechanisms governing temperature adaptation in cattle. This provides valuable insights for strategic breed selection across diverse climatic regions, thereby aiding livestock production amid evolving climate challenges.

The genomic natural history of the aurochs

Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia1. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs-European, Southwest Asian, North Asian and South Asian-each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago2, but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin.

Deep Ancestral Introgressions between Ovine Species Shape Sheep Genomes via Argali-Mediated Gene Flow

Previous studies revealed extensive genetic introgression between Ovis species, which affects genetic adaptation and morphological traits. However, the exact evolutionary scenarios underlying the hybridization between sheep and allopatric wild relatives remain unknown. To address this problem, we here integrate the reference genomes of several ovine and caprine species: domestic sheep, argali, bighorn sheep, snow sheep, and domestic goats. Additionally, we use 856 whole genomes representing 169 domestic sheep populations and their six wild relatives: Asiatic mouflon, urial, argali, snow sheep, thinhorn sheep, and bighorn sheep. We implement a comprehensive set of analyses to test introgression among these species. We infer that the argali lineage originated ∼3.08 to 3.35 Mya and hybridized with the ancestor of Pachyceriforms (e.g. bighorn sheep and snow sheep) at ∼1.56 Mya. Previous studies showed apparent introgression from North American Pachyceriforms into the Bashibai sheep, a Chinese native sheep breed, despite of their wide geographic separation. We show here that, in fact, the apparent introgression from the Pachyceriforms into Bashibai can be explained by the old introgression from Pachyceriforms into argali and subsequent recent introgression from argali into Bashibai. Our results illustrate the challenges of estimating complex introgression histories and provide an example of how indirect and direct introgression can be distinguished.

[Runs of Homozygosity Decipher Genetic Diversity in Cattle Breed Dwelling in the Colder Regions of the World]

BACKGROUND

Our study focuses on Yakutian cattle, a Siberian native breed, examining its inbreeding and diversity through genome-wide analysis of runs of homozygosity (ROHs). Yakutian cattle are adapted to Siberia's harsh sub-arctic conditions, enduring temperatures below -70°C. However, the population genetics studies on this breed are scanty, to document the genetic uniqueness in these cattle.

RESULTS

We analyzed 40 Yakutian cattle with strict quality control for ROH detection yielding 683 homozygous segments, averaging 17 per individual with an average length of 9 Mb. ROH regions were found to be involved in important pathways pertaining to cold adaptation. Autozygosity ranged from 1% to 12% of the genome, with a relatively low average inbreeding coefficient (FROH) of 0.057, as compared to other breeds. Also, the different diversity indicators, namely, principal component analysis, heterozygosity, and effective population size analysis, revealed the prevalence of genetic diversity within the breed.

CONCLUSION

Our findings on ROH are the first of its kind in Yakutian cattle that support their adaptability to colder environments, as evidenced by low inbreeding and high genetic diversity.

Development and validation of a 5K low-density SNP chip for Hainan cattle

BACKGROUND

This study aimed to design and develop a 5K low-density liquid chip for Hainan cattle utilizing targeted capture sequencing technology. The chip incorporates a substantial number of functional single nucleotide polymorphism (SNP) loci derived from public literature, including SNP loci significantly associated with immunity, heat stress, meat quality, reproduction, and other traits. Additionally, SNPs located in the coding regions of immune-related genes from the Bovine Genome Variation Database (BGVD) and Hainan cattle-specific SNP loci were included.

RESULTS

A total of 5,293 SNPs were selected, resulting in 9,837 DNA probes with a coverage rate of 85.69%, thereby creating a Hainan cattle-specific 5K Genotyping by Target Sequencing (GBTS) liquid chip. Evaluation with 152 cattle samples demonstrated excellent clustering performance and a detection rate ranging from 96.60 to 99.07%, with 94.5% of SNP sites exhibiting polymorphism. The chip achieved 100% gender coverage and displayed a heterozygosity rate between 14.20% and 29.65%, with a repeatability rate of 99.65-99.85%. Analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed the potential regulatory roles of exonic SNPs in immune response pathways.

CONCLUSION

The development and validation of the 5K GBTS liquid chip for Hainan cattle represent a valuable tool for genome analysis and genetic diversity assessment. Furthermore, it facilitates breed identification, gender determination, and kinship analysis, providing a foundation for the efficient utilization and development of local cattle genetic resources.

Introgression drives adaptation to the plateau environment in a subterranean rodent

BACKGROUND

Introgression 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.

RESULTS

Applying 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.

CONCLUSIONS

Introgression 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.

Uncovering structural variants in Creole cattle from Guadeloupe and their impact on environmental adaptation through whole genome sequencing

Structural variants play an important role in evolutionary processes. Besides, they constitute a large source of inter individual genetic variation that might represent a major factor in the aetiology of complex, multifactorial traits. Their importance in adaptation is becoming increasingly evident in literature. Yet, the characterization of the genomic landscape of structural variants in local breeds remains scarce to date. Herein, we investigate patterns and gene annotation of structural variants in the Creole cattle from Guadeloupe breed using whole genome sequences from 23 bulls representative of the population. In total, we detected 32821 ascertained SV defining 15258 regions, representing ~ 17% of the Creole cattle genome. Among these, 6639 regions have not been previously reported in the Database of Genomic Variants archive. Average number of structural variants detected per individual in the studied population is in the same order of magnitude of that observed in indicine populations and higher than that reported in taurine breeds. We observe an important within-individual variability where approximately half of the detected structural variants have low frequency (MAF < 0.25). Most of the detected structural variants (55%) occurred in intergenic regions. Genic structural variants overlapped with 7793 genes and the predicted effect of most of them is ranked as "modifier". Among the structural variants that were predicted to have a high functional impact on the protein, a 5.5 Kb in length, highly frequent deletion on chromosome 2, affects ALPI, a gene associated with the interaction between gut microbiota and host immune system. The 6639 newly identified structural variants regions include three deletions and three duplications shared by more than 80% of individuals that are significantly enriched for genes related to tRNA threonylcarbamoyladenosine metabolic process, important for temperature adaptation in thermophilic organisms, therefore suggesting a potential role in the thermotolerance of Creole cattle from Guadeloupe cattle to tropical climate. Overall, highly frequent structural variants that are specific to the Creole cattle population encompass olfactory receptor and immunity genes as well as genes involved in muscle tone, muscle development and contraction. Beyond mapping and characterizing structural variants in the Creole cattle from Guadeloupe breed, this study provides valuable information for a better understanding of the potential role of chromosomal rearrangements in adaptive traits in cattle.

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.

Genome-Wide Analysis of Genetic Diversity and Selection Signatures in Zaobei Beef Cattle

This investigation provides a comprehensive analysis of genomic diversity and selection signatures in Zaobei beef cattle, an indigenous breed known for its adaptation to hot and humid climates and superior meat quality. Whole-genome resequencing was conducted on 23 Zaobei cattle, compared with 46 Simmental cattle to highlight genetic distinctions. Population structure analysis confirmed the genetic uniqueness of Zaobei cattle. Using methods such as DASDC v1.01, XPEHH, and θπ ratio, we identified 230, 232, and 221 genes through DASDC, including hard sweeps, soft sweeps, and linkage sweeps, respectively. Coincidentally, 109 genes were identified when using XPEHH and θπ ratio methods. Together, these analyses revealed eight positive selection genes (ARHGAP15, ZNF618, USH2A, PDZRN4, SPATA6, ROR2, KCNIP3, and VWA3B), which are linked to critical traits such as heat stress adaptation, fertility, and meat quality. Moreover, functional enrichment analyses showed pathways related to autophagy, immune response, energy metabolism, and muscle development. The comprehensive genomic insights gained from this study provide valuable knowledge for breeding programs aimed at enhancing the beneficial traits in Zaobei cattle.

Whole-genome resequencing deciphers patterns of genetic diversity, phylogeny, and evolutionary dynamics in Kashmir cattle

Kashmir cattle, which were kept by local pastoralists for centuries, are exceptionally resilient and adaptive to harsh environments. Despite its significance, the genomic characteristics of this cattle breed remain elusive. This study utilized whole genome sequences of Kashmir cattle (n = 20; newly sequenced) alongside published whole genomes of 32 distinct breeds and seven core cattle populations (n = 135). The analysis identified ~25.87 million biallelic single nucleotide polymorphisms in Kashmir cattle, predominantly in intergenic and intron regions. Population structure analyses revealed distinct clustering patterns of Kashmir cattle with proximity to the South Asian, African and Chinese indicine cattle populations. Genetic diversity analysis of Kashmir cattle demonstrated lower inbreeding and greater nucleotide diversity than analyzed global breeds. Homozygosity runs indicated less consanguineous mating in Kashmir cattle compared with European taurine breeds. Furthermore, six selection sweep detection methods were used within Kashmir cattle and other cattle populations to identify genes associated with vital traits, including immunity (BOLA-DQA5, BOLA-DQB, TNFAIP8L, FCRL4, AOAH, HIF1AN, FBXL3, MPEG1, CDC40, etc.), reproduction (GOLGA4, BRWD1, OSBP2, LEO1 ADCY5, etc.), growth (ADPRHL1, NRG2, TCF12, TMOD4, GBP4, IGF2, RSPO3, SCD, etc.), milk composition (MRPS30 and CSF1) and high-altitude adaptation (EDNRA, ITPR2, AGBL4 and SCG3). These findings provide essential genetic insights into the characteristics and establish the foundation for the scientific conservation and utilization of Kashmir cattle breed.

Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data

Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors. Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors. Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.

Illuminating Genetic Diversity and Selection Signatures in Matou Goats through Whole-Genome Sequencing Analysis

(1) Background: Matou goats, native to Hunan and Hubei provinces in China, are renowned for their exceptional meat and skin quality. However, a comprehensive whole-genome-based exploration of the genetic architecture of this breed is scant in the literature. (2) Methods: To address this substantial gap, we used whole-genome sequences of 20 Matou goats and compared them with published genomic data of 133 goats of different breeds across China. This comprehensive investigation sought to assess genetic diversity, population structure, and the presence of genomic selection signals. (3) Results: The whole genome of Matou goat populations yielded a substantial catalog of over 19 million single nucleotide polymorphisms (SNPs), primarily distributed within intergenic and intron regions. The phylogenetic tree analysis revealed distinct clades corresponding to each goat population within the dataset. Notably, this analysis positioned Matou goats in a closer genetic affinity with Guizhou White goats, compared to other recognized goat breeds. This observation was corroborated by principal component analysis (PCA) and admixture analysis. Remarkably, Matou goats exhibited diminished genetic diversity and a notable degree of inbreeding, signifying a reduced effective population size. Moreover, the study employed five selective sweep detection methods (including PI, CLR, PI-Ratio, Fst, and XP-EHH) to screen top signal genes associated with critical biological functions, encompassing cardiomyocytes, immunity, coat color, and meat quality. (4) Conclusions: In conclusion, this study significantly advances our understanding of the current genetic landscape and evolutionary dynamics of Matou goats. These findings underscore the importance of concerted efforts in resource conservation and genetic enhancement for this invaluable breed.

Genome-Wide Identification and Evolutionary and Mutational Analysis of the Bos taurus Pax Gene Family

Bos taurus is known for its tolerance of coarse grains, adaptability, high temperature, humidity, and disease resistance. Primarily, cattle are raised for their meat and milk, and pinpointing genes associated with traits relevant to meat production can enhance their overall productivity. The aim of this study was to identify the genome, analyze the evolution, and explore the function of the Pax gene family in B. taurus to provide a new molecular target for breeding in meat-quality-trait cattle. In this study, 44 Pax genes were identified from the genome database of five species using bioinformatics technology, indicating that the genetic relationships of bovids were similar. The Pax3 and Pax7 protein sequences of the five animals were highly consistent. In general, the Pax gene of the buffalo corresponds to the domestic cattle. In summary, there are differences in affinity between the Pax family genes of buffalo and domestic cattle in the Pax1/9, Pax2/5/8, Pax3/7, and Pax4/6 subfamilies. We believe that Pax1/9 has an effect on the growth traits of buffalo and domestic cattle. The Pax3/7 gene is conserved in the evolution of buffalo and domestic animals and may be a key gene regulating the growth of B. taurus. The Pax2/5/8 subfamily affects coat color, reproductive performance, and milk production performance in cattle. The Pax4/6 subfamily had an effect on the milk fat percentage of B. taurus. The results provide a theoretical basis for understanding the evolutionary, structural, and functional characteristics of the Pax family members of B. taurus and for molecular genetics and the breeding of meat-production B. taurus species.

Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep

Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing ∼ 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated β-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. The haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with haplotype A had an increased hemoglobin-O2 affinity compared with those carrying haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.

Genome-wide association study provided insights into the polled phenotype and polled intersex syndrome (PIS) in goats

BACKGROUND

Breeding polled goats is a welfare-friendly approach for horn removal in comparison to invasive methods. To gain a comprehensive understanding of the genetic basis underlying polledness in goats, we conducted whole-genome sequencing of 106 Xinong Saanen dairy goats, including 33 horned individuals, 70 polled individuals, and 3 polled intersexuality syndrome (PIS) individuals.

METHODS

The present study employed a genome-wide association study (GWAS) and linkage disequilibrium (LD) analysis to precisely map the genetic locus underlying the polled phenotype in goats.

RESULTS

The analysis conducted in our study revealed a total of 320 genome-wide significant single nucleotide polymorphisms (SNPs) associated with the horned/polled phenotype in goats. These SNPs exhibited two distinct peaks on chromosome 1, spanning from 128,817,052 to 133,005,441 bp and from 150,336,143 to 150,808,639 bp. The present study identified three genome-wide significant SNPs, namely Chr1:129789816, Chr1:129791507, and Chr1:129791577, as potential markers of PIS-affected goats. The results of our LD analysis suggested a potential association between MRPS22 and infertile intersex individuals, as well as a potential association between ERG and the polled trait in goats.

CONCLUSION

We have successfully identified three marker SNPs closely linked to PIS, as well as several candidate genes associated with the polled trait in goats. These results may contribute to the development of SNP chips for early prediction of PIS in goats, thereby facilitating breeding programs aimed at producing fertile herds with polled traits.

Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens

The introduction of exotic breeds and the cultivation of new lines by breeding companies have posed challenges to native chickens in South China, including loss of breed characteristics, decreased genetic diversity, and declining purity. Understanding the population genetic structure and genetic diversity of native chickens in South China is crucial for further advancements in breeding efforts. In this study, we analyzed the population genetic structure and genetic diversity of 321 individuals from 10 different breeds in South China. By comparing commercial chickens with native ones, we identified selection signatures occurring between local chickens and commercial breeds. The analysis of population genetic structure revealed that the native chicken populations in South China exhibited a considerable level of genetic diversity. Moreover, the commercial lines of Xiaobai chicken and Huangma chicken displayed even higher levels of genetic diversity, which distinguished them from other native varieties at the clustering level. However, certain individuals within these commercial varieties showed a discernible genetic relationship with the native populations. Notably, both commercial varieties also retained a significant degree of genetic similarity to their respective native counterparts. In order to investigate the genomic changes occurring during the commercialization of native chickens, we employed 4 methods (Fst, ROD, XPCLR, and XPEHH) to identify potential candidate regions displaying selective signatures in Southern Chinese native chicken population. A total of 168 (identified by Fst and ROD) and 86 (identified by XPCLR and XPEHH) overlapping genes were discovered. Functional annotation analysis revealed that these genes may be associated with reproduction and growth (SAMSN1, HYLS1, ROBO3, FGF14, PRSS23), musculoskeletal development (DNER, MYBPC1, DGKB, ORC1, KLF10), disease resistance and environmental adaptability (PUS3, CRB2, CALD1, USP15, SGCD, LTBP1), as well as egg production (ADGRB3, ACSF3). Overall, native chickens in South China harbor numerous selective sweep regions compared to commercial chickens, enriching valuable genomic resources for future genetic research and breeding conservation.

Whole-genome sequencing reveals genomic diversity and selection signatures in Xia'nan cattle

BACKGROUND

The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia'nan cattle, a crossbreed of Charolais and Nanyang cattle, is China's first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia'nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia'nan cattle using whole-genome sequencing data from 30 Xia'nan cattle and 178 published cattle genomic data.

RESULT

The ancestry estimating composition analysis showed that the ancestry proportions for Xia'nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia'nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia'nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes (FST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the detected genes and found that these genes may influence body development (NR6A1), meat quality traits (MCCC1), growth traits (WSCD1, TMEM68, MFN1, NCKAP5), and immunity (IL11RA, CNTFR, CCL27, SLAMF1, SLAMF7, NAA35, and GOLM1).

CONCLUSION

We elucidated the genomic features and population structure of Xia'nan cattle and detected some selection signals in genomic regions potentially associated with crucial economic traits in Xia'nan cattle. This research provided a basis for further breeding improvements in Xia'nan cattle and served as a reference for genetic enhancements in other crossbreed cattle.

Unraveling genomic diversity and positive selection signatures of Qaidam cattle through whole-genome re-sequencing

Qaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low-oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole-genome resequencing technology, along with 192 published sets of whole-genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in Bos taurus, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross-population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance.

Whole-genome resequencing uncovers diversity and selective sweep in Kazakh cattle

The Kazakh cattle in the Xinjiang Uygur Autonomous Region of China are highly adaptable and have multiple uses, including milk and meat production, and use as draft animals. They are an excellent original breed that could be enhanced by breeding and hybrid improvement. However, the genomic diversity and signature of selection underlying the germplasm characteristics require further elucidation. Herein, we evaluated 26 Kazakh cattle genomes in comparison with 103 genomes of seven other cattle breeds from regions around the world to assess the Kazakh cattle genetic variability. We revealed that the relatively low linkage disequilibrium at large SNP distances was strongly correlated with the largest effective population size among Kazakh cattle. Using population structural analysis, we next demonstrated a taurine lineage with restricted Bos indicus introgression among Kazakh cattle. Notably, we identified putative selected genes associated with resistance to disease and body size within Kazakh cattle. Together, our findings shed light on the evolutionary history and breeding profile of Kazakh cattle, as well as offering indispensable resources for germplasm resource conservation and crossbreeding program implementation.

A High-Coverage Mesolithic Aurochs Genome and Effective Leveraging of Ancient Cattle Genomes Using Whole Genome Imputation

Ancient genomic analyses are often restricted to utilizing pseudohaploid data due to low genome coverage. Leveraging low-coverage data by imputation to calculate phased diploid genotypes that enables haplotype-based interrogation and single nucleotide polymorphism (SNP) calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archeological, evolutionary, and economic reasons. Here, we test this approach by sequencing a Mesolithic European aurochs (18.49×; 9,852 to 9,376 calBCE) and an Early Medieval European cow (18.69×; 427 to 580 calCE) and combine these with published individuals: two ancient and three modern. We downsample these genomes (0.25×, 0.5×, 1.0×, and 2.0×) and impute diploid genotypes, utilizing a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased SNPs. We recover high densities of correct calls with an accuracy of >99.1% at variant sites for the lowest downsample depth of 0.25×, increasing to >99.5% for 2.0× (transversions only, minor allele frequency [MAF] ≥ 2.5%). The recovery of SNPs correlates with coverage; on average, 58% of sites are recovered for 0.25× increasing to 87% for 2.0×, utilizing an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs, despite the highest temporal distance from the modern reference panel. Our imputed genomes behave similarly to directly called data in allele frequency-based analyses, for example consistently identifying runs of homozygosity >2 Mb, including a long homozygous region in the Mesolithic European aurochs.

POLB Regulates Proliferation and Apoptosis of Bovine Primary Myocytes

DNA polymerase β (DNA polymerase beta (POLB)) belongs to a member of the DNA polymerase X family, mainly involved in various biological metabolic processes, such as eukaryotic DNA replication, DNA damage repair, gene recombination, and cell cycle regulation. In this study, the muscle development-related gene POLB was screened by selection signature and RNA-seq analysis and then validated for the proliferation and apoptosis of bovine primary myocytes. It was also found that overexpression of the POLB gene had a pro-apoptosis effect, but interfering with the expression of the gene had no significant effect on cells. Then, the analysis of related apoptotic genes revealed that POLB overexpression affected CASP9 gene expression.

Research Progress and Applications of Bovine Genome in the Tribe Bovini

Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species.

Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data

OBJECTIVE

The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits.

METHODS

To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions.

RESULTS

The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity.

CONCLUSION

In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

Genomic insights into the population history and adaptive traits of Latin American Criollo cattle

Criollo cattle, the descendants of animals brought by Iberian colonists to the Americas, have been the subject of natural and human-mediated selection in novel tropical agroecological zones for centuries. Consequently, these breeds have evolved distinct characteristics such as resistance to diseases and exceptional heat tolerance. In addition to European taurine (Bos taurus) ancestry, it has been proposed that gene flow from African taurine and Asian indicine (Bos indicus) cattle has shaped the ancestry of Criollo cattle. In this study, we analysed Criollo breeds from Colombia and Venezuela using whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) array data to examine population structure and admixture at high resolution. Analysis of genetic structure and ancestry components provided evidence for African taurine and Asian indicine admixture in Criollo cattle. In addition, using WGS data, we detected selection signatures associated with a myriad of adaptive traits, revealing genes linked to thermotolerance, reproduction, fertility, immunity and distinct coat and skin coloration traits. This study underscores the remarkable adaptability of Criollo cattle and highlights the genetic richness and potential of these breeds in the face of climate change, habitat flux and disease challenges. Further research is warranted to leverage these findings for more effective and sustainable cattle breeding programmes.