Genetic Diversity and Selective Signature in Dabieshan Cattle Revealed by Whole-Genome Resequencing

Genetic Structure and Selection Signals for Extreme Environment Adaptation in Lop Sheep of Xinjiang

OBJECTIVE

Lop sheep species exhibit remarkable adaptability to desert pastures and extreme arid climates, demonstrating tolerance to rough feeding and high resistance to stress. However, little is known about the population genetic diversity of Lop sheep and the genetic mechanisms underlying their adaptability to extreme environments.

METHODS

Blood samples were collected from a total of 110 individuals comprising 80 Ruoqiang Lop sheep and 30 Yuli Lop sheep. A total of 110 Lop sheep were subjected to whole genome resequencing to analyze genetic diversity, population structure, and signatures of selection in both regions.

RESULTS

The genetic diversity of the Lop sheep population is substantial, and the degree of inbreeding is low. In comparison to the Lop sheep in Yuli County, the genetic diversity and linkage disequilibrium analysis results for the Lop sheep population in Ruoqiang County are slightly lower. Population structure analysis indicates that Ruoqiang and Yuli Lop sheep have differentiated into two independent groups. Using Yuli Lop sheep as the reference group, an analysis of the extreme environmental adaptability selection signal of Lop sheep was conducted. The FST and π ratio under the 1% threshold identified 1686 and 863 candidate genes, respectively, with their intersection yielding a total of 122 candidate genes. Functional annotation revealed that these genes are associated with various traits, including immune response (SLC12A2, FOXP1, PANX1, DYNLRB2, RAP1B, and SEMA4D), heat and cold resistance (DNAJC13, PLCB1, HIKESHI, and PITPNC1), desert adaptation (F13A1, PANX1, ST6GAL1, STXBP3, ACTN4, and ATP6V1A), and reproductive performance (RAP1B, RAB6A, PLCB1, and METTL15).

CONCLUSIONS

These research findings provide a theoretical foundation for understanding the survival and reproductive characteristics of Lop sheep in extreme environments, and they hold practical value for the conservation and utilization of Lop sheep genetic resources, as well as for genetic improvement efforts.

Leveraging Whole-Genome Resequencing to Uncover Genetic Diversity and Promote Conservation Strategies for Ruminants in Asia

Whole-genome resequencing (WGRS) is a critical branch of whole-genome sequencing (WGS), primarily targeting species with existing reference genomes. By aligning sequencing data to the reference genome, WGRS enables precise detection of genetic variations in individuals or populations. As a core technology in genomic research, WGS holds profound significance in ruminant studies. It not only reveals the intricate structure of ruminant genomes but also provides essential data for deciphering gene function, variation patterns, and evolutionary processes, thereby advancing the exploration of ruminant genetic mechanisms. However, WGS still faces several challenges, such as incomplete and inaccurate genome assembly, as well as the incomplete annotation of numerous unknown genes or gene functions. Although WGS can identify a vast number of genomic variations, the specific relationships between these variations and phenotypes often remain unclear, which limits its potential in functional studies and breeding applications. By performing WGRS on multiple samples, these assembly challenges can be effectively addressed, particularly in regions with high repeat content or complex structural variations. WGRS can accurately identify subtle variations among different individuals or populations and further elucidate their associations with specific traits, thereby overcoming the limitations of WGS and providing more precise genetic information for functional research and breeding applications. This review systematically summarizes the latest applications of WGRS in the analysis of ruminant genetic structures, genetic diversity, economic traits, and adaptive traits, while also discussing the challenges faced by this technology. It aims to provide a scientific foundation for the improvement and conservation of ruminant genetic resources.

Analysis of Population Structure and Selective Signatures for Milk Production Traits in Xinjiang Brown Cattle and Chinese Simmental Cattle

This study aims to elucidate the population structure and genetic diversity of Xinjiang brown cattle (XJBC) and Chinese Simmental cattle (CSC) while conducting genome-wide selective signatures analyses to identify selected genes associated with milk production traits in both breeds. Based on whole-genome resequencing technology, whole-genome single nucleotide polymorphisms (SNPs) of 83 Xinjiang brown cattle and 80 Chinese Simmental cattle were detected to resolve the genetic diversity and genetic structure of the two populations, whole-genome selective elimination analysis was performed for the two breeds of cattle using the fixation index (Fst) and nucleotide diversity (θπ ratio), and enrichment analysis was performed to explore their biological functions further. Both breeds exhibited relatively rich genetic diversity, with the Chinese Simmental cattle demonstrating higher genetic diversity than Xinjiang brown cattle. The IBS and G matrix results indicated that most individuals in the two populations were farther apart from each other. The PCA and neighbor-joining tree revealed no hybridization between the two breeds, but there was a certain degree of genetic differences among the individuals in the two breeds. Population structure analysis revealed that the optimal number of ancestors was three when K = 3. This resulted in clear genetic differentiation between the two populations, with only a few individuals having one ancestor and the majority having two or three common ancestors. A combined analysis of Fst and θπ was used to screen 112 candidate genes related to milk production traits in Xinjiang brown cattle and Chinese Simmental cattle. This study used genome-wide SNP markers to reveal the genetic diversity, population structure, and selection characteristics of two breeds. This study also screened candidate genes related to milk production traits, providing a theoretical basis for conserving genetic resources and improving genetic selection for milk production traits in Xinjiang brown cattle and Chinese Simmental cattle.

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.

Genomic Insights and Conservation Priorities for Kongshan Cattle: A Whole-Genome Resequencing Approach

Kongshan Cattle, indigenous to Sichuan Province and recognized as China's 56th local cattle breed in 2024, exhibit unique adaptations including superior resistance to harsh conditions. Despite a declining population due to the influx of foreign breeds, there is a significant focus on preserving their genetic diversity through advanced genomic techniques. This study utilized whole-genome resequencing, a cost-effective and information-rich method, to perform a comprehensive genetic assessment of the Kongshan Cattle. High-quality resequencing data yielded an average of 17.5 billion clean bases per sample, with high proportions of Q20 and Q30 bases and a balanced GC content. SNP analysis revealed an average of 14 million SNPs per sample, with a notable transition-to-transversion ratio and a significant portion of heterozygosity. Further analysis of genomic and coding regions identified substantial insertions and deletions, particularly in coding sequences affecting gene functionality. A detailed examination of these genetic variations highlighted genes, including NEIL2 and PNKP, which are integral to stress resistance pathways, indicating potential adaptive advantages. This study not only underscores the genetic diversity of Kongshan Cattle but also contributes to broader efforts in germplasm conservation.

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.

Deciphering the Genetic Landscape: Insights Into the Genomic Signatures of Changle Goose

The Changle goose (CLG), a Chinese indigenous breed, is celebrated for its adaptability, rapid growth, and premium meat quality. Despite its agricultural value, the exploration of its genomic attributes has been scant. Our study entailed whole-genome resequencing of 303 geese across CLG and five other Chinese breeds, revealing distinct genetic diversity metrics. We discovered significant migration events from Xingguo gray goose to CLG and minor gene flow between them. We identified genomic regions through selective sweep analysis, correlating with CLG's unique traits. An elevated inbreeding coefficient in CLG, alongside reduced heterozygosity and rare single nucleotide polymorphisms (RSNPs), suggests a narrowed genetic diversity. Genomic regions related to reproduction, meat quality, and growth were identified, with the GATA3 gene showing strong selection signals for meat quality. A non-synonymous mutation in the Sloc2a1 gene, which is associated with reproductive traits in the CLG, exhibited significant differences in allelic frequency. The roles of CD82, CDH8, and PRKAB1 in growth and development, alongside FABP4, FAF1, ESR1, and AKAP12 in reproduction, were highlighted. Additionally, Cdkal1 and Mfsd14a may influence meat quality. This comprehensive genetic analysis underpins the unique genetic makeup of CLG, providing a basis for its conservation and informed breeding strategies.

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 Sequencing for Identifying Candidate Genes Related to the Special Phenotypes of the Taihu Dianzi Pigeon

The Taihu Dianzi pigeon is a breed native to China, and its special piebalding, crest, and polydactyly phenotypes are the result of artificial and natural selection. Here, we analyzed the genetic differences among three kinds of pigeons with different phenotypes at the genomic level. A selective sweep was conducted based on the fixation index (FST) and nucleotide diversity (π) ratio, and the results revealed that MC1R was related to the formation of the distinctive piebalding of the Taihu Dianzi pigeon. Combined with the results of genome-wide association studies, we identified candidate genes associated with the crest (SMYD and STOX2) and polydactyly (SLC52A3 and ANGPT4). The candidate genes identified in this study and their variants may be useful for understanding the genetic mechanism underlying the special phenotypes of the Taihu Dianzi pigeon. This study provides new insights into the genetic factors that may influence the formation of the special piebalding, crest, and polydactyly characteristics in pigeons.

Evidence for selective sweeps in the MHC gene repertoire of various cattle breeds

Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle.

Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study

BACKGROUND

Eggs represent important sources of protein and are widely loved by consumers. Egg yolk taste is an important index for egg selection, and the moisture content of the egg yolk affects the taste. To understand the molecular mechanism underlying egg yolk moisture content, this study determined the phenotype and heritability of egg yolk water content and conducted a genome-wide association study (GWAS) using a mixed linear model.

RESULTS

We determined the phenotype and heritability of thermogelled egg yolk water content (TWC) and found that the average TWC was 47.73%. Moreover, significant variations occurred (41.06-57.12%), and the heritability was 0.11, which indicates medium-low heritability. Through the GWAS, 48 single nucleotide polymorphisms (SNPs) related to TWC (20 significantly, 28 suggestively) were obtained, and they were mainly located on chromosomes 10 and 13. We identified 36 candidate genes based on gene function and found that they were mainly involved in regulating fat, protein, and water content and embryonic development. FGF9, PIAS1, FEM1B, NOX5, GLCE, VDAC1, IGFBP7, and THOC5 were involved in lipid formation and regulation; AP3S2, GNPDA1, HSPA4, AP1B1, CABP7, EEF1D, SYTL3, PPP2CA, SKP1, and UBE2B were involved in protein folding and hydrolysis; and CSF2, SOWAHA, GDF9, FSTL4, RAPGEF6, PAQR5, and ZMAT5 were related to embryonic development and egg production. Moreover, MICU2, ITGA11, WDR76, BLM, ANPEP, TECRL, EWSR1, and P4HA2 were related to yolk quality, while ITGA11, WDR76, BLM, and ANPEP were potentially significantly involved in egg yolk water content and thus deserve further attention and research. In addition, this study identified a 19.31-19.92 Mb genome region on GGA10, and a linkage disequilibrium analysis identified strong correlations within this region. Thus, GGA10 may represent a candidate region for TWC traits.

CONCLUSION

The molecular genetic mechanism involved in TWC was revealed through heritability measurements and GWAS, which identified a series of SNPs, candidate genes, and candidate regions related to TWC. These results provide insights on the molecular mechanism of egg yolk moisture content and may aid in the development of new egg traits.

Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle

Dabieshan cattle (DBSC) are a valuable genetic resource for indigenous cattle breeds in China. It is a small to medium-sized breed with slower growth, but with good meat quality and fat deposition. Genetic markers could be used for the estimation of population genetic structure and genetic parameters. In this work, we genotyped the DBSC breeding population (n = 235) with the GeneSeek Genomic Profiler (GGP) 100 k density genomic chip. Genotype data of 222 individuals and 81,579 SNPs were retained after quality control. The average minor allele frequency (MAF) was 0.20 and the average linkage disequilibrium (LD) level (r²) was 0.67 at a distance of 0-50 Kb. The estimated relationship coefficient and effective population size (Ne) were 0.023 and 86 for the current generation. In addition, we used genotype data to estimate the genetic parameters of the population's phenotypic traits. Among them, height at hip cross (HHC) and shin circumference (SC) were rather high heritability traits, with heritability of 0.41 and 0.54, respectively. The results reflected the current cattle population's extent of inbreeding and history. Through the principal breeding parameters, genomic breeding would significantly improve the genetic progress of breeding.