BACKGROUND:Cattle have undergone complex evolutionary trajectories shaped by domestication, migration, and selection. Although runs of homozygosity (ROH) are a ubiquitous genomic feature, their full potential to decipher the evolutionary history and functional consequences in global cattle populations remains underexplored. We analyzed whole-genome sequences from 102 breeds across 17 geographic regions to conduct a global investigation of ROH landscapes, population structure, genomic inbreeding, and functional variants. RESULTS:ROH patterns revealed elevated homozygosity burdens in intensively selected European breeds, whereas South Chinese indicine showed a high short ROH burden, suggestive of a unique ancient demography. ROH-based principal component analysis (PCA) and admixture delineated taurine-indicine lineages, region-specific ancestries, inbreeding, and breeding effects. ROH-based inbreeding coefficient (FROH) exhibited greater stability for cross-population inbreeding assessment, showing a high correlation with excess of homozygosity-based inbreeding coefficient (FHOM) and a negative association with heterozygosity. Region-specific ROH hotspots, identified via permutation test, reflected a combination of local adaptation and demographic legacies. Trait-focused analyses, cross-validated with multiple selection scans, identified genes underlying growth, milk, and climate adaptation. Notably, we found missense mutations in CHEK2, SPG7, FANCA, and MSRB3, whose frequencies were significantly correlated with temperature and humidity. CONCLUSION:This study establishes ROH as a pivotal genomic marker for illuminating the dynamics of domestication, migration, inbreeding, and selection. Our findings offer valuable resources and insights for advancing genetic conservation and precision breeding in cattle under the pressures of climate change.

[This retracts the article DOI: 10.1016/j.omtn.2018.02.012.].

Circular RNAs (circRNAs) have emerged as critical regulators of skeletal muscle development, yet the functions of many muscle-derived circRNAs remain uncharacterized. In this study, we identified a novel circRNA, circAIDA, formed by exons 2 to 6 of the AIDA gene, based on bovine muscle sequencing data. Mechanistically, we demonstrate that circAIDA acts as a molecular sponge for miR-29a, thereby relieving the repression of its downstream targets, AKT3 and CLCN2. Functionally, circAIDA promotes bovine myoblast proliferation while inhibiting apoptosis and differentiation in vitro. Furthermore, experiments in vivo suggested circAIDA could attenuate regeneration of skeletal muscle in mice. In brief, we discovered a novel circAIDA/miR-29a interaction that regulates bovine myogenesis, providing new insights into the molecular networks controlling skeletal muscle development.

Skeletal muscle is a crucial tissue involved in body movement and energy metabolism, and its growth and development directly influence the economic value of livestock. This study investigates the effects of the TEX10 gene on the proliferation, differentiation, and apoptosis of bovine myoblasts, as well as the underlying molecular mechanisms. Using techniques such as CCK-8, EdU incorporation, qPCR, Western blotting, and immunofluorescence, we observed that TEX10 significantly promotes the expression of cell cycle factors, including CDK2 and PCNA, thereby increasing cell proliferation and the proportion of cells in the S phase. Overexpression and knockdown experiments demonstrated that TEX10 enhances the differentiation and myotube formation of myoblasts, while upregulating key genes such as MYOG and MYOD. Additionally, flow cytometry analysis of the cell cycle revealed that TEX10 inhibits apoptosis in bovine myoblasts. Transcriptomic analysis showed that TEX10 regulates several signaling pathways associated with proliferation, differentiation, and apoptosis, including PI3K-Akt, cAMP, and IL-17. Overall, these findings suggest that TEX10 plays a significant regulatory role in bovine muscle growth, providing a theoretical foundation for molecular breeding strategies aimed at improving yellow cattle.

Bohuai goat is a crossbreeding breed between Huai goat and Boer goat, which has higher meat yield and reproductive efficiency. To explore the genetic basis of these traits, we sequenced the whole genome of 289 samples from 8 Chinese local goat populations and Boer goats. Through variation detection and genetic diversity analysis, we identified 68,166,098 SNPs and assessed genetic diversity parameters such as nucleotide diversity, linkage disequilibrium, and homozygous regions (ROH). The analysis of population structure showed that there was a close genetic relationship between Bohuai goat and Boer goat, which was significantly different from that of Chinese native breeds. Fst, Pi_ratio and XPEHH methods were used to analyze the low reproduction rate population of Bohuai goat.. We found a strong selection in a region of BMPR1B on chr6, which may be associated with the high fertility of Bohuai goats and was also detected in the Vst. In addition, a CNVR fragment (GLIS3 gene) was found to be associated with spermatogenesis in the detection of CNV analysis. Our results provide insights for understanding the genetic diversity and selection of reproductive traits of Bohuai goats. They also offer evidence for the correlation between the BMPR1B gene and reproductive traits and provide information for molecular breeding strategies of other goat breeds.

Gayal (Bos frontalis) an endangered bovine species inhabitingChina, India, Bangladesh, Myanmar and Bhutan, has a mysterious evolutionary origin. Shaped by natural selection, its unique traits make it a valuable genetic resource; however, its populations are rapidly declining. In this study, comprehensive whole-genome resequencing of fifty-eight samples of Gayal from China, India, Myanmar and Bangladesh was performed. We identified over 44 million SNPs across four Gayal populations. Nucleotide diversity analysis revealed variations in genetic diversity, with the lowest occurring in India and the highest occurring in China. Phylogenetic tree analysis revealed three distinct clades representing China, India and Bangladesh-Myanmar, which were further confirmed by principal component and admixture analyses. The genetic exchanges between Gayal and other bovine species indicate limited influence from domestic cattle in both the Chinese and Bangladeshi Gayal populations. Mitochondrial DNA sequences and a phylogenetic tree highlighted the unique mitochondrial genome of Gayal. Genome-wide selection signals pinpointed candidate genes linked to mitochondrial function, immunity, musculoskeletal development, reproduction and growth performance. Distinct haplotype patterns emerged for the CCDC157, KIAA0753 and MTFP1 genes in the Chinese and Bangladesh-Myanmar Gayal populations, indicating artificial selection in the Chinese population. KEGG pathway and gene ontology enrichment analyses provided insights into processes related to neurodevelopment, cardiac function, tissue growth, immunity and metabolism. In summary, our study enhances our understanding of Gayal genetics, population structure and selection signals across four countries. This knowledge is crucial for conserving this endangered species amid its rapid decline.

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.

Jun dimerization protein D (JunD), a member of the activating protein-1 transcription factor family, serves as a key regulator of mammalian myogenesis by orchestrating cell cycle progression and coordinating the network of myogenic differentiation determinants. miR-206 exhibits tissue-specific expression in skeletal muscle, with abundant representation across miRNA expression profiles in multiple mammalian species. Although both JunD and miR-206 are critically involved in muscle development, their specific roles in yak skeletal muscle ontogeny remain poorly characterized, particularly regarding the regulatory axis involving miR-206-mediated targeting of JunD during myoblast proliferation and differentiation. To address this knowledge gap, this study used methods such as CCK-8, EdU, RT-qPCR, western blot, immunofluorescence, and the dual-luciferase reporter system. It was found that JunD significantly promoted the expression of cell cycle factors, such as CDK2 and PCNA, and increased cell proliferation and the proportion of S-phase cells. JunD overexpression or interference experiments demonstrated that it enhanced the differentiation and myotube formation ability of myoblasts and simultaneously upregulated the expression of key genes such as MYOG and MYOD. Additionally, the results of cell cycle detection by flow cytometry revealed that the JunD gene inhibited the apoptosis of yak myoblasts. Transcriptome analysis revealed that JunD regulated cAMP and other signaling pathways related to proliferation, differentiation, and apoptosis. The results of the dual-luciferase reporter assay showed a good binding relationship between miR-206 and JunD. The rescue experiments demonstrated that miR-206 regulated the expression of the JunD gene, thereby exerting its influence at the transcriptional level. This study marks the first identification of JunD in yaks and clarifies its role in the development of yak myoblasts through the miR-206-JunD regulatory axis. These findings provide new insights into the molecular breeding of cattle, contributing to the basic research into the breeding and muscle development of yaks.

BackgroundThe silkworm (Bombyx mori), has been farmed in China for over 5,000 years, and holds significant economic value. Recent genomic advances have deepened our understanding of silk production mechanisms, enabling the development of improved silkworm breeds. Further research is needed to identify effective molecular markers linked to silk production traits, as this will enhance genetic improvement efforts.ResultsIn the genome-wide association analysis study, we identified 40 significant single nucleotide polymorphisms (SNPs) and 28 candidate genes which were related to cocoon shell weight, cocoon width and whole cocoon weight in four silkworm strains in Henan. Through linkage imbalance block analysis, we found that the KWMTBOMO02490 (ATPase inhibitor-like protein) and KWMTBOMO12678 (OTU domain-containing protein 7B) were strongly selected. By using online databases, we found that the KWMTBOMO02490 gene was highly expressed in the posterior silk glands and may play an important role in the process of silk production.ConclusionThe candidate genes in this study may affect the production and health traits of silkworms, and may provide an important reference for silkworm breeding.

This study investigated genomic structural variations and their association with muscle development in Qinghai-Tibetan Plateau yaks to elucidate their genetic diversity and adaptive mechanisms. Whole-genome resequencing was performed on 145 Qinghai-Tibetan Plateau yaks, supplemented with sequence data from 12 wild yaks obtained from the National Center for Biotechnology Information (NCBI) database. Analyses characterized runs of homozygosity (ROH), copy number variations (CNV), and structural variations (SV). A genome-wide copy number variation map for Qinghai Plateau yaks was constructed. Qinghai-Tibetan Plateau yaks exhibited numerous ROHs (totaling 61,074 segments, covering 19,947.56 Mb), showing relatively high levels of genomic homozygosity compared to wild yaks (3255 segments, 1056.66 total length), and 1175 CNV regions and 59,694 SVs, primarily located in non-coding regions, were identified. Publicly available transcriptome data were integrated to identify candidate genes related to muscle development, followed by statistical validation of key candidates. Integrating genomic and transcriptomic data revealed 84 overlapping genes potentially involved in muscle development. Subsequent bioinformatic prioritization identified PTPN6, ATP2A1, LCP1, GNA15, ALOX5AP, FLT3, SLC34A3, and BCL11A as high-priority candidate genes potentially influencing this trait. These findings demonstrate that genomic variations significantly impact muscle development in Qinghai-Tibetan Plateau yaks, providing a valuable molecular basis for future yak breeding programs and adaptation research.

Structural variations (SVs) play crucial roles in the evolutionary adaptation of domesticated animals to natural and human-controlled environments, but SVs have not been explored in Tibetan cattle, which recently migrated and rapidly adapted to the high altitudes of the Qinghai-Tibetan Plateau (QTP). In this study, a de novo chromosome-level genome assembly for Tibetan cattle is constructed. It is found that using a lineage-specific reference genome significantly increased variant detection accuracy and completeness. Analysis of long-read sequencing data from 36 high-altitude QTP and 48 low-altitude cattle identified 222 528 SVs and 259 SV hotspot regions. Positively selected SVs in high-altitude cattle are related to energy metabolism erythropoiesis and angiogenesis, and peroxisomal metabolism. A 102-bp intronic deletion in GNPAT likely upregulated its expression. It is distinguished 7293 SVs that may be introgressed from yak, including variants upstream of the hypoxia-inducing gene EGLN1. Finally, a ≈2-Mb heterozygous inversion and two translocations on chromosome 6 are likely associated with the cattle gray coat via regulatory effects on the KIT gene. The results confirm the importance of SVs in evolutionary adaptation and the contribution yak-introgressed SVs to the rapid acclimatization of QTP 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.

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.

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.

Previous researches revealed a copy number variation (CNV) region in the bovine fibroblast growth factor 13 (FGF13) gene. However, its effects remain unknown. This study detected the various copy number types in seven Chinese cattle breeds and analysed their population genetic characteristics and effects on growth traits and transcription levels. Copy number Loss was more frequent in Caoyuan Red cattle and Xianan cattle than in the other breeds. Association analysis between CNV and growth traits of Qinchuan indicated that the CNV was significantly related to chest depth, hip width and hucklebone width (P < 0.05). Additionally, the growth traits of individuals with copy number Loss were significantly inferior to those with copy number Gain or Median (P < 0.05). Besides, we found two splicing isoforms, AS1 and AS2, in FGF13 gene, which resulted from alternative 5′ splicing sites of intron 1. These isoforms showed varied expression levels in various tissues. Moreover, CNV was significantly and negatively associated with the mRNA expression of AS1 (r = −0.525, P < 0.05). The CNVs in bovine FGF13 gene negatively regulated growth traits and gene transcription. These observations provide new insights into bovine FGF13 gene, delivering potentially useful information for future Chinese cattle breeding programs.

Skeletal muscle growth and development in livestock and poultry play a pivotal role in determining the quality and yield of meat production. However, the mechanisms of myogenesis are remained unclear due to it finely regulated by a complex network of biological macromolecules. In this study, leveraging previous sequencing data, we investigated a differentially expressed circular RNA (circSGCB) present in fetal and adult muscle tissues among various ruminant species, including cattle, goat, and sheep. Our analysis revealed that circSGCB is a single exon circRNA, potentially regulated by an adjacent bovine enhancer. Functional analysis through loss-of-function tests demonstrated that circSGCB exerts inhibitory effects on bovine myoblast proliferation while promoting myocytes generation. Furthermore, we discovered that circSGCB primarily localizes to the cytoplasm, where it functions as a molecular sponge by binding to bta-miR-27a-3p. This interaction releases the mRNAs of KLF3 gene and further activates downstream functional pathways. In vivo, studies provided evidence that up-regulation of KLF3 contributes to muscle regeneration. These findings collectively suggest that circSGCB operates via a competing endogenous RNA (ceRNA) mechanism to regulate KLF3, thereby influencing myogenesis in ruminants and highlights it may as potential molecular targets for enhancing meat production in livestock and poultry industries.

Circular RNA (circRNA), a stable ring-shaped RNA molecule found in eukaryotic cells, plays significant roles in biological regulation, particularly by interfering with transcription factor binding or enhancing gene expression. Using transcriptomic sequencing, we identified differentially expressed circRNAs in bovine muscle at various time points. Specifically, circDYRK1A was discovered and shown to enhance differentiation while suppressing proliferation of adult myoblasts. Rescue experiments further demonstrated that circDYRK1A regulates the KLF5 gene expression by interacting with miR21-5p, thus exerting its influence at the transcriptional level. This study marks the first identification of circDYRK1A in cattle and elucidates its role in bovine myoblast development through the circDYRK1A-miR21-5p-KLF5 regulatory axis. These findings contribute novel insights into molecular breeding of cattle and advance fundamental research on beef cattle breeding and muscle development.

(1) Background: Copy number variation (CNV) is a critical component of genome structural variation and has garnered significant attention. High-throughput screening of the KCNJ15 gene has revealed a correlation between the CNV region and the growth traits of goats. We aimed to identify the CNV of the KCNJ15 gene in five goat breeds and analyze its association with growth characteristics. (2) Methods: We utilized 706 goats from five breeds: Guizhou black goat (GZB), Guizhou white goat (GZW), Bohuai goat (BH), Huai goat (HH), and Taihang goat (TH). To evaluate the number of copies of the KCNJ15 gene using qPCR, we analyzed the correlation between the CNV and growth characteristics and then used a universal linear model. The findings revealed variations in the distribution of different copy number types among the different goat breeds. (3) Results: Association analysis revealed a positive influence of the CNV in the KCNJ15 gene on goat growth. In GZB, individuals with duplication types exhibited superior performance in terms of cannon bone circumference (p < 0.05). In HH, individuals with duplication types exhibited superior performance in terms of body slanting length (p < 0.05). Conversely, normal TH demonstrated better body height and body weight (p < 0.05), while in GZW, when CN = 3, it performed better than other types in terms of body weight and chest circumference (p < 0.05). However, in BH, it had no significant effect on growth traits. (4) Conclusions: We confirmed that the CNV in the KCNJ15 gene significantly influences the growth characteristics of four distinct goat breeds. The correlation between KCNJ15 gene CNVs and goat growth traits offers valuable insights to breeders, enabling them to employ precise and efficient breeding methods that enhance livestock welfare, productivity, and overall economic benefits in the industry.