Genomic sequencing analysis reveals copy number variations and their associations with economically important traits in beef cattle

Copy number variations within fibroblast growth factor 13 gene influence growth traits and alternative splicing in cattle

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.

Genome-wide association studies for economically important traits in mink using copy number variation

Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.

Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle

Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP array. Next, we performed a CNV-based genome-wide association analysis (GWAS) of six meat quality traits and identified 12 significant CNV segments corresponding to eight candidate genes, including PCDH15, CSMD3, etc. Using region-based association analysis, we further identified six CNV segments relevant to meat quality in beef cattle. Among these, TRIM77 and TRIM64 within CNVR4 on BTA29 were detected as candidate genes for backfat thickness (BFT). Notably, we identified a 34 kb duplication for meat color (MC) which was supported by read-depth signals, and this duplication was embedded within the keratin gene family including KRT4, KRT78, and KRT79. Our findings will help to dissect the genetic architecture of meat quality traits from the aspects of CNVs, and subsequently improve the selection process in breeding programs.

Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle

Qaidam cattle (CDM) are indigenous breed inhabiting Northwest China. In the present study, we newly sequenced 20 Qaidam cattle to investigate the copy number variants (CNVs) based on the ARS-UMD1.2 reference genome. We generated the CNV region (CNVR) datasets to explore the genomic CNV diversity and population stratification. The other four cattle breeds (Xizang cattle, XZ; Kazakh cattle, HSK; Mongolian cattle, MG; and Yanbian cattle, YB) from the regions of North China embracing 43 genomic sequences were collected and are distinguished from each of the other diverse populations by deletions and duplications. We also observed that the number of duplications was significantly more than deletions in the genome, which may be less harmful to gene formation and function. At the same time, only 1.15% of CNVRs overlapped with the exon region. Population differential CNVRs and functional annotations between the Qaidam cattle population and other cattle breeds revealed the functional genes related to immunity (MUC6), growth (ADAMTSL3), and adaptability (EBF2). Our analysis has provided numerous genomic characteristics of some Chinese cattle breeds, which are valuable as customized biological molecular markers in cattle breeding and production.

Identification and Characterization of Copy Number Variations Regions in West African Taurine Cattle

A total of 106 West African taurine cattle belonging to the Lagunaire breed of Benin (33), the N’Dama population of Burkina Faso (48), and N’Dama cattle sampled in Congo (25) were analyzed for Copy Number Variations (CNVs) using the BovineHDBeadChip of Illumina and two different CNV calling programs: PennCNV and QuantiSNP. Furthermore, 89 West African zebu samples (Bororo cattle of Mali and Zebu Peul sampled in Benin and Burkina Faso) were used as an outgroup to ensure that analyses reflect the taurine cattle genomic background. Analyses identified 307 taurine-specific CNV regions (CNVRs), covering about 56 Mb on all bovine autosomes. Gene annotation enrichment analysis identified a total of 840 candidate genes on 168 taurine-specific CNVRs. Three different statistically significant functional term annotation clusters (from ACt1 to ACt3) involved in the immune function were identified: ACt1 includes genes encoding lipocalins, proteins involved in the modulation of immune response and allergy; ACt2 includes genes encoding coding B-box-type zinc finger proteins and butyrophilins, involved in innate immune processes; and Act3 includes genes encoding lectin receptors, involved in the inflammatory responses to pathogens and B- and T-cell differentiation. The overlap between taurine-specific CNVRs and QTL regions associated with trypanotolerant response and tick-resistance was relatively low, suggesting that the mechanisms underlying such traits may not be determined by CNV alterations. However, four taurine-specific CNVRs overlapped with QTL regions associated with both traits on BTA23, therefore suggesting that CNV alterations in major histocompatibility complex (MHC) genes can partially explain the existence of genetic mechanisms shared between trypanotolerance and tick resistance in cattle. This research contributes to the understanding of the genomic features of West African taurine cattle.

Copy Number Variation (CNV): A New Genomic Insight in Horses

Simple Summary

This study aimed to contribute to our knowledge of CNVs, a type of genomic marker in equines, by producing, for the first time, a fine-scale characterization of the CNV regions (CNVRs) in the Pura Raza Española horse breed. We found not only the existence of a unique pattern of genomic regions enriched in CNVs in the PRE in comparison with the data available from other breeds but also the incidence of CNVs across the entire genome. Since these regions could affect the structure and dose of the genes involved, we also performed a gene ontology analysis which revealed that most of the genes overlapping in CNVRs were related to the olfactory pathways and immune response.

Abstract

Copy number variations (CNVs) are a new-fangled source of genetic variation that can explain changes in the phenotypes in complex traits and diseases. In recent years, their study has increased in many livestock populations. However, the study and characterization of CNVs in equines is still very limited. Our study aimed to investigate the distribution pattern of CNVs, characterize CNV regions (CNVRs), and identify the biological pathways affected by CNVRs in the Pura Raza Española (PRE) breed. To achieve this, we analyzed high-density SNP genotyping data (670,804 markers) from a large cohort of 654 PRE horses. In total, we identified 19,902 CNV segments and 1007 CNV regions in the whole population. The length of the CNVs ranged from 1.024 kb to 4.55 Mb, while the percentage of the genome covered by CNVs was 4.4%. Interestingly, duplications were more abundant than deletions and mixed CNVRs. In addition, the distribution of CNVs across the chromosomes was not uniform, with ECA12 being the chromosome with the largest percentage of its genome covered (19.2%), while the highest numbers of CNVs were found in ECA20, ECA12, and ECA1. Our results showed that 71.4% of CNVRs contained genes involved in olfactory transduction, olfactory receptor activity, and immune response. Finally, 39.1% of the CNVs detected in our study were unique when compared with CNVRs identified in previous studies. To the best of our knowledge, this is the first attempt to reveal and characterize the CNV landscape in PRE horses, and it contributes to our knowledge of CNVs in equines, thus facilitating the understanding of genetic and phenotypic variations in the species. However, further research is still needed to confirm if the CNVs observed in the PRE are also linked to variations in the specific phenotypical differences in the breed.

Effect of genetic variants in the SMAD1 and SMAD5 genes promoter on growth and beef quality traits in cattle

The SMAD1 and SMAD5 genes belong to mothers against decapentaplegic proteins family, which participate in the BMP pathway to control skeletal myogenesis and growth. In the present study, we analyzed the associations between polymorphisms of SMAD1 and SMAD5 genes promoter and important economical traits in Qinchuan cattle. Four SNPs in the SMAD1 gene promoter and three SNPs in the SMAD5 promoter were identified by sequencing of 448 Qinchuan cattles. Allelic and frequency analyses of these SNPs resulted in eight haplotypes both in the promoters of the two genes promoter and identified potential cis-regulatory transcription factor (TF) components. In addition, correlation analysis showed that cattle SMAD1 promoter activity of individuals with Hap4 (P < 0.01) was stronger than that of individuals with Hap2. while the transcriptional activity of individuals with Hap3 within SMAD5 gene promoter was significantly (P < 0.01) higher followed by H2. Uniformly, diplotypes H4-H6 of SMAD1 gene and H1-H3 of SMAD5 gene performed significant (P < 0.01) associations with body measurement and improved carcass quality traits. All these results have indicated that polymorphisms in SMAD1 and SMAD5 genes promoter could impact the transcriptional regulation and then affect muscle content in beef cattle. Moreover, both the SMAD1 and SMAD5 genes were expressed ubiquitously in 10 tissues and had higher expression in the longissimus thoracis tissue from 6-month-old and 12-month-old cattle than in cattle of other ages. We can conclude that SMAD1 and SMAD5 genes may play an important role in muscle growth and development, and the variants mapped within SMAD1 and SMAD5 genes can be utilized in molecular marker-assisted selection for cattle carcass quality and body measurement traits in breed improvement programs of Qinchuan cattle.

Investigation of Copy Number Variations (CNVs) of the Goat PPP3CA Gene and Their Effect on Litter Size and Semen Quality

Simple Summary

PPP3CA is one of the candidate genes for goat reproduction, but no studies have been carried out yet. Therefore, the purpose of this study was to determine the associations between copy number variations in the goat PPP3CA gene and litter size and semen quality in goats, including Shaanbei white cashmere goats (SBWC) (n = 353) and Guizhou Heima (GZHM) goats (n = 64). Based on the association analysis, the results showed that only CNV1 (copy number variation 1) and CNV2 (copy number variation 2) were distinctly related to the first-birth litter size in female goats (p = 7.6802 × 10⁻¹¹; p = 5.0895 × 10⁻⁹), and they were also significantly associated with the semen quality of SBWC goats (p < 0.05). These findings prove that the PPP3CA gene plays an important role in reproduction traits in goats.

Abstract

Copy number variations (CNVs) have many forms of variation structure, and they play an important role in the research of variety diversity, biological evolution and disease correlation. Since CNVs have a greater impact on gene regulation and expression, more studies are being finalized on CNVs in important livestock and poultry species. The protein phosphatase 3 catalytic subunit alpha (PPP3CA) is a key candidate gene involved in the goat fecundity trait, and has important effects on precocious puberty, estrogen signal transduction pathways and oocyte meiosis. Additionally, PPP3CA also has a dephosphorylation effect in the process of spermatogonial stem cell meiosis and spermatogenesis. So far, there is no research on the relationship between the copy number variations of the PPP3CA gene and reproduction traits. Therefore, the purpose of this study was to determine the association between copy number variations in the goat PPP3CA gene and litter size and semen quality in Shaanbei white cashmere goats (SBWC) (n = 353) and Guizhou Heima goats (n = 64). Based on the association analysis, the results showed that only CNV1 and CNV2 within the PPP3CA gene were distinctly related to the first-birth litter size in female goats (p = 7.6802 × 10⁻¹¹; p = 5.0895 × 10⁻⁹, respectively) and they were also significantly associated with the semen quality of SBWC goats (p < 0.05). In addition, individuals with Loss genotypes demonstrated better phenotypic performance compared to those with other types. Therefore, CNV1 and CNV2 of the PPP3CA gene are potentially useful for breeding, as they are linked to important goat reproduction traits.