Copy number variation of MYLK4 gene and its growth traits of Capra hircus (goat)

Genomics and transcriptomics identify quantitative trait loci affecting growth-related traits in silver pomfret (Pampus argenteus)

Pampus argenteus, a species distributed throughout the Indo-West Pacific, plays a significant role in the yield of aquaculture species. However, cultured P. argenteus has always been characterised by unbalanced growth synchronisation among individuals, slow growth rate, and lack of excellent germplasm resources. Therefore, we conducted mass selection for fast-growing strain P. argenteus for several consecutive years. Various genetic improvement programs have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In the present study, we combined bulked segregant analysis and transcriptome sequencing to identify candidate single nucleotide polymorphisms (SNPs) and key genes for growth-related traits in P. argenteus. A total of 7,280,936 SNPs and 2,212,379 insertions/deletions were identified in the extreme phenotypes of the fast-growing and slow-growing groups. Based on the examination of SNP frequency differences and sliding-window analysis, 42 SNPs were identified as candidate markers. Moreover, 14 of the 42 SNPs linked to growth-related traits were confirmed to be credible SNPs, and eight growth-related genes were screened, namely myb-binding protein 1 A, insulin A/B chains, α-1B adrenoceptor, engulfment and cell motility protein 3, myosin light chain kinase family member 4, insulin receptor located, unconventional myosin-9b, and matrilin-1. An optimal three-factor model (SNP4&SNP12&SNP14) was constructed using the generalized multifactor dimensionality reduction method, and its accuracy was verified as 67.72 %. These results may benefit genetic studies and accelerate genetic improvement of fast-growing strains of P. argenteus.

Identification of novel genetic loci related to dromedary camel (Camelus dromedarius) morphometrics, biomechanics, and behavior by genome-wide association studies

In the realm of animal breeding for sustainability, domestic camels have traditionally been valued for their milk and meat production. However, key aspects such as zoometrics, biomechanics, and behavior have often been overlooked in terms of their genetic foundations. Recognizing this gap, the present study perfomed genome-wide association analyses to identify genetic markers associated with zoometrics-, biomechanics-, and behavior-related traits in dromedary camels (Camelus dromedarius). 16 and 108 genetic markers were significantly associated (q < 0.05) at genome and chromosome-wide levels of significance, respectively, with zoometrics- (width, length, and perimeter/girth), biomechanics- (acceleration, displacement, spatial position, and velocity), and behavior-related traits (general cognition, intelligence, and Intelligence Quotient (IQ)) in dromedaries. In most association loci, the nearest protein-coding genes are linkedto neurodevelopmental and sensory disorders. This suggests that genetic variations related to neural development and sensory perception play crucial roles in shaping a dromedary camel's physical characteristics and behavior. In summary, this research advances our understanding of the genomic basis of essential traits in dromedary camels. Identifying specific genetic markers associated with zoometrics, biomechanics, and behavior provides valuable insights into camel domestication. Moreover, the links between these traits and genes related to neurodevelopmental and sensory disorders highlight the broader implications of domestication and modern selection on the health and welfare of dromedary camels. This knowledge could guide future breeding strategies, fostering a more holistic approach to camel husbandry and ensuring the sustainability of these animals in diverse agricultural contexts.

Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data

The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy for identifying shared variants within a population and uncovering important genomic regions related to complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, identify ROH islands and annotated genes within these candidate regions using whole-genome sequencing data from 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. Subsequent to quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for further analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3-1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. Within these segments, we identified 63 ROH islands housing 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2 and SLC24A4), body size/weight (MYLK4, PRIM2, FABP2, EYS and PHF3), immune capacity (IL2, IL21, PTP4A1, SEMA4C, JAK2, CCNA2 and TNIP3) and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2 and HSPA4L). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed 56 and 9 significant terms (FDR-corrected p-value < 0.05), respectively, among which cGMP-PKG signalling pathway, regulation of actin cytoskeleton, and calcium signalling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to our understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.

Investigation of the association between goat DNMT3B gene polymorphism and growth traits

The DNA methyltransferase 3 beta (DNMT3B) gene is key for DNA methylation and has been well recognized in regulating growth and development. A previous observation indicated that an 11-bp indel of DNMT3B affected the reproductive traits in goats, yet the effect of this polymorphism on body measurement traits in goats has not been reported. This study aims to investigate the associations between DNMT3B gene polymorphism and goat growth traits. We investigated this 11-bp indel in 2184 goats and three genotypes have been found in Shaanbei white cashmere goat (SBWC): insertion/insertion (II), deletion/deletion (DD) and insertion/deletion (ID). Only ID and DD genotypes were detected in Nubian goats and Guizhou heima goat (GZHM). The allele frequencies analyzed revealed that the 'D' allele frequencies were higher in all three goat breeds. Further association analysis demonstrated that this indel is markedly associated with the cannon circumference (CC) and cannon circumference index (CCI) of SBWC and cannon circumference (CC) of Nubian goats (p < .05). The CC and CCI are essential indicators to measure the growth status of goats. In summary, our study sheds some light on the potential impact of the 11-bp indel polymorphism of the DNMT3B gene on improving the growth traits in goats.

Association between the copy number variation of CCSER1 gene and growth traits in Chinese Capra hircus (goat) populations

Recently, Coiled-coil serine-rich protein 1 (CCSER1) gene is reported to be related to economic traits in livestock, and become a hotspot. In our study, we detected CCSER1 gene CNV in 693 goats from six breeds (GZB, GZW, AN, BH, HG, TH) by quantitative real-time PCR (qPCR) and the association analysis between the types of CNV and growth traits. Then, CCSER1 gene expression pattern was discovered in seven tissues from NB goats. Our results showed that the CCSER1 gene copy numbers were distributed differently in the aforementioned six breeds. The type of CCSER1 gene CNV was significantly associated with body weight and heart girth traits in GZW goat, in which individuals with deletion type were dominant in body weight trait (P < 0.05), while the normal type individuals were more advantageous in heart girth trait (P < 0.01); and there was a significant association with heart girth in TH goat (P < 0.05), which normal type was the dominant one. The expression profile revealed that CCSER1 gene has the highest level in the lung, followed by the small intestine and heart. In conclusion, our result is dedicated to an in-depth study of the novel CCSER1 gene CNV site and to provide essential information for Chinese goats molecular selective breeding in the future.

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats

Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs-for group of traits withers height, rump height, body length, 2 SNPs-for withers height and rump height, 1 SNP-for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats.

Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds

BACKGROUND

Elucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution to genetic diversity and association with important pathophysiological states. The present study aimed to elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X and 30X). Post-quality control, the sequence reads were aligned to the latest draft release of the Bubaline genome. The genome-wide CNVs were elucidated using a read-depth approach in CNVnator with different bin sizes. Adjacent CNVs were concatenated into copy number variation regions (CNVRs) in different breeds and their genomic coverage was elucidated.

RESULTS

Overall, the average size of CNVR was lower at 30X coverage, providing finer details. Most of the CNVRs were either deletion or duplication type while the occurrence of mixed events was lesser in number on a comparative basis in all breeds. The average CNVR size was lower at 30X coverage (0.201 Mb) as compared to 10X (0.013 Mb) with the finest variants in Banni buffaloes. The maximum number of CNVs was observed in Murrah (2627) and Pandharpuri (25,688) at 10X and 30X coverages, respectively. Whereas the minimum number of CNVs were scored in Surti at both coverages (2092 and 17,373). On the other hand, the highest and lowest number of CNVRs were scored in Jaffarabadi (833 and 10,179 events) and Surti (783 and 7553 events) at both coverages. Deletion events overnumbered duplications in all breeds at both coverages. Gene profiling of common overlapped genes and longest CNVRs provided important insights into the evolutionary history of these breeds and indicate the genomic regions under selection in respective breeds.

CONCLUSION

The present study is the first of its kind to elucidate the high-resolution CNV map in major buffalo populations using a read-depth approach on whole genome resequencing data. The results revealed important insights into the divergence of major global buffalo breeds along the evolutionary timescale.

Goat Pleomorphic Adenoma Gene 1 (PLAG1): mRNA Expression, CNV Detection and Associations with Growth Traits

The pleomorphic adenoma gene 1 (PLAG1) gene, as the major gene responsible for growth, plays a vital role in myogenesis. Meanwhile, the relationship between copy number variation (CNV) of this gene and growth traits in goats remains unclear. Therefore, this study investigated four aspects: bioinformatics analysis, mRNA expression (n = 6), CNV detection (n = 224), and association analysis. The findings indicated that the gene had a large number of conserved motifs, and the gene expression level was higher in fetal goats than in adult goats. Three CNV loci were selected from the database, among which CNV1 was located in the bidirectional promoter region and was associated with goat growth traits. CNV analysis showed that CNV2 and CNV3 of the PLAG1 gene were associated with growth traits such as body weight, heart girth, height at hip cross, and hip width (p < 0.05), with CNV1 loss genotype being the superior genotype, and CNV2 and CNV3 median and gain genotypes of being superior genotypes. This finding further confirms that the PLAG1 gene is the dominant gene for growth traits, which will serve as theoretical guidance for goat breeding.

Goat MyoD1: mRNA expression, InDel and CNV detection and their associations with growth traits

The Myogenic differentiation 1 (MyoD1) gene is a crucial regulator of muscle formation and differentiation. However, there are few studies on the mRNA expression pattern of the goat MyoD1 gene and its effect on goat growth and development. To address this, we investigated the mRNA expression of the MyoD1 gene in several tissues of fetal and adult goats, containing heart, liver, spleen, lung, kidney and skeletal muscle. The results focused on the expression of the MyoD1 gene in skeletal muscle of fetal goats was much higher than adult goats, suggesting its important role in skeletal muscle formation and development. Following, a total of 619 Shaanbei White Cashmere goats (SBWCs) were used to monitor the InDel (Insertion/Deletion) and CNV (Copy Number Variation) variations of the MyoD1 gene. Three InDel loci were identified, and there was no significant correlation with goat growth traits. Furthermore, a CNV locus containing the MyoD1 gene exon with three types (Loss type, Normal type, Gain type) were identified. The association analysis results showed that the CNV locus was significantly associated with body weight, height at hip cross, heart girth and hip width in SBWCs (P < 0.05). Meanwhile, the Gain type of CNV exhibited the best growth traits and good consistency among three types in goats, suggesting its potential as a DNA marker for marker-assisted breeding of goats. Overall, our study provided a scientific basis for breeding goats with better growth and development traits.

Analysis of Potential Genes and Economic Parameters Associated with Growth and Heat Tolerance in Sheep (Ovis aries)

This study explored the potential genes and economic factors that might be associated with growth and heat tolerance in two sheep breeds. Data on growth performance from the third month to six months of age were obtained based on records. In comparison to Aboudeleik lambs, Barki lambs developed considerably greater starting body weight, final body weight, final body weight gain, daily weight gain, and percentage increase in BW/month. Single nucleotide polymorphisms (SNPs) were found between lambs of the two breeds using PCR-DNA sequencing of CAST, LEP, MYLK4, MEF2B, STAT5A, TRPV1, HSP90AB1, HSPB6, HSF1, ST1P1, and ATP1A1 genes. Lambs from each breed were divided into groups based on detected SNPs in genes related to growth. The least squares means of the differentiated groups revealed a significant correlation of detected SNPs with growth and heat tolerance attributes (p ≤ 0.05). Barki lambs elicited greater total variable costs, total costs, total return, and net return values. The Barki sheep provided the best economic efficiency value when comparing the percentage difference between net profit and economic efficiency. Together with economic considerations, SNPs found may be used as proxies for marker-assisted selection of the best breed of sheep for traits related to growth and heat tolerance.

Copy Number Variation of the SOX6 Gene and Its Associations with Growth Traits in Ashidan Yak

Copy number variation (CNV) is a fundamental type of structural variation of the genome affecting the economic traits of livestock. The SOX6 gene (sex-determining region Y-box 6), as a transcription factor, has multiple functions with regard to sex determination, embryonic growth, the nervous system development, as well as bone, and various organ formation. This study employed quantitative real-time fluorescence quota PCR (qPCR) for detecting the SOX6-CNV of the 311 Ashidan yaks and analyzed the correlation of the SOX6-CNV with four phenotypes (including body weight, withers height, body length, and chest girth) of the yaks aged 6, 12, 18, and 30 months using ANOVA and multiple comparisons. Furthermore, the SOX6 gene expression was identified in seven different tissues of the yaks. The experiment results demonstrated the expression of SOX6 in each tissue, and the kidney and muscle tissue were found to have higher relative expression levels. Based on the processing by IBM SPSS software, SOX6-CNV was significantly correlated with the chest girth of the 6-months old yaks (p < 0.05) and 30-months yaks (p < 0.05), and withers height of 6 months yaks (p < 0.05) and 18-months yaks (p < 0.05), as well as the normal type of CNV, was chosen for yak breeding. In conclusion, SOX6 might be prominently involved in promoting growth and development of yaks, suggesting that the SOX6 gene can be used in breeding yaks by molecular marker-assisted selection (MAS). The study also offered some important insights into the references and clues for the genetic breeding of yaks.

Association of HSF1 gene copy number variation with growth traits in the Ashidan yak

Copy Number Variation (CNV) is the major manner for the variation of genome structure, which is associated with numerous important traits. The heat shock factor 1 (HSF1) gene is a stress response transcriptional regulator. It participates in the heat shock response, simultaneously participated in the development of tissue. The objective of this research was to explore the influence of CNV of the HSF1 gene on the growth traits of the Ashidan yak. In this study, the growth traits (withers height, body weight, chest girth, and body length) of 274 Ashidan yaks were divided into four stages (6, 12, 18, and 30 months old). Moreover, quantitative polymerase chain reaction (qPCR) was exploited for determining the HSF1 gene relative expression level, and SPSS software was utilized for the statistical analysis. The outcomes indicated that HSF1-CNV was significantly associated with body length (p < 0.05) and was extremely significant associated with withers height (p < 0.01) of 18-month-old Ashidan yaks. Besides, the HSF1 relative expression in heart and muscle was higher than that existed in other tissues (p < 0.01). The outcomes suggested that the CNV of HSF1 gene would affect the growth and development of the Ashidan yak, which is conducive to the early breeding of yak.

Copy Number Variations in the MICALL2 and MOGAT2 Genes Are Associated with Ashidan Yak Growth Traits

Copy number variations (CNVs) are a result of genomic rearrangement affecting DNA regions over 1 kb in length, and can include inversions, translocations, deletions, and duplications. The molecule interacting with CasL-like protein 2 (MICALL2) gene is primarily associated with mitochondrial protein targeting and exhibits predicted stress fiber colocalization. The monoacylglycerol O-acyltransferase 2 (MOGAT2) gene encodes an enzyme responsible for catalyzing diacylglycerol synthesis from 2-monoacylglycerol and fatty acyl-CoA. For this study, blood samples were obtained from 315 yaks, and the body weight, body length, withers height, and chest girth of these animals were measured at 6, 12, 18, and 30 months of age. Genomic DNA was harvested from the collected blood samples, and CNVs in these samples were detected by qPCR. The resultant data were compared using ANOVAs, revealing significant associations between MICALL2 gene CNVs and body weight at 6 months of age (p < 0.05), body length and chest girth at 30 months of age (p < 0.05), and withers height at 18 months of age (p < 0.01) in Ashidan yaks. Similarly, MOGAT2 CNVs were significantly associated with body weight at 6 and 30 months of age (p < 0.05), and with withers height at 18 months of age (p < 0.01) in these Ashidan yaks. MICALL2 and MOGAT2 gene expression was further analyzed in yak tissue samples, revealing that MICALL2 was most highly expressed in the adipose tissue, whereas MOGAT2 was most highly expressed in the lung. These results thus confirmed the relationship between CNVs in the MICALL2 and MOGAT2 genes and Ashidan yak growth traits, providing a valuable gene locus that can be leveraged for future marker-assisted yak breeding efforts.

Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats

The objective of this study was to identify the SNPs and candidate genes related to body weight and seven body conformation traits at the age of 8 months in the Russian aboriginal Karachai goats (n = 269) by conducting genome-wide association studies (GWAS), using genotypes generated by Goat SNP BeadChip (Illumina Inc., USA). We identified 241 SNPs, which were significantly associated with the studied traits, including 47 genome-wide SNPs (p < 10−5) and 194 suggestive SNPs (p < 10−4), distributed among all goat autosomes except for autosome 23. Fifty-six SNPs were common for two and more traits (1 SNP for six traits, 2 SNPs for five traits, 12 SNPs for four traits, 20 SNPs for three traits, and 21 SNPs for two traits), while 185 SNPs were associated with single traits. Structural annotation within a window of 0.4 Mb (±0.2 Mb from causal SNPs) revealed 238 candidate genes. The largest number of candidate genes was identified at Chr13 (33 candidate genes for the five traits). The genes identified in our study were previously reported to be associated with growth-related traits in different livestock species. The most significant genes for body weight were CRADD, HMGA2, MSRB3, MAX, HACL1 and RAB15, which regulate growth processes, body sizes, fat deposition, and average daily gains. Among them, the HMGA2 gene is a well-known candidate for prenatal and early postnatal development, and the MSRB3 gene is proposed as a candidate gene affecting the growth performance. APOB, PTPRK, BCAR1, AOAH and ASAH1 genes associated with withers height, rump height and body length, are involved in various metabolic processes, including fatty acid metabolism and lipopolysaccharide catabolism. In addition, WDR70, ZBTB24, ADIPOQ, and SORCS3 genes were linked to chest width. KCNG4 was associated with rump height, body length and chest perimeter. The identified candidate genes can be proposed as molecular markers for growth trait selection for genetic improvement in Karachai goats.

Copy number variation (CNV) of the AHR gene in the Ashidan yak and its association with growth traits

Copy number variation (CNV) is a principal genomic structure variation affecting the gene expression through the dose-effect and change of gene regulatory region. It plays an important role in regulating the various complex traits of vertebrates. The aromatic hydrocarbon receptor (AHR) is a member of ligand-dependent transcription factors which belong to the alkaline helix-loop-helix PASS family. It is used as a conservative environmental sensor during biological evolution. This study, tracked the growth data (body weight, withers height, body length, chest girth) of 332 yaks in four stages (6, 12, 18, and 30 months) were tracked. The CNV of the yaks was analyzed using real-time quantitative PCR, and the correlation between CNV of AHR and yak growth traits was analyzed using the SPSS and R software. The AHR gene expression profiles were assessed in different tissues of the 18-month-old yak. The statistical analysis indicated the AHR-CNV of the Ashidan yak to significantly correlate with the body length (P < 0.05), and was found to be correlated with the withers height at 18 months old (P < 0.01) with extreme significance. To sum up, this study for the first time discussed the relationship between AHR-CNV and the growth traits of the Ashidan yak. The results indicated that the AHR gene might become a new molecular marker in the breeding yak.

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.

Copy number variations of the KAT6A gene are associated with body measurements of Chinese sheep breeds

Copy number variation (CNV) is one kind of genomic structure variations and presents as gains and losses of genomic fragments. More recently, we have made an atlas of CNV maps for livestock. In the future, it is a primary focus to determine the phenotypic effects of candidate CNVs. Lysine Acetyltransferase 6 A (KAT6A) is a protein coding gene and plays a critical role in many cellular processes. However, the effects of KAT6A CNVs on sheep body measurements remains unknown. In this study, we performed quantitative polymerase chain reaction (qPCR) to detect the presences and distributions of three CNV regions within KAT6A gene in 672 sheep from four Chinese breeds. Association analysis indicated that the three CNVs of KAT6A gene were significantly associated with body measurement(s) in Small-tailed Han sheep (STH) and Hu sheep (HU) (p < 0.05), while no effects on Large-tailed Han sheep (LTH) were observed (p > 0.05) were observed. Additionally, only one CNV was significantly associated with body measurement (body length) in Chaka sheep (CK) (p < 0.05). Our study provided evidence that the CNV(s) of KAT6A gene could be used as candidate marker(s) for molecular breedings of STH, HU, and CK breeds.

Copy number variation of CADM2 gene revealed its association with growth traits across Chinese Capra hircus (goat) populations

Copy number variations (CNVs) are the wide structural variations ranging from 50 bp to several Mb at genome which can affect gene expression and further impacting growth and development traits of livestock. Comparing with single nucleotide polymorphisms (SNPs), CNVs can better explain the genetic and phenotypic diversity, are increasingly important in biological research. As a member of immunoglobulin super-family, cell adhesion molecule 2 (CADM2) plays a vital role in cancer development and metabolic regulation. Here, we tested the CNV of CADM2 gene in 443 goats across five breeds (Guizhou white goat, GZW; Guizhou black goat, GZB; Africa Nubian goat, AN; Boer goat × Huai goat, BH; Boer goat, BG) and detected its association with phenotypic traits. Subsequently, we analyzed the CADM2 gene expression level in different tissues of NB goats (n = 3, Nubian × Black) and the transcriptional expression in lung is much higher than others. The results showed that the CNV of CADM2 has a significant association with withers height and body length in GZB goat (P < 0.01), in which individuals with type of deletion were superior to those with duplication or normal type in term of body hight and body length (P < 0.01). In summary, this study confirmed the association between CNV of CADM2 gene and growth traits, and our research data indicated the CADM2-CNV may considered as a prospective candidate for the molecular marker-assisted selection breeding of goat growth traits, which conducived to accelerating the genetic amelioration in Chinese goats.