Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle

Expression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so, the genomic variation is often called from short-read alignments, which are unable to comprehensively resolve structural variation. Here we build a pangenome from 16 HiFi haplotype-resolved cattle assemblies to identify small and structural variation and genotype them with PanGenie in 307 short-read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-called small variation and confidently genotype close to 21 million small and 43,000 structural variants in the larger population. We validate 85% of these structural variants (with MAF > 0.1) directly with a subset of 25 short-read samples that also have medium coverage HiFi reads. We then conduct e/sQTL mapping with this comprehensive variant set in a subset of 117 cattle that have testis transcriptome data, and find 92 structural variants as causal candidates for eQTL and 73 for sQTL. We find that roughly half of the top associated structural variants affecting expression or splicing are transposable elements, such as SV-eQTL for STN1 and MYH7 and SV-sQTL for CEP89 and ASAH2 Extensive linkage disequilibrium between small and structural variation results in only 28 additional eQTL and 17 sQTL discovered when including SVs, although many top associated SVs are compelling candidates.

Unravelling novel and pleiotropic genes for cannon bone circumference and bone mineral density in Yorkshire pigs

Leg weakness is a prevalent health condition in pig farms. The augmentation of cannon bone circumference and bone mineral density can effectively improve limb strength in pigs and alleviate leg weakness. This study measured forelimb cannon bone circumference (fCBC) and rear limb cannon bone circumference (rCBC) using an inelastic tapeline and rear limb metatarsal area bone mineral density (raBMD) using a dual-energy X-ray absorptiometry bone density scanner. The samples of Yorkshire castrated boars were genotyped using a 50K single-nucleotide polymorphism (SNP) array. The SNP-chip data were imputed to the level of whole-genome sequencing data (iWGS). This study used iWGS data to perform genome-wide association studies and identified novel significant SNPs associated with fCBC on SSC6, SSC12, and SSC13, rCBC on SSC12 and SSC14, and raBMD on SSC7. Based on the high phenotypic and genetic correlations between CBC and raBMD, multi-trait meta-analysis was performed to identify pleiotropic SNPs. A significant potential pleiotropic quantitative trait locus (QTL) regulating both CBC and raBMD was identified on SSC15. Bayes fine mapping was used to establish the confidence intervals for these novel QTLs with the most refined confidence interval narrowed down to 56 kb (15.11 to 15.17 Mb on SSC12 for fCBC). Furthermore, the confidence interval for the potential pleiotropic QTL on SSC15 in the meta-analysis was narrowed down to 7.45 kb (137.55 to137.56 Mb on SSC15). Based on the biological functions of genes, the following genes were identified as novel regulatory candidates for different phenotypes: DDX42, MYSM1, FTSJ3, and MECOM for fCBC; SMURF2, and STC1 for rCBC; RGMA for raBMD. Additionally, RAMP1, which was determined to be located 23.68 kb upstream of the confidence interval of the QTL on SSC15 in the meta-analysis, was identified as a potential pleiotropic candidate gene regulating both CBC and raBMD. These findings offered valuable insights for identifying pathogenic genes and elucidating the genetic mechanisms underlying CBC and BMD.

Multitrait meta-analyses identify potential candidate genes for growth-related traits in Holstein heifers

Understanding the underlying pleiotropic relationships among growth and body size traits is important for refining breeding strategies in dairy cattle for optimal body size and growth rate. Therefore, we performed single-trait GWAS for monthly-recorded body weight (BW), hip height, body length, and chest girth from birth to 12 mo of age in Holstein animals, followed by stepwise multiple regression of independent or lowly-linked markers from GWAS loci using conditional and joint association analyses (COJO). Subsequently, we conducted a multitrait meta-analysis to detect pleiotropic markers. Based on the single-trait GWAS, we identified 170 significant SNPs, in which 59 of them remained significant after the COJO analyses. The most significant SNP, located at BTA7:3,676,741, explained 2.93% of the total phenotypic variance for BW6 (BW at 6 mo of age). We identified 17 SNPs with potential pleiotropic effects based on the multitrait meta-analyses, which resulted in 3 additional SNPs in comparison to those detected based on the single-trait GWAS. The identified quantitative trait loci regions overlap with genes known to influence human growth-related traits. According to positional and functional analyses, we proposed HMGA2, HNF4G, MED13L, BHLHE40, FRZB, DMP1, TRIB3, and GATAD2A as important candidate genes influencing the studied traits. The combination of single-trait GWAS and meta-analyses of GWAS results improved the efficiency of detecting associated SNPs, and provided new insights into the genetic mechanisms of growth and development in Holstein cattle.

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.

The association of gene polymorphisms with milk production and mastitis resistance phenotypic traits in dairy cattle

The aim of this study was to evaluate the association between gene polymorphisms (SNPs) and mastitis indicators and their relationship with milk production profitability in dairy herd.A functional analysis was also performed of five genes containing the studied SNPs and those located close by. DNA was isolated from the hair bulb of 320 dairy cows kept in three herds and SNP-microarray analysis was performed. The data on 299 cows was subjected to final statistical analysis using AI-REML method with one-trait repeatability test-day animal model and pedigree information using the DMU4 package. Five from 35 SNPs significantly associated with mastitis indicators or production traits and located within a gene or no more than 500,000 nucleotides from the gene were selected for the functional and economic analysis. A questionnaire was also developed to collect associated economic data of 219 cows from three herds, such as the value of milk production and direct costs incurred over three years; this allowed the gross margin, direct profitability index and direct costs incurred to produce one liter of milk to be determined, among others. None of the five studied SNPs were related to protein content. The rs110785912(T/A), found near CXCR4, and rs136813430(T/C), located in the TLR4 gene exon, were associated with lnSCC, while rs110455063(C/G), located near IGFI, was associated with milk yield, fat and total solid contents. rs109421300(T/C), associated with fat/protein content ratio, as well as fat and total solid content, is located in the DGAT1 gene intron. rs41587003(A/C), located in the DLG2 gene intron, was associated with lactose content. The economic analysis revealed differences between the variants of the three tested SNPs. The T/C variant of the rs136813430(T/C) SNP was characterized by the highest gross margin, the highest direct profitability index and the lowest costs incurred to produce 1 liter of milk. The T/A variant of rs110785912(T/A) was related to low lnSCC and was characterized by the highest direct profitability index. In turn, the C/C variant of the rs41587003(T/C) was related to the lowest level of lactose and the highest costs of milk production. It appears that rs136813430(T/C) may be the most promising of the tested SNPs for increasing the profitability of milk production. To our knowledge, it is the first effort to assess directly a correlation between the DNA polymorphism and economic output of a dairy enterprise.

Genome-Wide Association Study for Body Conformation Traits and Fitness in Czech Holsteins

The aim of this study was a genome-wide association study (GWAS) on conformation traits using 25,486 genotyped Czech Holsteins, with 35,227 common SNPs for each genotype. Linear trait records were collected between 1995 and 2020. The Interbull information from Multiple Across Country Evaluation (MACE) was included for bulls that mostly had daughter records in a foreign country. When using the Bonferroni correction, the number of SNPs that were either significant or approached the significance threshold was low-dairy capacity composite on BTA4, feet and legs composite BTA21, total score BTA10, stature BTA24, body depth BTA6, angularity BTA20, fore udder attachment BTA10. Without the Bonferroni correction, the total number of significant or near of significance SNPs was 32. The SNPs were localized on BTA1,2,4,5,6,7,8,18,22,25,26,28 for dairy capacity composite, BTA15,21 for feet and legs composite, BTA10 for total score, BTA24 stature, BTA6,23 body depth, BTA20 angularity, BTA2 rump angle, BTA9,10 rear legs rear view, BTA2,19 rear legs side view, BTA10 fore udder attachment, BTA2 udder depth, BTA10 rear udder height, BTA12 central alignment, BTA24 rear teat placement, BTA8,29 rear udder width. The results provide biological information for the improvement of body conformation and fitness in the Holstein population.

Adult health and transition stage-specific rotenone-mediated Drosophila model of Parkinson’s disease: Impact on late-onset neurodegenerative disease models

Parkinson’s disease (PD) affects almost 1% of the population worldwide over the age of 50 years. Exposure to environmental toxins like paraquat and rotenone is a risk factor for sporadic PD which constitutes 95% of total cases. Herbicide rotenone has been shown to cause Parkinsonian symptoms in multiple animal models. Drosophila is an excellent model organism for studying neurodegenerative diseases (NDD) including PD. The aging process is characterized by differential expression of genes during different life stages. Hence it is necessary to develop life-stage-matched animal models for late-onset human disease(s) such as PD. Such animal models are critical for understanding the pathophysiology of age-related disease progression and important to understand if a genotropic drug/nutraceutical can be effective during late stages. With this idea, we developed an adult life stage-specific (health and transition phase, during which late-onset NDDs such as PD sets in) rotenone-mediated Drosophila model of idiopathic PD. Drosophila is susceptible to rotenone in dose-time dependent manner. Rotenone-mediated fly model of sporadic PD exhibits mobility defects (independent of mortality), inhibited mitochondrial complex I activity, dopaminergic (DAergic) neuronal dysfunction (no loss of DAergic neuronal number; however, reduction in rate-limiting enzyme tyrosine hydroxylase (TH) synthesis), and alteration in levels of dopamine (DA) and its metabolites; 3,4-Dihydroxyphenylacetic acid (DOPAC) and Homovanilic acid (HVA) in brain-specific fashion. These PD-linked behaviors and brain-specific phenotypes denote the robustness of the present fly model of PD. This novel model will be of great help to decipher life stage-specific genetic targets of small molecule mediated DAergic neuroprotection; understanding of which is critical for formulating therapeutic strategies for PD.

Whole genome resequencing reveals the genetic contribution of Kazakh and Swiss Brown cattle to a population of Xinjiang Brown cattle

Xinjiang Brown cattle is characterized by wide environmental adaptation from its female parent (Kazakh cattle) and good production performance from its male parent (Swiss Brown cattle). However, the genetic basis underlying these characteristics hasnotbeenexplored. Here we compared 50 genomes of Xinjiang Brown cattle to the genomes of other eight breeds worldwide to analyze patterns of genetic variation in the Xinjiang Brown cattle. We found canonical genomic characteristics of cross breed with the lowest linkage disequilibrium and the highest effective population size. At the global level, Xinjiang Brown cattle had 9.88% Kazakh cattle and 90.12% Swiss Brown cattle inheritance. Our local ancestry inference revealed the segments with the excess of Kazakh cattle blood enriched in genes or pathways involved in digestion,absorption,metabolism and disease. More importantly, we also observed the completely fixed haplotypes inherited from Swiss Brown cattle harboring genes (LCORL, GHR, MEF2D, PCSK1 and MSRB3), KEGG pathways, cattle QTLs or human NHGRIGWAS catalog related to body measurement and growth traits. Our findings will not only help understand the process of cross breeding but can provide basic materials for further QTL mapping and improvement of important traits in Xinjiang Brown cattle.

Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes

Background

Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleotide polymorphisms, SNPs) for genome-wide association studies (GWAS) of 18 fertility and reproduction traits in Holstein cattle. Aiming to identify pleiotropic variants and increase detection power, multiple-trait analyses were performed using a method to efficiently combine the estimated SNP effects of single-trait GWAS based on a chi-square statistic.

Results

There were 87, 72, and 84 significant SNPs identified for heifer, cow, and sire traits, respectively, which showed a wide and distinct distribution across the genome, suggesting that they have relatively distinct polygenic nature. The biological functions of immune response and fatty acid metabolism were significantly enriched for the 184 and 124 positional candidate genes identified for heifer and cow traits, respectively. No known biological function was significantly enriched for the 147 positional candidate genes found for sire traits. The most important chromosomes that had three or more significant QTL identified are BTA22 and BTA23 for heifer traits, BTA8 and BTA17 for cow traits, and BTA4, BTA7, BTA17, BTA22, BTA25, and BTA28 for sire traits. Several novel and biologically important positional candidate genes were strongly suggested for heifer (SOD2, WTAP, DLEC1, PFKFB4, TRIM27, HECW1, DNAH17, and ADAM3A), cow (ANXA1, PCSK5, SPESP1, and JMJD1C), and sire (ELMO1, CFAP70, SOX30, DGCR8, SEPTIN14, PAPOLB, JMJD1C, and NELL2) traits.

Conclusions

These findings contribute to better understand the underlying biological mechanisms of fertility and reproduction traits measured in heifers, cows, and sires, which may contribute to improve genomic evaluation for these traits in dairy cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08555-z.

Identification of important genomic footprints using eight different selection signature statistics in domestic cattle breeds

In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, we used eight different statistical tools (Tajima's D, Fu & Li's D*, CLR, ROH, iHS, F_ST, FLK, and hapFLK) on seven indigenous and five exotic cattle breeds. We further performed composite analysis by comparing their covariance matrix. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3, CXCL5, IRF8, and MYOM1). The outcome of this investigation provides a basis for detecting selective sweeps that explain the genetic variation of traits. They may possess functional importance for multiple cattle breeds in different subcontinents. However, further studies are required to improve the findings using high-density arrays or whole-genome sequencing with higher resolution and greater sample sizes.

A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

Background

Semen quality and insemination success are monitored in artificial insemination bulls to ensure high male fertility rates. Only ejaculates that fulfill minimum quality requirements are processed and eventually used for artificial inseminations. We examined 70,990 ejaculates from 1343 Brown Swiss bulls to identify bulls from which all ejaculates were rejected due to low semen quality. This procedure identified a bull that produced 12 ejaculates with an aberrantly small number of sperm (0.2 ± 0.2 × 109 sperm per mL) which were mostly immotile due to multiple morphological abnormalities.

Results

The genome of this bull was sequenced at a 12× coverage to investigate a possible genetic cause. Comparing the sequence variant genotypes of this bull with those from 397 fertile bulls revealed a 1-bp deletion in the coding sequence of the QRICH2 gene which encodes the glutamine rich 2 protein, as a compelling candidate causal variant. This 1-bp deletion causes a frameshift in translation and a premature termination codon (ENSBTAP00000018337.1:p.Cys1644AlafsTer52). The analysis of testis transcriptomes from 76 bulls showed that the transcript with the premature termination codon is subject to nonsense-mediated mRNA decay. The 1-bp deletion resides in a 675-kb haplotype that includes 181 single nucleotide polymorphisms (SNPs) from the Illumina BovineHD Bead chip. This haplotype segregates at a frequency of 5% in the Brown Swiss cattle population. Our analysis also identified another bull that carried the 1-bp deletion in the homozygous state. Semen analyses from the second bull confirmed low sperm concentration and immotile sperm with multiple morphological abnormalities that primarily affect the sperm flagellum and, to a lesser extent, the sperm head.

Conclusions

A recessive loss-of-function allele of the bovine QRICH2 gene likely causes low sperm concentration and immotile sperm with multiple morphological abnormalities. Routine sperm analyses unambiguously identify homozygous bulls for this allele. A direct gene test can be implemented to monitor the frequency of the undesired allele in cattle populations.

Bull fertility and semen quality are not correlated with dairy and production traits in Brown Swiss cattle

Undisturbed reproduction is key for successful breeding of beef and dairy cattle. Improving reproductive ability can be difficult because of antagonistic relationships with other economically relevant traits. In cattle, thorough investigation of female fertility revealed unfavorable genetic correlations with various production phenotypes. However, the correlation between male reproductive ability and production traits remains poorly understood. Here, we investigated the genetic relationships among and between male fertility characteristics and economically relevant traits in a population of Brown Swiss cattle. We performed GWAS with imputed genotypes at nearly 12 million sequence variants for semen quality (sperm head and tail anomalies, motility, concentration, and volume), male fertility, and 57 production phenotypes. Allele substitution effects were then correlated on a trait-by-trait basis to estimate genetic correlations. Correlations between male reproductive characteristics and traits of economic value were small and ranged from -0.0681 to 0.0787. Among the semen quality parameters, sperm motility was negatively correlated with anomalies (head: r = -0.7083 ± 0.0002; tail: r = -0.7739 ± 0.0002) and volume (r = -0.1266 ± 0.0003), whereas volume was negatively correlated with concentration (r = -0.3503 ± 0.0002). Sire nonreturn rate was negatively correlated with sperm anomalies (head: r = -0.1640 ± 0.0002; tail: r = -0.1580 ± 0.0002) and positively correlated with motility (r = 0.1598 ± 0.0002). A meta-analysis of male reproductive traits identified 2 quantitative trait loci: a previously described region on chromosome 6 showed pleiotropic effects and a novel region on chromosome 11 was associated with sperm head anomalies. In conclusion, our results suggest that selection for economically important dairy and production phenotypes has little impact on semen quality and fertility of Brown Swiss bulls.

Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle

Bone weight is critical to affect body conformation and stature in cattle. In this study, we conducted a genome-wide association study for bone weight in Chinese Simmental beef cattle based on the imputed sequence variants. We identified 364 variants associated with bone weight, while 350 of them were not included in the Illumina BovineHD SNP array, and several candidate genes and GO terms were captured to be associated with bone weight. Remarkably, we identified four potential variants in a candidate region on BTA6 using Bayesian fine-mapping. Several important candidate genes were captured, including LAP3, MED28, NCAPG, LCORL, SLIT2, and IBSP, which have been previously reported to be associated with carcass traits, body measurements, and growth traits. Notably, we found that the transcription factors related to MED28 and LCORL showed high conservation across multiple species. Our findings provide some valuable information for understanding the genetic basis of body stature in beef cattle.

Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.

Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data

Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.

Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle

BACKGROUND

The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process.

RESULTS

A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit.

CONCLUSIONS

The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.

Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats

The way in which living organisms mobilize a combination of long-term adaptive mechanisms and short-term phenotypic plasticity to face environmental variations is still largely unknown. In the context of climate change, understanding the genetic and epigenetic bases for adaptation and plasticity is a major stake for preserving genomic resources and the resilience capacity of livestock populations. We characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco. We produced for each individual Whole-Genome Sequence at 12X coverage and MeDIP-Seq data, to identify regions under selection and those differentially methylated. For both species, the analysis of genetic differences (F_ST) along the genome between animals from localities with high vs. low temperature annual variations detected candidate genes under selection in relation to environmental perception (5 genes), immunity (4 genes), reproduction (8 genes) and production (11 genes). Moreover, we found for each species one differentially methylated gene, namely AGPTA4 in goat and SLIT3 in sheep, which were both related, among other functions, to milk production and muscle development. In both sheep and goats, the comparison between genomic regions impacted by genetic and epigenetic variations suggests that climatic variations impacted similar biological pathways but different genes.

Detection of Genomic Regions with Pleiotropic Effects for Growth and Carcass Quality Traits in the Rubia Gallega Cattle Breed

Simple Summary

The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. We have developed a ssGWAS by backsolving the SNP effects after implementing a ssGBLUP. The results showed an apparent heterogeneity of the additive genetic variance across the genome. Some of the genomic regions explaining the most of this additive variance were shared across traits, indicating the presence of pleiotropic effects, which were reflected in their genetic correlations.

Abstract

The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS (single-step Genome Wide Association Studies) by backsolving the SNP (single nucleotide polymorphisms) effects. Therefore, the objective of this study was to identify genomic regions associated with the genetic variability in growth and carcass quality traits. We implemented a ssGBLUP by using a database that included records for Birth Weight (BW-327,350 records-), Weaning Weight (WW-83,818-), Cold Carcass Weight (CCW-91,621-), Fatness (FAT-91,475-) and Conformation (CON-91,609-). The pedigree included 464,373 individuals, 2449 of which were genotyped. After a process of filtering, we ended up using 43,211 SNP markers. We used the GBLUP and SNPBLUP model equivalences to obtain the effects of the SNPs and then calculated the percentage of variance explained by the regions of the genome between 1 Mb. We identified 7 regions of the genome for CCW; 8 regions for BW, WW, FAT and 9 regions for CON, which explained the percentage of variance above 0.5%. Furthermore, a number of the genome regions had pleiotropic effects, located at: BTA1 (131–132 Mb), BTA2 (1–11 Mb), BTA3 (32–33 Mb), BTA6 (36–38 Mb), BTA16 (24–26 Mb), and BTA 21 (56–57 Mb). These regions contain, amongst others, the following candidate genes: NCK1, MSTN, KCNA3, LCORL, NCAPG, and RIN3.

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility

Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to assess ejaculate volume, sperm concentration, sperm motility, sperm head and tail anomalies and insemination success. The heritability of the six semen traits was between 0 and 0.26. Genome-wide association testing on 607,511 SNPs revealed a QTL on bovine chromosome 6 that was associated with sperm motility (P = 2.5 x 10⁻²⁷), head (P = 2.0 x 10⁻⁴⁴) and tail anomalies (P = 7.2 x 10⁻⁴⁹) and insemination success (P = 9.9 x 10⁻¹³). The QTL harbors a recessive allele that compromises semen quality and male fertility. We replicated the effect of the QTL on fertility (P = 7.1 x 10⁻³²) in an independent cohort of 2481 Brown Swiss bulls. The analysis of whole-genome sequencing data revealed that a synonymous variant (BTA6:58373887C>T, rs474302732) in WDR19 encoding WD repeat-containing protein 19 was in linkage disequilibrium with the fertility-associated haplotype. WD repeat-containing protein 19 is a constituent of the intraflagellar transport complex that is essential for the physiological function of motile cilia and flagella. Bioinformatic and transcription analyses revealed that the BTA6:58373887 T-allele activates a cryptic exonic splice site that eliminates three evolutionarily conserved amino acids from WDR19. Western blot analysis demonstrated that the BTA6:58373887 T-allele decreases protein expression. We make the remarkable observation that, in spite of negative effects on semen quality and bull fertility, the BTA6:58373887 T-allele has a frequency of 24% in the Brown Swiss population. Our findings are the first to uncover a variant that is associated with quantitative variation in semen quality and male fertility in cattle.

In cattle farming, artificial insemination is the most common method of breeding. To ensure high fertilization rates, ejaculate quality and insemination success are closely monitored in artificial insemination bulls. We analyse semen quality, insemination success and microarray-called genotypes at more than 600,000 genome-wide SNP markers of 794 bulls to identify a recessive allele that compromises semen quality. We take advantage of whole-genome sequencing to pinpoint a variant in the coding sequence of WDR19 encoding WD repeat-containing protein 19 that activates a novel exonic splice site. Our results indicate that cryptic splicing in WDR19 is associated with reduced male reproductive performance. This is the first report of a variant that contributes to quantitative variation in bovine semen quality.

Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa

Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%-98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise F ST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise F ST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.