Speed Index in the Racing Quarter Horse: A Genome-wide Association Study

The racing line of Quarter Horses is characterized by great sprinting speed over short distances on straight tracks. To perform selection on racing horses, the speed index (SI) and conformation traits are often used. A genome-wide association study (GWAS) on 112 racing Quarter Horses was performed for the SI trait, and markers and genes associated were reported. The GWAS was carried out using the Qxpak.5 software and the genotyping data obtained from the Equine SNP50 BeadChip. A total of eight significant single-nucleotide polymorphisms (SNPs) (P < .0001; Q = 0.25) distributed on Equus caballus autosomal chromosomes 2, 4, 10, 18, and 27 were found and served as markers for genomic regions mined for candidate genes associated with SI. For candidate gene, annotation was considered 100 kb windows upstream and downstream to each important SNP. The highlighted genes were GRM8, GRIK2, NEB, ANK1, and KAT6A because their function could be related to racing performance. Future studies should consider a validation study with an independent population, and sequencing of these candidate genes should be done to identify causal alleles.     

Impact of MYOD family genes on pork traits in Large White and Landrace pigs

Summary Porcine myogenic differentiation genes ( MYOD ) family play a key role in growth and muscle development and are therefore considered as candidate genes for meat production traits. The objective of the study was to investigate the polymorphisms at four loci belonging to the MYOD genes family and analyse their associations with variation in meat production traits in Czech pig breeds. To verify the associations between the polymorphisms and the selected meat traits, altogether 254 pigs, including full- and half-sibs, of Large White and Landrace breeds were tested. The studied meat characteristics were weight of neck, loin, shoulder and ham, lean meat content (LMC), backfat thickness, intramuscular fat (IMF), remission, dry matter content and test daily gain. Statistically significant associations were observed between MYOG gene and fat and neck weight, and between MYF5 gene and IMF and LMC. High significant differences were observed between genotypes AA and AB of MYOD1 in IMF and between genotypes AB and BB of MYF5 in loin weight.     

A Genome-Wide Association Study for Morphometric Traits in Quarter Horse

A genome-wide association study for morphometric traits was conducted in 184 Quarter Horses, 120 from a racing population, and 64 from a cutting population, which were genotyped using the Illumina EquineSNP50 chip. Association analysis was performed with 42,058 single-nucleotide polymorphisms (SNPs) (after quality control) using Qxpak5 software. The following traits were measured: weight (W), rump length (RL), and body length (BL). These morphometric traits are important for the best performance in race and cutting events. For weight, three SNPs associated (P < .0001) were found on chromosomes (Equus caballus autosomes [ECA]) 2 and 3. For rump length, eight SNPs associated (P < .0001) were found on ECA 2, 3, 6, 7, 9, 21, and 26. On ECA 3 and ECA 8, two SNPs were associated (P < .0001) with body length. So, a total of 13 important chromosomal regions were identified with Q values of 0.53 (SNPs for W), 0.40 (SNPs for RL), and 0.99 (SNPs for BL). Positional and functional candidate genes emerging from this study were WWOX and AAVPR1A. Further studies are required to confirm these associations in other populations.     

Polymorphisms in MCT1, CD147, PDK4, and DMRT3 genes in Arabian and Quarter Horses

Monocarboxylate transporter isoform 1 (MCT1) and its ancillary protein, CD147 function to transport H⁺ and lactate ions, retarding systemic acidosis and fatigue. The PDK4 gene is involved in the adenosine triphosphate production, and the DMRT3 gene is involved in the locomotor system. This study investigated polymorphisms of MCT1, CD147, PDK4, and DMRT3 in Arabian and Quarter Horses to associate polymorphisms with performance. Arabian Horses were divided into high performance and untrained horses groups based on success in endurance competition, whereas Quarter Horses were separated by a speed index. Polymorphisms were analyzed by sequencing (MCT1 and CD147), ARMS-PCR (PDK4), and PCR-RFLP (DMRT3). To compare the frequencies of SNPs, the Fisher's exact test was performed in the software R at 5% of significance. The A alleles from the polymorphisms Lys457Gln:1573A>C of MCT1 and Ile51Val:168A>G of CD147 were essentially fixed in both breeds. Only two Arabian from the high performance and one from the untrained horses group appeared AC in MCT1. For the DMRT3 polymorphism (g.22999655C>A:ECA23), all the animals were CC, except one Arabian in the high and two Quarter Horses in the low performance group that were AC. For the PDK4 polymorphism (g.38973231A>G:ECA4), Arabian showed a significantly greater frequency of the G allele than Quarter Horses (P < .01). Considering the kind of exercise practiced by each breed, it is likely that the PDK4 polymorphism influences the pathway to energy production.     

Evaluation of candidate genes related to litter traits in Indian pig breeds

Improvement in litter traits is the key to profitable pig farming that directly enhances the economic standing of the farmers in developing countries. The present study aimed to explore oestrogen receptor (ESR), epidermal growth factor (EGF), follicle-stimulating hormone beta subunit (FSHβ), prolactin receptor (PRLR) and retinol-binding protein 4 (RBP4) genes as possible candidate genetic markers for litter traits in indigenous pigs of India. The breeds included in the study were Ghungroo, Mali, Niang Megha and Tenyi Vo, and the reproductive traits considered were litter size at birth (LSB), number born alive (NBA), litter weight at birth (LWB), litter size at weaning (LSW) and litter weight at weaning (LWW) at their first parity. PCR-RFLP and primer-based mutation detection methods were used to identify polymorphism, and associations between the genotypes and the traits were analysed using a general linear model. The Ghungroo pigs recorded the best litter performances among the breeds (p < .05, LWB p < .01). Different alleles and genotypes of the genes under study were detected. Short interspersed nuclear element (SINE) −/− genotype of FSHβ revealed significantly higher litter traits (p < .05, LSB p < .01). The LWW was also found to be significantly influenced by ESR BB and AB, EGF AB and BB, and PRLR CC genotypes (p < .05). Although we did not find statistically significant and consistently superior litter traits with respect to different genotypes of other studied genes than genotype SINE −/− of the FSHβ, PRLR CC genotype demonstrated superior performances for all the litter traits. Our study revealed the FSHβ as a potential candidate genetic marker for litter traits in indigenous pig breeds of India.     

Multivariate genetic analysis to account for preselection and disqualified races in the genetic evaluation of racing performances in German trotters

Abstract

The genetic associations between racing performance and preselection of horses considered as the binary trait racing status (trotters without or with at least one racing performance in life were classified as 0 and 1, respectively) as well as disqualified races (disqualified and non-disqualified trotters were classified as 1 and 0, respectively) were analysed in German trotters. Variance components for racing performance traits square root of rank at finish, racing time per km, and log of earnings with racing status were estimated based on an animal model using REML. Heritabilities of racing status, racing time and rank at finish were 0.30, 0.21, and 0.06, respectively. The genetic correlations between racing status and racing time or rank at finish were ?0.74 and ?0.32, indicating that horses started at least once showed a higher genetic potential in racing time or finishing ability than never started horses. This showed the high preselection of German trotters especially based on racing time. To account for this preselection, it was recommended for additional use of racing status in the German evaluation system. Breeding values of the three racing performance traits were estimated by two distinct models, in- or excluding racing status and compared by using three criteria. Racing time per km showed the highest correlation (r=0.98) between breeding values evaluated by these two distinct models. Therefore, incorrect selection rate of horses using breeding values from the model without racing status, was lowest for racing time per km (9.7%). Selection response increased about 1% for this trait after including racing status in the model. For the estimation of rank at finish, inclusion of racing status in the multiple trait model was much more important as indicated by a low correlation between breeding values (r=0.29) and high percentage of incorrectly selected stallions (97.5%). The trait disqualified races was first analysed using an univariate threshold model. Heritability of this trait was low (h ²=0.12) and repeatability (r=0.43) showed a moderate magnitude. Using a linear multiple trait animal model, disqualified races showed a low heritability (h ²=0.05) and a moderate favourable genetic correlation (r _g=0.43) with racing time per km. Consequently, selection on racing time per km is expected to improve indirectly the reliability of racing performance. Combined selection of reduction in disqualified races and racing time may even further improve the reliability of racing trotters.     

Frequency distribution of a Cys430Ser polymorphism in peroxisome proliferator-activated receptor-gamma coactivator-1 (PPARGC1) gene sequence in Chinese and Western pig breeds

Identification of major genes, that genetically impact fat tissue formation is important for successful selection of lean animals with good meat quality. Because of its central role in fat cell differentiation and muscle fibre type determination, PPARGC1 is a potential candidate gene affecting fattening traits and pig meat quality. In this study, a T/A substitution at position 1378 (GenBank accession no. AY346131 ) in the porcine PPARGC1 gene causing a Cys430Ser amino acid substitution at position 430 was genotyped on a total of 239 animals, including 101 from seven Chinese and 138 from six Western pig breeds. Bayesian analysis revealed that the mean frequency of allele T (Cys) was 92.64 ± 4.82% in Chinese pigs, and 45.99 ± 4.13% in Western pigs. The 95% interval of the posterior mean frequency of allele T was 0.82–1.00 in Chinese pigs and 0.38–0.54 in Western pigs, indicating these two groups of pigs diverged at this locus during genetic evolution of the breed. Because marked differences in fat and lean tissue deposition exist between Western and Chinese pig breeds, this Cys430Ser exchange in the PPARGC1 gene deserves further evaluation to determine its phenotypic effect on fattening and carcass traits in commercial pig populations.     

Affecting Lipid Metabolism Salivary MicroRNAs Expressions in Arabian Racehorses Before and After the Race

The active roles of microribonucleic acids (miRNAs) in gene regulation have made miRNAs a key point for the scientific world in the study of physiological processes. Although saliva includes the largest number of miRNAs, there is no miRNA study in saliva on horses has been found. Our study is the first study on miRNAs isolation from saliva in horses. In the present study, saliva was studied in Arabian racehorses to better understand the molecular mechanisms of expression levels that are effective in lipid metabolism of miRNAs and their target genes during the race. Identification of lipid metabolism of miRNAs and their target genes is an opportunity to provide information about biomarkers in Arabian racehorses on energy supply for race performance. Arabian racehorses have low glycogen content and high triglyceride storage capability, thanks to the high amount of oxidative type I fiber in their muscle tissue. Therefore, Arabian racehorses can provide higher levels of energy using more fat. The aim of this study is to determine the prerace and postrace expression levels of eight miRNAs in saliva that are known to affect lipid metabolism in Arabian racehorses. The expression level of eca-miR-33a was found to be statistically significant (P < .05). Target genes of eca-miR-33a have been copredicted as ABCA1, CROT, ABHD2, and SATB2, with three validated databases and other analysis tools. In conclusion, these findings revealed that both eca-miR-33a and its target genes could be potential core genes that play important roles in lipid metabolism in Arabian racehorses to provide energy during the race.     

中国不同牛种DGAT1基因遗传多样性及经济性状关联分析研究进展

乙酰辅酯A∶二酰甘油酰基转移酶(DGAT1)是甘油三脂合成过程中唯一的关键酶,对动物机体脂肪代谢、沉积起重要作用,已成为研究奶牛泌乳性状和肉牛主要经济性状的重要候选基因之一。近年来,随着相关研究的不断深入,研究者普遍认为DGAT1基因对奶牛的产奶量、乳脂率、乳蛋白率、乳糖率、乳脂肪酸及空怀天数、输精次数、初配年龄等繁殖性状均有显著影响,且与肉牛体脂也存在相关性。作者主要介绍了DGAT1基因的遗传多态性及其与经济性状关联分析在中国各地区不同品种奶牛、肉牛、水牛和牦牛上的研究进展,指出该基因对奶牛的产奶性能及肉牛的肉质性状、生长性状具有重要的调控作用。但由于环境条件、品种及选育背景等因素影响,DGAT1基因遗传多态性对不同地区不同牛群体的经济性状影响不尽相同。因此,要将DGAT1基因实际应用在品种选育工作中还需明确该基因对研究群体的具体遗传效应,并结合其他候选基因进行综合分析。     

Identification of new semen trait-related candidate genes in Duroc boars through genome-wide association and weighted gene co-expression network analyses

Semen traits are crucial in commercial pig production since semen from boars is widely used in artificial insemination for both purebred and crossbred pig production. Revealing the genetic architecture of semen traits potentially promotes the efficiencies of improving semen traits through artificial selection. This study is aimed to identify candidate genes related to the semen traits in Duroc boars. First, we identified the genes that were significantly associated with three semen traits, including sperm motility (MO), sperm concentration (CON), and semen volume (VOL) in a Duroc boar population through a genome-wide association study (GWAS). Second, we performed a weighted gene co-expression network analysis (WGCNA). A total of 2, 3, and 20 single-nucleotide polymorphisms were found to be significantly associated with MO, CON, and VOL, respectively. Based on the haplotype block analysis, we identified one genetic region associated with MO, which explained 6.15% of the genetic trait variance. ENSSSCG00000018823 located within this region was considered as the candidate gene for regulating MO. Another genetic region explaining 1.95% of CON genetic variance was identified, and, in this region, B9D2, PAFAH1B3, TMEM145, and CIC were detected as the CON-related candidate genes. Two genetic regions that accounted for 2.23% and 2.48% of VOL genetic variance were identified, and, in these two regions, WWC2, CDKN2AIP, ING2, TRAPPC11, STOX2, and PELO were identified as VOL-related candidate genes. WGCNA analysis showed that, among these candidate genes, B9D2, TMEM145, WWC2, CDKN2AIP, TRAPPC11, and PELO were located within the most significant module eigengenes, confirming these candidate genes’ role in regulating semen traits in Duroc boars. The identification of these candidate genes can help to better understand the genetic architecture of semen traits in boars. Our findings can be applied for semen traits improvement in Duroc boars.     

Associations of natural variation in the CD163 and other candidate genes on host response of nursery pigs to porcine reproductive and respiratory syndrome virus infection

Pigs with complete resistance to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) have been produced by genetically knocking out the CD163 gene that encodes a receptor of the PRRSV for entry into macrophages. The objectives of this study were to evaluate associations of naturally occurring single nucleotide polymorphisms (SNPs) in the CD163 gene and in three other candidate genes (CD169, RGS16, and TRAF1) with host response to PRRSV-only infection and to PRRS vaccination and PRRSV/porcine circovirus 2b (PCV2b) coinfection. SNPs in the CD163 gene were not included on SNP genotyping panels that were used for previous genome-wide association analyses of these data. An additional objective was to identify the potential genetic interaction of variants at these four candidate genes with a mutation in the GBP5 gene that was previously identified to be associated with host response to PRRSV infection. Finally, the association of SNPs with expression level of the nearby gene was tested. Several SNPs in the CD163, CD169, and RGS16 genes were significantly associated with host response under PRRSV-only and/or PRRSV/PCV2b coinfection. The effects of all SNPs that were significant in the PRRSV-only infection trials depend on genetic background. The effects of some SNPs in the CD163, CD169, and RGS16 genes depend on genotype at the putative causative mutation in the GBP5 gene, which indicates a potential biological interaction of these genes with GBP5. In addition, genome-wide association results for the PRRSV-only infection trials revealed that SNPs located in the CDK5RAP2 or MEGF9 genes, near the TRAF1 gene, had suggestive effects on PRRS viral load, which indicates that these SNPs might contribute to PRRSV neuropathogenesis. In conclusion, natural genetic variants in the CD163, CD169, and RGS16 genes are associated with resistance to PRRSV and/or PCV2b infection and appear to interact with the resistance quantitative trait locus in the GBP5 gene. The identified SNPs can be used to select for increased natural resistance to PRRSV and/or PRRSV-PCV2b coinfection.     

Association analysis of novel polymorphisms in 2′, 5′‐oligoadenylate synthetase gene with reproductive traits in indigenous and cross‐bred cattle of Indian Origin

2′, 5′‐Oligoadenylate synthetases (OAS) are important components of an interferon‐mediated antiviral pathway. No polymorphisms in exonic regions of bovine OAS1 gene have been identified and associated with reproduction traits. The objective of the study was to detect and evaluate the effects of mutations in exonic region of bovine OAS1 gene with reproduction traits in cattle. DNA samples collected from 250 individual cows of two Indian dairy breeds (Sahiwal and Frieswal) of cattle were used in the study. The genetic variants of the OAS1 gene were identified with polymerase chain reaction–single‐strand conformation polymorphism (PCR‐SSCP) and sequence analysis using seven set of primer pairs. The PCR‐SSCP analysis revealed polymorphism in the fragments comprising of exon 2, exon 5 and first fragment of exon 6 while the fragments of exons 1, 3, 4 and second fragment of exon 6 were monomorphic in Sahiwal and Frieswal cattle. The mutations in the amplified region comprising of exon 2 were found to have significant association with age at first breeding and calving, service period, dry period and pregnancy rate. Significant associations were found between SNPs in the exon 5 and service and dry periods of the animal, whereas the genetic variants in the first fragment of the exon 6 showed significant association with age at first breeding and calving. To our knowledge, this study demonstrated for the first time that the polymorphisms in OAS1 gene were associated with reproductive traits and it can be chosen as a candidate gene for improvement of reproductive performance of cattle.     

SNP genetic polymorphisms of MDR-1, CYP1A2 and CYPB11 genes in four canine breeds upon toxicological evaluation

The fields of pharmacogenetics and pharmacogenomics have become increasingly promising regarding the clinical application of genetic data to aid in prevention of adverse reactions. Specific screening tests can predict which animals express modified proteins or genetic sequences responsible for adverse effects associated with a drug. Among the genetic variations that have been investigated in dogs, the multidrug resistance gene (MDR) is the best studied. However, other genes such as CYP1A2 and CYP2B11 control the protein syntheses involved in the metabolism of many drugs. In the present study, the MDR-1, CYP1A2 and CYP2B11 genes were examined to identify SNP polymorphisms associated with these genes in the following four canine breeds: Uruguayan Cimarron, Border Collie, Labrador Retriever and German Shepherd. The results revealed that several SNPs of the CYP1A2 and CYP2B11 genes are potential targets for drug sensitivity investigations.     

Genome‐wide association study for fatty acid composition in Japanese Black cattle

Fatty acid composition is one of the important traits in beef. The aim of this study was to identify candidate genomic regions for fatty acid composition by genome‐wide association study with 50 K single nucleotide polymorphism (SNP) array in Japanese Black cattle. A total of 461 individuals and 40 657 SNPs were used in this study. We applied genome‐wide rapid association using mixed model and regression (GRAMMAR) and genomic control approaches to estimate the associations between genotypes and fatty acid composition. In addition, two SNPs in fatty acid synthase (FASN) (T1952A) and stearoyl‐CoA desaturase (SCD) (V293A) genes were also genotyped. Association analysis revealed that 30 significant SNPs for several fatty acids (C14:0, C14:1, C16:1 and C18:1) were located in the BTA19 FASN gene located within this region but the FASN mutation had no significant effect on any traits. We also detected one significant SNP for C18:1 on BTA23 and two SNPs for C16:0 on BTA25. The region around 17 Mb on BTA26 harbored two significant SNPs for C14:1 and SNP in SCD in this region showed the strongest association with C14:1. This study demonstrated novel candidate regions in BTA19, 23 and 25 for fatty acid composition.     

Phenotypic and genetic parameter estimates for racing traits of Arabian horses in Turkey

The racing records for Arabian horses used in the study were obtained from the Turkish Jockey Club. The traits used in the study were racing time, best racing time, rank, annual earnings, earnings per start, log annual earnings and log earnings per start. Genetic parameters were estimated by the restricted maximum likelihood (REML) procedure using the DFREML program. The effects of age, sex and origin of horse were significant for each trait. The effect of year was significant on time and earning traits, but not rank. The effect of month on time traits was also significant. Heritability estimates of the entire data set were 0.280, 0.281, 0.069, 0.139, 0.174, 0.152 and 0.171 for racing time, best racing time, rank, annual earnings, earnings per start, log annual earnings and log earnings per start respectively. Estimates of repeatability varied from 0.349 to 0.500 for racing time, from 0.430 to 0.524 for best racing time and from 0.129 to 0.171 for rank depending on the data set used in the analyses. Best racing time was the most appropriate trait for selection in this study, as this might lead to genetic improvement than other traits.     

Genetic mapping using 1.4M SNP array refined loci for fatty acid composition traits in Chinese Erhualian and Bamaxiang pigs

Chinese indigenous pigs display marked genetic and phenotypic differences compared with western commercial pigs. In this study, we tested the association between 660K SNPs and longissimus muscle fatty acid composition traits in Chinese Erhualian (n = 331) and Bamaxiang (n = 315) pigs based on a customized 1.4 million SNP array. We identified a total of 64 significant associations for 20 fatty acid composition traits at the p‐value threshold of 1 × 10^?6 among which 42 associations in low linkage disequilibrium (r² < .2) with previously reported loci were considered novel. We substantially improved the strength and precision of the associations at four previously detected loci near FADS2, ELOVL7, ELOVL6 and FASN genes, facilitating follow‐up candidate gene studies. Moreover, we also identified loci near ABCD2, ACSBG1, ELOVL5, HPGDS, DAGT2, ACAD10 and ACSL1 genes with function relevant to metabolism of fatty acids. In this study, valuable genetic variants and candidate genes associated with fatty acid composition traits were identified in Erhualian and Bamaxiang pigs. Some identified loci could be used to improve pork nutrition in pig breeding practice. Using the SNP array with higher marker density and less ascertainment bias improved QTL detection power and precision in Chinese indigenous pigs.     

几个中国地方猪群体遗传结构和产仔数性状选择信号分析

旨在对几个中国地方猪品种进行群体遗传结构分析,并筛选与中国地方猪产仔数相关的基因组选择信号及候选基因.本研究下载了6个中国地方品种猪共计102头个体的Illumina PorcineSNP60芯片数据,构建了包括19头迪庆藏猪、16头明光小耳猪、16头五指山猪在内的低产仔数组和包括11头姜曲海猪、20头蓝塘猪、20头梅...     

Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep

Ovulation rate and prolificacy are the most important reproductive traits that have major impact on the efficiency of lamb meat production. Here, we compared the whole genomes of the Romanov sheep, known as one of the high prolific breeds, and four other sheep breeds namely Assaf, Awassi, Cambridge and British du cher, to identify genetic mechanisms underlying prolificacy in sheep. Selection signature analysis revealed 637 and 477 protein‐coding genes under positive selection from F_ST and nucleotide diversity (Pi) statistics, respectively. Further analysis showed that several candidate genes including LEPR, PDGFRL and KLF5 genes are involved in sheep prolificacy. The identified candidate genes in the selected regions are novel and provide new insights into the genetic mechanisms underlying prolificacy in sheep and can be useful in sheep breeding programmes to develop improved breeds for high reproductive efficiency.