RESUMO
Birth and weaning weights, average daily weight gain, and Kleiber ratio are important indicator traits in selection decision. The phenotypic expression of these traits is determined by the genetic background, environmental effects, and their interactions. The objective of this study was to estimate genetic parameters regarding birth (BW) and weaning weights (WW) and average daily weight gain (ADWG), Kleiber ratio (KR), and obtain the effects of sex, birth type, herd, and year. The data consisted of 2274 Kilis goats with pedigree information obtained from 53 bucks and 774 does in 4 generations. The restricted maximum likelihood (REML) procedure was conducted with an animal linear mixed model. Sex, birth type, herd, and year were found to be statistically significant (p value < 0.001) for all traits. Moderate direct heritabilities (ha2) for BW, WW, ADW, and KR were found to be as 0.18 ± 0.03, 0.50 ± 0.04, 0.47 ± 0.04, and 0.37 ± 0.05, respectively. The proportion of maternal permanent environmental effect (c2) to the total phenotypic variance (σ2p) was estimated as 0.00 ± 0.00, 0.12 ± 0.02, 0.11 ± 0.02, and 0.18 ± 0.03 for BW, WW, ADWG, and KR, respectively. The genetic, phenotypic, and environmental correlations between the pre-weaning growth traits were found to be ranging from - 0.02 to 0.99. Thus, our study suggests moderate heritabilities and positive and relatively high genetic correlations among the observed pre-weaning growth traits. These results have implications in terms of providing rapid genetic progress for these traits in breeding programs of Kilis goats.
Assuntos
Cabras , Aumento de Peso , Animais , Peso Corporal/genética , Desmame , Cabras/genética , Aumento de Peso/genética , Peso ao Nascer/genética , FenótipoRESUMO
Sheep are considered as a major contributor of global food security. Moreover, sheep preweaning growth traits as well as in vivo carcass composition traits such as ultrasonic measurements of Longissimus dorsi muscle depth (UMD) and back-fat thickness (UFD) are crucially important indicators of meat yield and hot carcass composition. Despite their relative importance for productivity and profitability of a sheep production system, detected QTL for these traits are quite scarce. Therefore, we implemented GWAS for these traits using animal mixed model-based association approach provided by GenABEL in Esme sheep. Three genome-wide and 14 individual chromosome-wide associated SNPs were discovered. As a result, ESRP1, LOC105613082, ZNF641, DUSP5, TEAD1, SMOX, PTPRT, RALYL, POM121C, PHIP, LOC101106051, ZIM3, PEG3, TRPC7, FBXL4, LOC105610397, LOC105616489 and DNAAF2 were suggested as candidates. Some of the discovered genes and involved pathways were already annotated to contribute growth and development in various species including human, mice and cattle. All in all, the results of this study are expected to strongly contribute to shed a light on the underlying molecular mechanisms behind growth and carcass composition traits, with potential implications on studies aiming faster genetic improvement, targeted low-resolution SNP panel designs and genome-editing studies.
Assuntos
Estudos de Associação Genética/veterinária , Locos de Características Quantitativas , Ovinos , Animais , Composição Corporal/genética , Carne/análise , Camundongos , Fenótipo , Polimorfismo de Nucleotídeo Único , Ovinos/genéticaRESUMO
Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [-log10(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log10(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.
Assuntos
Cruzamento/métodos , Indústria de Laticínios , Estudo de Associação Genômica Ampla , Cabras/genética , Lactação/genética , Glândulas Mamárias Animais/anatomia & histologia , Animais , Indústria de Laticínios/métodos , Feminino , Membro Anterior/anatomia & histologia , Marcadores Genéticos , Genômica/métodos , Genótipo , Membro Posterior/anatomia & histologia , Casco e Garras/anatomia & histologia , Leite/química , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genéticaRESUMO
Male reproductive parameters are often used for the functional examination and evaluation of predicted genetic values for future aspects. However, these traits are relatively reliable until the measurable effects are expressed on desired traits. Therefore, we aimed to associate the single nucleotide polymorphism (SNP) genotype of the investigated characteristics and reproductive loci. A total of 46 male dogs are divided into three age groups (I ≤ 3 years, n = 19; II 4-6 years; n = 19, and III ≥7 years, n = 8). The testis, scrotum and body weight, libido sexualis and ejaculation time for each fraction were monitored as functional traits, while the pH, fractional semen volume, motility, concentration, and abnormal and dead spermatozoa rate were recorded as spermatological traits. The Affymetrix Canine 127 K SNP genotyping array v2 (Affymetrix Inc., California, USA) was used for SNP genotyping. In the primary results, the scrotal circumference was found to be higher in group II compared to other groups (p < 0.05) and the lowest total abnormal spermatozoa rate was found in group I (p < 0.05). The normal spermatozoa rate was found to be significantly above the threshold in relation to the SNP in chromosome 17. In conclusion, this study represents an exciting first step towards SNP association with dog semen spermatological parameters. Future studies might be undertaken to evaluate this SNP region for gene-knockout and expression analysis and for fine mapping to validate and/or discover the exact position of the effect region.
Assuntos
Cães/genética , Reprodução/genética , Espermatozoides/fisiologia , Fatores Etários , Animais , Ejaculação/fisiologia , Estudo de Associação Genômica Ampla , Libido/fisiologia , Masculino , Polimorfismo de Nucleotídeo Único , Escroto/anatomia & histologia , Análise do Sêmen/veterinária , Motilidade dos Espermatozoides/genética , Testículo/anatomia & histologiaRESUMO
Serum biochemical indicators serve as vital proxies that reflect the physiological state and functions of different organs. The genetic parameters and molecular mechanisms underlying serum biochemical indicators of sheep (Ovis aries) have not been well understood. Therefore, the aim of the present study was to identify the genetic architecture and genomic loci underlying ten serum biochemical indicators in sheep, including alanine transaminase, aspartate transferase, lactate dehydrogenase, cholesterol, glucose, phosphorus, calcium, creatinine, urea and total protein levels. We implemented genetic parameter estimations and GWASs for each trait in 422 Akkaraman lambs. Overall, low to moderate heritability estimates were found in the range of 0.14-0.55. Additionally, low to high genetic correlations were observed among traits. In total, 23 SNP loci were associated with serum biochemical indicators leading to 19 genes. These were SPTA1, MGST2, CACUL1, IGFBP7, PARD3, PHB1, SLC15A5, TRIM35, RGS6, NUP93, CNTNAP2, SLC7A11, B3GALT5, DPP10, HST2ST1, NRP1, LRP1B, MAP3K9 and ENSOARG00020040484.1, as well as LOC101103187, LOC101117162, LOC105611309 and LOC101118029. To our knowledge, these data provide the first associations between SPTA1 and serum cholesterol and between ENSOARG00020040484.1 and serum glucose. The current findings provide a comprehensive inventory of the relationships between serum biochemical parameters, genetic variants and disease-relevant characteristics. This information may facilitate the identification of therapeutic targets and fluid biomarkers and establish a strong framework for comprehending the pathobiology of complex diseases as well as providing targets for sheep genetic improvement programs.
Assuntos
Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Animais , Ovinos/genética , Ovinos/sangue , Estudo de Associação Genômica Ampla , Colesterol/sangue , Biomarcadores/sangueRESUMO
The objective of this study was to uncover the genetic background of wool quality, a production trait, by estimating genomic heritability and implementing GWAS in Akkaraman sheep. The wool characteristics measured included fibre diameter (FD) and staple length (SL) at the age of 8 months and yearling fibre diameter (YFD), yearling staple length (YSL) and yearling greasy fleece weight (YGFW) at 18 months of age. Animals were genotyped using the Axiom 50 K Ovine Genotyping Array. Maximum likelihood estimations of a linear mixed model (LMM) were used to estimate genomic heritability, where GWAS was conducted following a score test of each trait. Genomic heritability estimates for the traits ranged between 0.22 and 0.63, indicating that phenotypes have a moderate range of heritability. One genome- and six chromosome-wide significant SNPs were associated with the wool traits in Akkaraman lambs. Accordingly, TRIM2, MND1, TLR2, RNF175, CEP290, TMTC3, RERE, SLC45A1, SOX2, MORN1, SKI, FAAP20, PRKCZ, GABRD, CFAP74, CALML6 and TMEM52 genes as well as nine uncharacterized regions (LOC101118971, LOC105609137, LOC105603067, LOC101122892, LOC106991694, LOC106991467, LOC106991455, LOC105616534 and LOC105609719) were defined as plausible candidates. The findings of this study shed light on the genetics of wool quality and yield for the Akkaraman breed and suggests targets for breeders during systematic breeding programmes.
Assuntos
Genoma , Lã , Ovinos , Animais , Fenótipo , Genótipo , Genoma/genética , GenômicaRESUMO
The aim of this study was to estimate genomic heritability and the impact that genetic backgrounds have on blood parameters in Akkaraman sheep by conducting genome-wide association studies and regional heritability mapping analysis. Genomic heritability estimates for blood parameters ranged from 0.00 to 0.55, indicating that measured phenotypes have a low to moderate heritability. A total of 7 genome- and 13 chromosome-wide significant SNPs were associated with phenotypic changes in 15 blood parameters tested. Accordingly, SCN7A, SCN9A, MYADM-like, CCDC67, ITGA9, MGAT5, SLC19A1, AMPH, NTRK2, MSRA, SLC35F3, SIRT6, CREB3L3, and NAV3 genes as well as three undefined regions (LOC101117887, LOC106991526 and LOC105608461) were suggested as candidates. Most of the identified genes were involved in basic biological processes that are essential to immune system function and cellular growth; specific functions include cellular transport, histone deacetylation, cell differentiation, erythropoiesis, and endocytosis. The top significant SNP for HCT, MCH, and MCHC was found within a genomic region mainly populated by the MYADM-like gene family. This region was previously suggested to be under historical selection pressure in many sheep breeds from various parts of the world. These results have implications on animal breeding program studies due to the effect that the genetic background has on blood parameters, which underlying many productive and wellness related traits.
Assuntos
Estudo de Associação Genômica Ampla , Genoma , Ovinos/genética , Animais , Estudo de Associação Genômica Ampla/métodos , Genômica , Polimorfismo de Nucleotídeo Único , FenótipoRESUMO
Genome-wide association studies (GWAS) have been used as an effective tool to understand the genetics of complex traits such as gastrointestinal parasite (GIP) resistance. The aim of this study was to understand the genetics of gastrointestinal parasite (nematodes, Moniezia spp., Eimeria spp.) resistance in Akkaraman sheep by performing genomic heritability estimations and conducting GWAS to uncover responsible genomic regions. This is one of the first studies to examine the genetic resistance of Akkaraman sheep to the tapeworm parasite. The samples from 475 animals were genotyped using the Axiom 50K Ovine Genotyping Array. Genomic heritability estimates ranged from 0.00 to 0.34 for parasite resistance traits. This indicates that measured phenotypes have low to moderate heritability estimates. A total of two genome-wide significant SNP associated with TNEM3 and ATRNL1 genes and 10 chromosome-wide significant SNPs related with 10 genes namely NELL1, ST6GALNAC3, HIPK1, SYT1, ALK, ZNF596, TMCO5A, PTH2R, LARGE1, and SCG2 were suggested as candidates for parasite resistance traits. The majority of these candidate genes were involved in several basic biological processes that are essential and important for immune system functions and cellular growth; specifically, inflammatory responses, cellular transport, cell apoptosis, cell differentiation, histone de-acetylation, and endocytosis. These results have implications for animal breeding program studies due to the effect that the genetic background has on parasite resistance, which underlies many productive, health, and wellness-related traits.
Assuntos
Nematoides , Parasitos , Ovinos/genética , Animais , Estudo de Associação Genômica Ampla/veterinária , Nematoides/fisiologia , Genótipo , GenômicaRESUMO
In the current study, the genetic architecture of growth and linear type traits were investigated in Akkaraman sheep. Estimations of genomic heritability, genetic correlations, and phenotypic correlations were implemented for 17 growth and linear type traits of 473 Akkaraman lambs by the univariate and multivariate analysis of animal mixed models. Correspondingly, moderate heritability estimates, as well as high and positive genetic/phenotypic correlations were found between growth and type traits. On the other hand, 2 genome-wide and 19 chromosome-wide significant single nucleotide polymorphisms were found to be associated with the traits as a result of animal mixed model-based genome-wide association analyses. Accordingly, we propose several genes located on different chromosomes (e.g., PRDM2, PTGDR, PTPRG, KCND2, ZNF260, CPE, GRID2, SCD5, SPIDR, ZNF407, HCN3, TMEM50A, FKBP1A, TLE4, SP1, SLC44A1, and MYOM3) as putative quantitative trait loci for the 22 growth and linear type traits studied. In our study, specific genes (e.g., TLE4, PTGDR, and SCD5) were found common between the traits studied, suggesting an interplay between the genetic backgrounds of these traits. The fact that four of the proposed genes (TLE4, MYOM3, SLC44A1, and TMEM50A) are located on sheep chromosome 2 confirms the importance of these genomic regions for growth and morphological structure in sheep. The results of our study are therefore of great importance for the development of efficient selection indices and marker-assisted selection programs, as well as for the understanding of the genetic architecture of growth and linear traits in sheep.