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1.
J Dairy Sci ; 103(10): 9177-9194, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32713698

RESUMO

The objectives of our study were to expand phenotypic characterization of digital cushion thickness (DCT) to the Jersey breed and include mature bulls and to identify breed-specific quantitative trait loci (QTL) for DCT within the Jersey or Holstein breeds and common QTL across breeds and sexes to better understand biological regulation and guide future use of marker-assisted selection. In a cohort of 698 cows and 85 bulls (Holstein and Jersey) from 8 farms in New York State, data were collected on DCT, body condition score (BCS), withers height, and sacral height. All animals underwent sonographic examination of the digital cushion evaluated at the sole ulcer site for the right front and hind feet. Linear mixed models were conducted on DCT separately for cows and bulls with fixed effects of time point, breed, age, digit, and BCS group. The models included random effects to control for the random subset of animals per farm, repeated measures, and multiple measurements from each animal. The phenotypic results indicated that DCT varied by time point, breed, age, digit, and BCS group for cows and by breed, age, digit, and BCS group for bulls. For the genotypic study, 616 cow DNA samples were genotyped on the Illumina BovineHD 777K BeadChip (Illumina Inc., San Diego, CA), whereas 76 bull DNA samples were genotyped on different platforms ranging from 5K to 150K. Multiple genome-wide association studies were conducted to highlight pertinent phenotyping parameters and genetic markers for genomic selection. Data were separated into 8 data sets based on different combinations of breed and sex. Each data set was assessed for quality of markers and samples before conducting genome-wide association studies for DCT, testing the inheritance models and genetic variation of digit, foot, and average thickness. Ten markers passed the Bonferroni correction threshold and 9 passed false discovery rate from 10 genome-wide association studies using a combination of the covariates breed, sex, genotyping batch plate, age, BCS, withers height, and sacral height. Of the 43 candidate genes, 8 novel biologically plausible genes were identified on Bos taurus autosomes 3, 4, 7, and 9: SFRS18 and LRRFIP1 function in fat deposition, whereas AHR, BZW2, EFNA5, USP45, and VAV3 effect bone growth, and SOSTDC1 is related to epidermal keratinocyte function. The genetic markers associated with DCT in this study were explored for variation between cows and bulls within and across breeds for their potential use in marker-assisted selection.


Assuntos
Bovinos/genética , Casco e Garras/anatomia & histologia , Animais , Bovinos/anatomia & histologia , Estudos de Coortes , Feminino , Marcadores Genéticos , Variação Genética , Estudo de Associação Genômica Ampla/veterinária , Genótipo , Modelos Lineares , Masculino , New York , Locos de Características Quantitativas , Especificidade da Espécie
2.
J Anim Sci ; 98(7)2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32687196

RESUMO

Whole-genome sequencing of 217 animals from three Danish commercial pig breeds (Duroc, Landrace [LL], and Yorkshire [YY]) was performed. Twenty-six million single-nucleotide polymorphisms (SNPs) and 8 million insertions or deletions (indels) were uncovered. Among the SNPs, 493,099 variants were located in coding sequences, and 29,430 were predicted to have a high functional impact such as gain or loss of stop codon. Using the whole-genome sequence dataset as the reference, the imputation accuracy for pigs genotyped with high-density SNP chips was examined. The overall average imputation accuracy for all biallelic variants (SNP and indel) was 0.69, while it was 0.83 for variants with minor allele frequency > 0.1. This study provides whole-genome reference data to impute SNP chip-genotyped animals for further studies to fine map quantitative trait loci as well as improving the prediction accuracy in genomic selection. Signatures of selection were identified both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during breed development or subsequent divergent selection. However, the fixation indices did not indicate a strong divergence among these three breeds. In LL and YY, the integrated haplotype score identified genomic regions under recent selection. These regions contained genes for olfactory receptors and oxidoreductases. Olfactory receptor genes that might have played a major role in the domestication were previously reported to have been under selection in several species including cattle and swine.


Assuntos
Variação Genética , Genômica , Suínos/genética , Animais , Cruzamento , Dinamarca , Frequência do Gene , Estudo de Associação Genômica Ampla/veterinária , Genótipo , Locos de Características Quantitativas
3.
Anim Genet ; 51(5): 722-730, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32662094

RESUMO

In order to find SNPs and genes affecting shank traits, we performed a GWAS in a chicken F2 population of eight half-sib families from five hatches derived from reciprocal crosses between an Arian fast-growing line and an Urmia indigenous slow-growing chicken. A total of 308 birds were genotyped using a 60K chicken SNP chip. Shank traits including shank length and diameter were measured weekly from birth to 12 weeks of age. A generalized linear model and a compressed mixed linear model (CMLM) were applied to achieve the significant regions. The value of the average genomic inflation factor (λ statistic) of the CMLM model (0.99) indicated that the CMLM was more effective than the generalized linear model in controlling the population structure. The genes surrounding significant SNPs and their biological functions were identified from NCBI, Ensembl and UniProt databases. The results indicated that 12 SNPs at 12 different ages passed the LD-adjusted 5% Bonferroni significant threshold. Two SNPs were significant for shank length and nine SNPs were significant for shank diameter. The significant SNPs were located near to or inside 11 candidate genes. The results showed that a number of significant SNPs in the middle ages were higher than the rest. The MXRA8 gene was related to the significant SNP at week 1 that promotes proliferation of growth plate chondrocytes. A unique SNP of Gga_rs16689511 located on chicken Z chromosome within the LOC101747628 gene was related to shank length at three different ages of birds (weeks 8, 9 and 11). The significant SNPs for shank diameter were found at weeks 4 and 7 (four and five SNPs respectively). The identifications of SNPs and genes here could contribute to a better understanding of the genetic control of shank traits in chicken.


Assuntos
Galinhas/genética , Estudo de Associação Genômica Ampla/veterinária , Membro Posterior/anatomia & histologia , Polimorfismo de Nucleotídeo Único , Animais , Galinhas/anatomia & histologia , Feminino , Irã (Geográfico) , Masculino , Análise de Sequência com Séries de Oligonucleotídeos/veterinária
4.
Anim Genet ; 51(5): 741-751, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32720725

RESUMO

The chicken gizzard is the primary digestive and absorptive organ regulating food intake and metabolism. Body weight is a typical complex trait regulated by an interactive polygene network which is under the control of an interacting network of polygenes. To simplify these genotype-phenotype associations, the gizzard is a suitable target organ to preliminarily explore the mechanism underlying the regulation of chicken growth through controlled food intake. This study aimed to identify key food intake-related genes through combinatorial GWAS and transcriptome analysis. We performed GWAS of body weight in an F2 intercrossed population and transcriptional profiling analysis of gizzards from chickens with different body weight. We identified a major 10 Mb quantitative trait locus (QTL) on chromosome 1 and numerous minor QTL distributed among 24 chromosomes. Combining data regarding QTL and gizzard gene expression, two hub genes, MLNR and HTR2A, and a list of core genes with small effect were found to be associated with food intake. Furthermore, the neuroactive ligand-receptor interaction pathway was found to play a key role in regulating the appetite of chickens. The present results show the major-minor gene interactions in metabolic pathways and provide insights into the genetic architecture and gene regulation during food intake in chickens.


Assuntos
Peso Corporal/genética , Galinhas/fisiologia , Ingestão de Alimentos/genética , Moela das Aves/metabolismo , Locos de Características Quantitativas , Animais , Galinhas/genética , Galinhas/crescimento & desenvolvimento , Perfilação da Expressão Gênica/veterinária , Estudo de Associação Genômica Ampla/veterinária , RNA-Seq/veterinária
5.
Poult Sci ; 99(6): 2833-2840, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32475416

RESUMO

Several genomic methods were applied for predicting shell quality traits recorded at 4 different hen ages in a White Leghorn line. The accuracies of genomic prediction of single-step GBLUP and single-trait Bayes B were compared with predictions of breeding values based on pedigree-BLUP under single-trait or multitrait models. Breaking strength (BS) and dynamic stiffness (Kdyn) measurements were collected on 18,524 birds from 3 consecutive generations, of which 4,164 animals also had genotypes from an Affymetrix 50K panel containing 49,591 SNPs after quality control edits. All traits had low to moderate heritability, ranging from 0.17 for BS to 0.34 for Kdyn. The highest accuracies of prediction were obtained for the multitrait single-step model. The use of marker information resulted in higher prediction accuracies than pedigree-based models for almost all traits. A genome-wide association study based on a Bayes B model was conducted to detect regions explaining the largest proportion of genetic variance. Across all 8 shell quality traits analyzed, 7 regions each explaining over 2% of genetic variance and 54 regions each explaining over 1% of genetic variance were identified. The windows explaining a large proportion of genetic variance overlapped with several potential candidate genes with biological functions linked to shell formation. A multitrait repeatability model using a single-step method is recommended for genomic evaluation of shell quality in layer chickens.


Assuntos
Criação de Animais Domésticos/métodos , Galinhas/fisiologia , Casca de Ovo/fisiologia , Estudo de Associação Genômica Ampla/veterinária , Genômica/métodos , Animais , Teorema de Bayes , Cruzamento , Galinhas/genética , Feminino , Genoma , Masculino
6.
Poult Sci ; 99(6): 2873-2887, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32475420

RESUMO

The function of the sperm storage tubules is directly correlated with the fertility of laying hens. However, little is known about the molecular mechanisms regulating the fertility traits in chicken. To identify genetic markers associated with reproductive traits, we calculated fertility rate at 61 to 69 wk (51 D) of Jing Hong chickens parent generation as the phenotype and the genotype were detected by the chicken 600K Affymetrix Axiom High Density single nucleotide polymorphisms (SNP)-array. The genome-wide association study using 190 Jing Hong hens showed that the 20 SNP in chromosomes 3 and 13 were significantly associated with fertility rate. To verify these results, a total of 1900 Jing Hong laying hens from 2 populations (P1 and P2) were further genotyped by polymerase chain reaction-restriction fragments length polymorphisms method. The association analysis results revealed that 12 polymorphisms (AX-75769978, AX-76582632, AX-75730546, AX-75730496, AX-75730588, AX-76530282, AX-76530329, AX-76529310, AX-75769906, AX-75755394, AX-80813697 and AX-76582809) out of 20 showed highly significant effects (P < 0.0001) on fertility rate in P1, P2 and P1+P2. Six haplotypes (TTAA, TTGG, TTAG, CTAA, CTGG, and CTAG) were inferred based on significant loci (AX-75730546 and AX-76530282) also showed significant association with fertility rate, where haplotype CTAG was shown to be markedly associated with the significantly highest (P < 0.0001) fertility rate (in P1, 86.42 ± 0.59; P2, 85.98 ± 0.59 and P1+P2, 86.16 ± 0.42) followed by other haplotypes for the irrespective of population studied. Collectively, we report for the first time that 12 SNP in the chromosomes 3 and 13 were significantly associated with fertility rate during the later stage of egg production, which could be used as the potential genetic markers that would be able to facilitate in the selection and improvement of fertility rate through chicken breeding.


Assuntos
Cruzamento , Galinhas/genética , Fertilidade/genética , Estudo de Associação Genômica Ampla/veterinária , Polimorfismo de Nucleotídeo Único , Animais , Galinhas/crescimento & desenvolvimento , Marcadores Genéticos , Reação em Cadeia da Polimerase/veterinária , Polimorfismo de Fragmento de Restrição
7.
Poult Sci ; 99(6): 2895-2901, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32475422

RESUMO

Reproduction trait is one of the most important economic traits in poultry industry. This study was aimed to investigate the mRNA expression levels, single nucleotide polymorphisms (SNP) of POMC gene, and the association with reproduction traits in chickens. Five SNP (g.958 G > A, g.1374 G > C, g.1393 G > A, g.1817 C > T, and g.1918G > A) were detected in introns of POMC gene in 317 Zhenning yellow chickens. Association analysis revealed that g.958 G > A and g.1817 C > T showed significantly associations with fertilization rate, hatching rate of hatching eggs, and hatching rate of fertilized eggs in chickens. Simultaneously, g.1374 G > C and g.1918G > A were both associated with egg weight at 300 D of age (P < 0.05). The SNP of g.958 G > A, g.1393 G > A, and g.1817 C > T were all associated with E2 hormone levels (P < 0.05). The result of mRNA expression levels in different tissues showed that POMC mRNA expression level in the pituitary was higher than those in the other tissues and varied in different genotypes. In conclusion, the results in this study provided new evidences that polymorphisms of the POMC gene have potential effects on reproduction traits in chickens. The 5 SNP detected in this study could be potential markers for improving reproduction traits in chickens.


Assuntos
Proteínas Aviárias/genética , Galinhas/fisiologia , Expressão Gênica , Estudo de Associação Genômica Ampla/veterinária , Polimorfismo Genético , Pró-Opiomelanocortina/genética , Reprodução/genética , Animais , Proteínas Aviárias/metabolismo , Galinhas/genética , Pró-Opiomelanocortina/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
8.
Poult Sci ; 99(6): 2902-2910, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32475423

RESUMO

Chicken plumage color is an important economical trait in poultry breeding, as triple-yellow indigenous broilers are preferred over western commercial broilers in the Chinese market. However, the studies on the pigmentation of plumage coloration are relatively rare at present. Here, we performed a genome-wide mapping study on an F2 intercross, whose 2 founders were one hybrid commercial line "High Quality chicken Line A" that originated from the Anak red chicken and one indigenous line "Huiyang Beard" chicken that is a classical "triple-yellow" Chinese indigenous breed. Moreover, we used an automatic colorimeter that can quantitatively assess the colorations in L∗, a∗, and b∗ values. One major quantitative trait locus (QTL) on chromosome 2 was thus identified by both genome-wide association and linkage analyses, which could explain 10 to 20% of the total phenotypic variance of the b∗ measurements of the back plumage color. Using linkage analysis, 2 additional QTL on chromosome 1 and 20 were also found to be significantly associated with the plumage coloration in this cross. With additional samples from Anak red and Huiyang Beard chickens as well as pooled resequencing data from the 2 founders of this cross, we then further narrowed down the QTL regions and identified several candidate genes, such as CABLES1, CHST11, BCL2L1, and CHD22. As the effects of QTL found in this study were substantial, quantitatively measuring the coloration rather than the descriptive measurements provides stronger statistical power for the analyses. In addition, this major QTL on chromosome 2 that was associated with feather pigmentation at the genome-wide level will facilitate the future chicken breeding for yellow plumage color. In conclusions, we mapped 3 associated QTL on chromosome 1, 2, and 20. The candidate genes identified in this study shed light in the genetic basis of yellow plumage color in chicken.


Assuntos
Galinhas/fisiologia , Ligação Genética , Estudo de Associação Genômica Ampla/veterinária , Pigmentação/genética , Locos de Características Quantitativas , Animais , Cruzamento , Galinhas/genética , Cor , Fenótipo
9.
Zool Res ; 41(4): 471-475, 2020 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-32543792

RESUMO

Cis-regulatory elements play an important role in the development of traits and disease in organisms (Ma et al., 2020; Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements (ENCODE) (Davis et al., 2018) and Functional Annotation of Animal Genomes (FAANG) (FAANG Consortium et al., 2015) offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms. In this study, we developed a tool (OrthReg) for annotating conserved orthologous cis-regulatory elements in targeted genomes using an annotated reference genome. Cross-species validation of this annotation tool using human and mouse ENCODE data confirmed the robustness of this strategy. To explore the efficiency of the tool, we annotated the pig genome and identified more than 28 million regulatory annotation records using the reference human ENCODE data. With this regulatory annotation, some putative regulatory non-coding variants were identified within domestication sweeps in European and East Asian pigs. Thus, this tool can utilize data produced by ENCODE, FAANG, and similar projects, and can be easily extended to customized experimental data. The extensive application of this tool will help to identify informative single nucleotide polymorphisms (SNPs) in post-genome-wide association studies and resequencing analysis of organisms with limited regulatory annotation data.


Assuntos
Sequência de Bases , Sequência Conservada , Estudo de Associação Genômica Ampla/métodos , Genoma , Camundongos/genética , Sus scrofa/genética , Animais , Estudo de Associação Genômica Ampla/veterinária , Humanos
10.
Anim Genet ; 51(4): 624-628, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32510640

RESUMO

Milk production is one of the most important characteristics of dairy sheep, and the identification of genes affecting milk production traits is critical to understanding the genetics and improve milk production in future generations. Three statistical techniques, namely GWAS, ridge-regression BLUP and BayesC π , were used to identify SNPs in significant association with three milk production traits (milk yield, fat yield and protein yield) in a crossbred dairy sheep population. The results suggested that chromosomes 1, 3, 4, 5, 7 and 11 were likely to harbor genes important to milk production because these chromosomes had the greatest top-100-SNP variance contributions on the three milk production traits. The GWAS analysis identified between 74 and 288 genome-wide significant SNP (P < 0.05) whereas the BayesCπ model revealed between six and 63 SNPs, each with >95% posterior probability of inclusion as having a non-zero association effect on at least one of the three milk production traits. Positional candidate genes for milk production in sheep were searched, based on the sheep genomic assembly OAR version 3.1, such as those which map position coincided with or was located within 0.1 Mbp of a genome-wide suggestive or significant SNP. These identified SNPs and candidate genes supported some previous findings and also added new information about genetic markers for genetic improvement of lactation in dairy sheep, but keeping in mind that the majority of these positional candidate genes are not necessarily true causative loci for these traits and future validations are thus necessary.


Assuntos
Estudo de Associação Genômica Ampla/veterinária , Leite/metabolismo , Carneiro Doméstico/genética , Animais , Cruzamento , Feminino , Modelos Genéticos , Modelos Estatísticos , Carneiro Doméstico/metabolismo
11.
Vet Clin North Am Equine Pract ; 36(2): 341-352, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32534851

RESUMO

A role for a genetic contribution to equine metabolic syndrome (EMS) and pars pituitary intermedia dysfunction (PPID) has been hypothesized. Heritability estimates of EMS biochemical measurements were consistent with moderately to highly heritable traits. Further, genome-wide association analyses have identified hundreds of regions of the genome contributing to EMS and candidate variants have been identified. The genetics of PPID has not yet been proven. Continued research for the specific genetic risk factors for both EMS and PPID is crucial for gaining a better understanding of the pathophysiology of both conditions and allowing development of genetic tests.


Assuntos
Doenças do Sistema Endócrino/veterinária , Doenças dos Cavalos/genética , Doenças Metabólicas/veterinária , Animais , Doenças do Sistema Endócrino/genética , Estudo de Associação Genômica Ampla/veterinária , Cavalos , Doenças Metabólicas/genética
12.
Anim Genet ; 51(4): 601-606, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32511786

RESUMO

We report haplotype-based GWASs for 33 blood parameters measured in 843 Italian Large White pigs. In the single-trait analysis, a total of 30 QTL for number of basophils, six erythrocyte traits (haemoglobin, haematocrit, mean corpuscular haemoglobin, mean corpuscular haemoglobin concentration, mean corpuscular volume and red blood cell count) and two clinical-biochemical traits (alkaline phosphatase and Ca2+ contents) were identified. In the multiple-trait analysis, a total of five QTL affected three different clusters of traits. Only four of these QTL were already reported in the single-marker and multi-marker GWASs we previously carried out on the same pig population. QTL on SSC11 and SSC17 showed effects on multiple traits. These results further dissected the genetic architecture of parameters that could be used as proxies in breeding programmes for more complex traits. In addition, these results might help to better define the pig as an animal model for several blood-related biological functions.


Assuntos
Análise Química do Sangue/veterinária , Estudo de Associação Genômica Ampla/veterinária , Haplótipos , Animais , Itália , Masculino , Sus scrofa
13.
Animal ; 14(12): 2443-2451, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32538338

RESUMO

Leg weakness (LW) issues are a great concern for pig breeding industry. And it also has a serious impact on animal welfare. To dissect the genetic architecture of limb-and-hoof firmness in commercial pigs, a genome-wide association study was conducted on bone mineral density (BMD) in three sow populations, including Duroc, Landrace and Yorkshire. The BMD data were obtained by ultrasound technology from 812 pigs (including Duroc 115, Landrace 243 and Yorkshire 454). In addition, all pigs were genotyped using genome-by-sequencing and a total of 224 162 single-nucleotide polymorphisms (SNPs) were obtained. After quality control, 218 141 SNPs were used for subsequent genome-wide association analysis. Nine significant associations were identified on chromosomes 3, 5, 6, 7, 9, 10, 12 and 18 that passed Bonferroni correction threshold of 0.05/(total SNP numbers). The most significant locus that associated with BMD (P value = 1.92e-14) was detected at approximately 41.7 Mb on SSC6 (SSC stands for Sus scrofa chromosome). CUL7, PTK7, SRF, VEGFA, RHEB, PRKAR1A and TPO that are located near the lead SNP of significant loci were highlighted as functionally plausible candidate genes for sow limb-and-hoof firmness. Moreover, we also applied a new method to measure the BMD data of pigs by ultrasound technology. The results provide an insight into the genetic architecture of LW and can also help to improve animal welfare in pigs.


Assuntos
Estudo de Associação Genômica Ampla , Locos de Características Quantitativas , Animais , Densidade Óssea/genética , Cruzamento , Feminino , Estudo de Associação Genômica Ampla/veterinária , Fenótipo , Polimorfismo de Nucleotídeo Único , Sus scrofa/genética , Suínos/genética
14.
Anim Genet ; 51(5): 811-814, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32548856

RESUMO

Thermal stress limits beef cattle production and a shorter hair coat is a key thermoregulative adaptation that allows cattle to lose heat more efficiently. The objective of this study was to identify genetic variants associated with the length of the undercoat and topcoat of cattle utilizing 1456 Brangus heifers genotyped with the Bovine GGP F250 array. Seven SNPs in the PCCA gene were significantly associated with undercoat length. PCCA belongs to the biotin transport and metabolism pathway. Biotin deficiency has been reported to cause hair loss. Four SNPs in an 110 kb including a missense mutation in the PRLR gene were significantly associated with topcoat length. Whereas the association of this polymorphism with hair length is novel, the SLICK mutation in PRLR has previously been demonstrated to significantly impact hair length in cattle. These newly detected genetic variants may contribute to a shorter hair coat and more thermotolerant animals.


Assuntos
Bovinos/fisiologia , Variação Genética/fisiologia , Cabelo/fisiologia , Termotolerância/genética , Animais , Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária
15.
Anim Genet ; 51(4): 595-600, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32363597

RESUMO

The number of teats is a morphological trait that influences the mothering ability of the sows and thus their reproduction performances. In this study, we carried out GWASs for the total number of teats and other 12 related parameters in 821 Italian Large White heavy pigs. All pigs were genotyped with the Illumina PorcineSNP60 BeadChip array. For four investigated parameters (total number of teats, the number of teats of the left line, the number of teats of the right line and the maximum number of teats comparing the two sides), significant markers were identified on SSC7, in the region of the vertnin (VRTN) gene. Significant markers for the numbers of posterior teats and the absolute difference between anterior and posterior teat numbers were consistently identified on SSC6. The most significant SNP for these parameters was an intron variant in the TOX high mobility group box family member 3 (TOX3) gene. For the other four parameters (absolute difference between the two sides; anterior teats; the ratio between the posterior and the anterior number of teats; and the absence or the presence of extra teats) only suggestively significant markers were identified on several other chromosomes. This study further supported the role of the VRTN gene region in affecting the recorded variability of the number of teats in the Italian Large White pig population and identified a genomic region potentially affecting the biological mechanisms controlling the developmental programme of morphological features in pigs.


Assuntos
Estudo de Associação Genômica Ampla/veterinária , Glândulas Mamárias Animais/anatomia & histologia , Sus scrofa/genética , Animais , Feminino , Genótipo , Itália , Fenótipo , Sus scrofa/anatomia & histologia
16.
BMC Vet Res ; 16(1): 138, 2020 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-32414370

RESUMO

BACKGROUND: Salmonella enterica serovars are a major cause of foodborne illness and have a substantial impact on global human health. In Canada, Salmonella is commonly found on swine farms and the increasing concern about drug use and antimicrobial resistance associated with Salmonella has promoted research into alternative control methods, including selecting for pig genotypes associated with resistance to Salmonella. The objective of this study was to identify single-nucleotide variants in the pig genome associated with Salmonella susceptibility using a genome-wide association approach. Repeated blood and fecal samples were collected from 809 pigs in 14 groups on farms and tonsils and lymph nodes were collected at slaughter. Sera were analyzed for Salmonella IgG antibodies by ELISA and feces and tissues were cultured for Salmonella. Pig DNA was genotyped using a custom 54 K single-nucleotide variant oligo array and logistic mixed-models used to identify SNVs associated with IgG seropositivity, shedding, and tissue colonization. RESULTS: Variants in/near PTPRJ (p = 0.0000066), ST6GALNAC3 (p = 0.0000099), and DCDC2C (n = 3, p < 0.0000086) were associated with susceptibility to Salmonella, while variants near AKAP12 (n = 3, p < 0.0000358) and in RALGAPA2 (p = 0.0000760) may be associated with susceptibility. CONCLUSIONS: Further study of the variants and genes identified may improve our understanding of neutrophil recruitment, intracellular killing of bacteria, and/or susceptibility to Salmonella and may help future efforts to reduce Salmonella on-farm through genetic approaches.


Assuntos
Polimorfismo de Nucleotídeo Único , Salmonelose Animal/genética , Salmonella/isolamento & purificação , Sus scrofa/genética , Animais , Derrame de Bactérias , Canadá , Fezes/microbiologia , Estudo de Associação Genômica Ampla/veterinária , Imunoglobulina G/análise , Linfonodos/microbiologia , Tonsila Palatina/microbiologia , Salmonella/imunologia , Salmonelose Animal/imunologia , Salmonelose Animal/microbiologia , Sus scrofa/sangue , Sus scrofa/microbiologia , Suínos , Doenças dos Suínos/genética , Doenças dos Suínos/imunologia , Doenças dos Suínos/microbiologia
17.
Anim Sci J ; 91(1): e13383, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32410280

RESUMO

The objectives of this study were to estimate genetic parameters and to perform a genome-wide association study (GWAS) for predicted methane-related traits in Japanese Black steers. The methane production and yield traits were predicted using on-farm measurable traits, such as dry matter intake and average daily gain. A total of 4,578 Japanese Black steers, which were progenies of 362 sires genotyped with imputed 551,995 single nucleotide polymorphisms (SNPs), had phenotypes of predicted methane-related traits during the total fattening period (52 weeks). For the estimation of genetic parameters, the estimated heritabilities were moderate (ranged from 0.57 to 0.60). In addition, the estimated genetic correlations of methane production traits with most of carcass traits and feed-efficiency traits were unfavorable, but those of methane yield traits were favorable or low. For the GWAS, no genome-wide significant SNP was detected, but a total of four quantitative trait locus (QTL) regions that explained more than 5.0% of genetic variance were localized on the genome, and some candidate genes associated with growth and feed-efficiency traits were located on the regions. Our results suggest that the predicted methane-related traits are heritable and some QTL regions for the traits are localized on the genome in Japanese Black steers.


Assuntos
Fenômenos Fisiológicos da Nutrição Animal/genética , Bovinos/genética , Bovinos/metabolismo , Dieta/veterinária , Estudo de Associação Genômica Ampla/veterinária , Genoma/genética , Metano/metabolismo , Característica Quantitativa Herdável , Animais , Masculino , Fenótipo , Polimorfismo de Nucleotídeo Único
18.
BMC Vet Res ; 16(1): 165, 2020 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-32460776

RESUMO

BACKGROUND: Johne's disease (JD) is a chronic intestinal inflammatory disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) infection in ruminants. Since there are currently no effective vaccine or treatment options available to control JD, genetic selection may be an alternative strategy to enhance JD resistance. Numerous Single Nucleotide Polymorphisms (SNPs) have been reported to be associated with MAP infection status based on published genome-wide association and candidate gene studies. The main objective of this study was to validate these SNPs that were previously identified to be associated with JD by testing their effect on Holstein bulls' estimated breeding values (EBVs) for milk ELISA test scores, an indirect indicator of MAP infection status in cattle. RESULTS: Three SNPs, rs41810662, rs41617133 and rs110225854, located on Bos taurus autosomes (BTA) 16, 23 and 26, respectively, were confirmed as significantly associated with Holstein bulls' EBVs for milk ELISA test score (FDR < 0.01) based on General Quasi Likelihood Scoring analysis (GQLS) analysis. Single-SNP regression analysis identified four SNPs that were associated with sire EBVs (FDR < 0.05). This includes two SNPs that were common with GQLS (rs41810662 and rs41617133), with the other two SNPs being rs110494981 and rs136182707, located on BTA9 and BTA16, respectively. CONCLUSIONS: The findings of this study validate the association of SNPs with JD MAP infection status and highlight the need to further investigate the genomic regions harboring these SNPs.


Assuntos
Doenças dos Bovinos/genética , Paratuberculose/genética , Polimorfismo de Nucleotídeo Único/genética , Animais , Cruzamento , Bovinos/genética , Doenças dos Bovinos/microbiologia , Resistência à Doença/genética , Ensaio de Imunoadsorção Enzimática/veterinária , Estudo de Associação Genômica Ampla/veterinária , Masculino , Leite/química , Mycobacterium avium subsp. paratuberculosis
19.
J Anim Sci ; 98(5)2020 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-32365208

RESUMO

Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P < 5 × 10-8) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P > × 10-6) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P < 5 × 10-8). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.


Assuntos
Doenças dos Bovinos/genética , Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária , Complicações do Trabalho de Parto/veterinária , Parto/genética , Locos de Características Quantitativas , Animais , Bovinos/classificação , Doenças dos Bovinos/patologia , Feminino , Complicações do Trabalho de Parto/genética , Parto/fisiologia , Fenótipo , Polimorfismo de Nucleotídeo Único , Gravidez , Sequenciamento Completo do Genoma
20.
Poult Sci ; 99(5): 2349-2361, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32359570

RESUMO

There have been several genome-wide association study (GWAS) reported for carcass, growth, and meat traits in chickens. Most of these studies have been based on single SNPs GWAS. In contrast, haplotype-based GWAS reports have been limited. In the present study, 2 Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) and genotyped with the chicken 60K SNP chip were used to perform a haplotype-based GWAS. The lean and fat chicken lines were selected for abdominal fat content for 11 yr. Abdominal fat weight was significantly different between the 2 lines; however, there was no difference for body weight between the lean and fat lines. A total of 132 haplotype windows were significantly associated with abdominal fat weight. These significantly associated haplotype windows were primarily located on chromosomes 2, 4, 8, 10, and 26. Seven candidate genes, including SHH, LMBR1, FGF7, IL16, PLIN1, IGF1R, and SLC16A1, were located within these associated regions. These genes may play important roles in the control of abdominal fat content. Two regions on chromosomes 3 and 10 were significantly associated with testis weight. These 2 regions were previously detected by the single SNP GWAS using this same resource population. TCF21 on chromosome 3 was identified as a potentially important candidate gene for testis growth and development based on gene expression analysis and the reported function of this gene. TCF12, which was previously detected in our SNP by SNP interaction analysis, was located in a region on chromosome 10 that was significantly associated with testis weight. Six candidate genes, including TNFRSF1B, PLOD1, NPPC, MTHFR, EPHB2, and SLC35A3, on chromosome 21 may play important roles in bone development based on the known function of these genes. In addition, several regions were significantly associated with other carcass and growth traits, but no candidate genes were identified. The results of the present study may be helpful in understanding the genetic mechanisms of carcass and growth traits in chickens.


Assuntos
Galinhas/fisiologia , Estudo de Associação Genômica Ampla/veterinária , Haplótipos , Carne/análise , Gordura Abdominal/metabolismo , Animais , Galinhas/genética , Galinhas/crescimento & desenvolvimento , Feminino , Masculino , Seleção Genética
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