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1.
Bamaxiang pig is from Guangxi province in China, characterized by its small body size and two‐end black coat colour. It is an important indigenous breed for local pork market and excellent animal model for biomedical research. In this study, we performed genomewide association studies (GWAS) on 43 growth and carcass traits in 315 purebred Bamaxiang pigs based on a 1.4 million SNP array. We observed considerable phenotypic variability in the growth and carcass traits in the Bamaxiang pigs. The corresponding SNP based heritability varied greatly across the 43 traits and ranged from 9.0% to 88%. Through a conditional GWAS, we identified 53 significant associations for 35 traits at p value threshold of 10?6. Among which, 26 associations on chromosome 3, 7, 14 and X passed a genomewide significance threshold of 5 × 10?8. The most remarkable loci were at around 30.6 Mb on chromosome 7, which had growth stage‐dependent effects on body lengths and cannon circumferences and showed large effects on multiple carcass traits. We discussed HMGA1 NUDT3, EIF2AK1, TMEM132C and AFF2 that near the lead SNP of significant loci as plausible candidate genes for corresponding traits. We also showed that including phenotypic covariate in GWAS can help to reveal additional significant loci for the target traits. The results provide insight into the genetic architecture of growth and carcass traits in Bamaxiang pigs.  相似文献   

2.
Boar reproductive traits are economically important for the pig industry. Here we conducted a genome‐wide association study (GWAS) for 13 reproductive traits measured on 205 F2 boars at day 300 using 60 K single nucleotide polymorphism (SNP) data imputed from a reference panel of 1200 pigs in a White Duroc × Erhualian F2 intercross population. We identified 10 significant loci for seven traits on eight pig chromosomes (SSC). Two loci surpassed the genome‐wide significance level, including one for epididymal weight around 60.25 Mb on SSC7 and one for semen temperature around 43.69 Mb on SSC4. Four of the 10 significant loci that we identified were consistent with previously reported quantitative trait loci for boar reproduction traits. We highlighted several interesting candidate genes at these loci, including APN, TEP1, PARP2, SPINK1 and PDE1C. To evaluate the imputation accuracy, we further genotyped nine GWAS top SNPs using PCR restriction fragment length polymorphism or Sanger sequencing. We found an average of 91.44% of genotype concordance, 95.36% of allelic concordance and 0.85 of r2 correlation between imputed and real genotype data. This indicates that our GWAS mapping results based on imputed SNP data are reliable, providing insights into the genetic basis of boar reproductive traits.  相似文献   

3.
旨在解析太湖流域地方猪品种内部遗传结构,鉴定梅山猪亚群间、二花脸群体间和米猪群体间体重体尺性状差异的候选基因.试验采集440头猪样本(代表太湖流域地方猪最全面血统)进行基因芯片分型,并使用该基因分型数据集进行多种群体遗传学分析,明确太湖流域地方猪品种内部的遗传结构,并鉴定梅山猪亚群间、以及二花脸和米猪群体间体重体尺性状...  相似文献   

4.
Decreased calving performance not only directly impacts the economic efficiency of dairy cattle farming but also influences public concern for animal welfare. Previous studies have revealed a QTL on Bos taurus autosome (BTA) 18 that has a large effect on calving traits in Holstein cattle. In this study, fine mapping of this QTL was performed using imputed high‐density SNP chip (HD) genotypes followed by imputed next‐generation sequencing (NGS) variants. BTA18 was scanned for seven direct calving traits in 6113 bulls with imputed HD genotypes. SNP rs136283363 (BTA18: 57 548 213) was consistently the most significantly associated SNP across all seven traits [e.g. p‐value = 2.04 × 10?59 for birth index (BI)]. To finely map the QTL region and to explore pleiotropic effects, we studied NGS variants within the targeted region (BTA18: 57 321 450–57 625 355) for associations with direct calving traits and with three conformation traits. Significant variants were prioritized, and their biological relevance to the traits was interpreted. Considering their functional relationships with direct calving traits, SIGLEC12, CD33 and CEACAM18 were proposed as candidate genes. In addition, pleiotropic effects of this QTL region on direct calving traits and conformation traits were observed. However, the extent of linkage disequilibrium combined with the lack of complete annotation and potential errors in the Bos taurus genome assembly hampered our efforts to pinpoint the causal mutation.  相似文献   

5.
The aim of the present study was to detect quantitative trait loci affecting fatty acid composition in back fat and intramuscular fat in a Duroc pig population comprising seventh‐generation pedigrees using genome‐wide association studies (GWAS). In total, 305 animals were genotyped using single nucleotide polymorphisms (SNPs) array and five selected SNPs from regions containing known candidate genes related to fatty acid synthesis or metabolism. In total, 24 genome‐wide significant SNP regions were detected in 12 traits, and 76 genome‐wide suggestive SNP regions were detected in 33 traits. The Sus scrofa chromosome (SSC) 7 at 10.3 Mb was significantly associated with C17:0 in intramuscular fat, while the SSC9 at 13.6 Mb was significantly associated with C14:0 in intramuscular fat. The SSC12 at 1.0 Mb was significantly associated with C14:0 in back fat and the SSC14 at 121.0 Mb was significantly associated with C18:0 in intramuscular fat. These regions not only replicated previously reported loci containing some candidate genes involved in fatty acid composition (fatty acid synthase and stearoyl‐CoA desaturase) but also included several additional related loci.  相似文献   

6.
Chinese Erhualian pigs are known for prolificacy with distinct reproductive traits compared with Western commercial breeds. In this study, a four‐generation intercross resource population was constructed using White Duroc boars and Chinese Erhualian sows as founder animals, and a total of 14 male reproductive traits were recorded in 411 F2/F3 boars including the testis and epididymis weights, the seminiferous tubular diameter and spermatogenesis at 60, 90 and 300 days of age, semen characteristics, serum testosterone concentration and libido level at 300 days of age. The White Duroc–Erhualian boars showed remarkable segregations in the traits measured except for the seminiferous tubular diameter and had high ratio (13.9%) of the abnormality of spermatogenesis, providing a good experimental population for detecting quantitative trait loci affecting these male reproductive traits. Furthermore, the correlations among nine male reproductive traits at 300 days of age indicated that the testis weight and the body weight were strongly correlated with the sperm production, supporting the two traits as important parameters for boar selection to increase sperm production and ultimately improve boar fertility. The libido level in the White Duroc–Erhualian boars that was evaluated by a new and easily recorded scoring system showed a significant correlation with serum testosterone concentration. Yet, both libido and serum testosterone concentration were not correlated with the sperm production. Results of this study provided new information on the male reproductive physiology and genetics in Chinese Erhualian and White Duroc boars.  相似文献   

7.
The average daily gain (ADG) and body weight (BW) are very important traits for breeding programs and for the meat production industry, which have attracted many researchers to delineate the genetic architecture behind these traits. In the present study, single‐ and multi‐trait genome‐wide association studies (GWAS) were performed between imputed whole‐genome sequence data and the traits of the ADG and BW at different stages in a large‐scale White Duroc × Erhualian F2 population. A bioinformatics annotation analysis was used to assist in the identification of candidate genes that are associated with these traits. Five and seven genome‐wide significant quantitative trait loci (QTLs) were identified by single‐ and multi‐trait GWAS, respectively. Furthermore, more than 40 genome‐wide suggestive loci were detected. On the basis of the whole‐genome sequence association study and the bioinformatics analysis, NDUFAF6, TNS1 and HMGA1 stood out as the strongest candidate genes. The presented single‐ and multi‐trait GWAS analysis using imputed whole‐genome sequence data identified several novel QTLs for pig growth‐related traits. Integrating the GWAS with bioinformatics analysis can facilitate the more accurate identification of candidate genes. Higher imputation accuracy, time‐saving algorithms, improved models and comprehensive databases will accelerate the identification of causal genes or mutations, which will contribute to genomic selection and pig breeding in the future.  相似文献   

8.
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.  相似文献   

9.
试验采集了435头240日龄苏太猪和760头240日龄白色杜洛克×二花脸F2资源家系猪的血清以检测其血糖和糖基化血清蛋白指标,并利用Illumina porcine 60 K SNP芯片判定个体的基因型,同时进行了全基因组SNP与2个性状关联性分析,以及定位影响苏太猪和白色杜洛克×二花脸F2资源家系猪个体240日龄血糖和糖基化血清蛋白的QTL。结果表明,试验共定位到5个影响血糖和糖基化血清蛋白的QTL,且均为5%染色体显著水平,但其中2个可能是假阳性结果,这些QTL位于不同染色体区域,解释表型变异为3.719%和3.724%。  相似文献   

10.
Among many factors, lipid metabolism within the follicular environment emerges as an important indicator of oocyte quality. In the literature a crucial significance is described concerning follicular fluid (FF) composition as well as messenger RNA (mRNA) expression in follicular cells. The aim of this study was to describe the relationship between oocyte, FF and follicular cells with regard to lipid metabolism. The set of data originating from individual follicles comprised: lipid droplets (LD) number in oocytes (BODIPY staining), mRNA expression of seven genes in cumulus and granulosa cells (SCD, FADS2, ELOVL2, ELOVL5, GLUT1, GLUT3, GLUT8; real time polymerase chain reaction) and fatty acid (FA) composition in FF (gas chromatography). Obtained results demonstrate significant correlation between oocyte lipid droplets number and FA composition in FF. However, gene expression studies show significant correlation between LD number and GLUT1 gene only. Moreover, the present experiment revealed correlations between FA content in FF and expression of several genes (SCD, FADS2, ELOVL5, GLUT8) in granulosa cells, whereas only the SCD gene in cumulus cells. We suggest that the results of our experiment indicate the importance of glucose : lipid metabolism balance, which contributes to better understanding of energy metabolism conversion between oocytes and the maternal environment.  相似文献   

11.
Immune traits play pivotal roles in animal immune capacity development and disease resistance. Single nucleotide polymorphisms (SNPs) are common forms of genetic variations among individuals, which are thought to account for the majority of inherited phenotypic variations. In this study, we performed genomewide association, using the Illumina 60K SNP BeadChip studies to detect molecular markers and candidate genes associated with immune traits in an F2 population. Sixteen immune traits were measured. We identified 85 significant SNPs (p < 2.98 × 10?6) with 5% as the genomewide significance threshold, 380 SNPs of suggestive significance (p < 5.96 × 10?5) from simple model (general linear model, GLM) and 15 SNPs of suggestive significance (p < 5.96 × 10?5) from the compressed mixed linear model (MLM), which were also found in GLM (six significant SNPs and seven suggestive SNPs). Three significant SNPs (GGaluGA151406, Gga_rs14554319 and Gga_rs13593979) and candidate genes (LYRM4 and KTN1) were found to be associated with avian influenza antibody titres, and the first two SNPs are from the results of two‐model analysis. For the immune organs, through the analysis of GLM, 19 SNPs were found to be significantly associated with the thymus weight, 61 SNPs were significantly associated with the bursa of Fabricius weight, six of which were located within a 34‐Mb region (125 846 474–159 649 698 bp) on chicken chromosome 1 (GGA1). A candidate region relevant to haematological traits from GLM was found in GGA4 and 9 loci were located on it. Three loci (GGaluGA348521, Gga_rs16098446 and GGaluGA348518) within 179 kb (16 286 868–16 466 134 bp) on GGAZ from GLM provided evidence that this genomic segment may be relevant to red blood cell volume distribution width (RDW). Our study provides a list of significant SNPs and candidate genes that will be valuable information for unveiling the underlying molecular mechanism of immune regulation.  相似文献   

12.
The aim of this study was to identify candidate regions associated with sexual precocity in Bos indicus. Nellore and Brahman were set as validation and discovery populations, respectively. SNP selected in Brahman to validate in Nellore were from gene regions affecting reproductive traits (G1) and significant SNP (p ≤ 10–3) from a meta-analysis (G2). In the validation population, early pregnancy (EP) and scrotal circumference (SC) were evaluated. To perform GWAS in validation population, we used regression and Bayes C. SNP with p ≤ 10–3 in regression and Bayes factor ≥3 in Bayes C were deemed significant. Significant SNP (for EP or SC) or SNP in their ±250 Kb vicinity region, which were in at least one discovery set (G1 or G2), were considered validated. SNP identified in both G1 and G2 were considered candidate. For EP, 145 SNP were validated in G1 and 41 in G2, and for SC, these numbers were 14 and 2. For EP, 21 candidate SNP were detected (G1 and G2). For SC, no candidate SNP were identified. Validated SNP and their vicinity region were located close to quantitative trait loci or genes related to reproductive traits and were enriched in gene ontology terms related to reproductive success. These are therefore strong candidate regions for sexual precocity in Nellore and Brahman.  相似文献   

13.
Pigs show extensive variation in exterior appearance. This variation has been explored as one of the selection targets to form breeding features in the pig industry. In this study, a customized Affymetrix Axiom Pig1.4M array plate was used to conduct genome‐wide association studies (GWAS) for two exterior traits—spotted coat color (SC) and facial type (FT)—in Chinese Dongxiang spotted pigs. Two and 12 single nucleotide polymorphisms (SNPs) were identified to be associated with SC and FT at the 5% genome‐wide significant level, respectively. Of these SNPs, two associated with SC were located around the DACH1 gene on Sus Scrofa chromosome (SSC)11. Eleven SNPs associated with FT were located within a 7.68 Mb region (29.03–36.71 Mb) on SSC7. Based on the GWAS results and the biological functions of genes, we highlight EDNRB as a candidate gene for SC and HMGA1 and RPS10 as the potential genes affecting facial variation. The findings contribute to the final characterization of causative genes and mutations underlying the effects of the SSC7 and SSC11 loci and improve our understanding of the genetic basis of phenotypic variation in Chinese indigenous pigs.  相似文献   

14.
Despite the wide range of observed phenotypic diversities and adaptation to different ecological conditions, little has been studied regarding the genetics of adaptation in the genome of indigenous cattle breeds of developing countries. Here, we investigated the linkage disequilibrium (LD) and identified the subset of outlier loci that are highly differentiated among cattle populations adapted to different ecological conditions in Ethiopia. Specifically, we genotyped 47 unrelated animals sampled from high‐ versus low‐altitude environments using a Bovine 50K SNP BeadChip. Linkage disequilibrium was assessed using both D′ and r2 between adjacent SNPs. We calculated FST and heterozygosity at different significance levels as measures of genetic differentiation for each locus between high‐ and low‐altitude populations following the hierarchical island model approach. We identified 816 loci (p < 0.01) showing selection signals and are associated with genes that might have roles in local adaptation. Some of them are associated with candidate genes that are involved in metabolism (ATP2A3, CA2, MYO18B, SIK3, INPP4A, and IREB2), hypoxia response (BDNF, TFRC, and PML) and heat stress (PRKDC, CDK1, and TFDC). Average r2 and D′ values were 0.14 ± 0.21 and 0.57 ± 0.34, respectively, for a minor allele frequency (MAF) ≥ 0.05 and were found to increase with increasing MAF value. The outlier loci identified in the studied Ethiopian cattle populations indicate the presence of genetic variation produced/shaped by adaptation to different environmental conditions and provide a basis for further validation and functional analysis using a reasonable sample size and high‐density markers.  相似文献   

15.
Ventro‐cranial chronic pleuritis can be a result of pleuropneumonia and enzootic pneumonia. These diseases cause severe losses in intensive pig production worldwide, but host resistance is difficult to breed for. It could be beneficial to use marker‐assisted selection, and a step towards this is to identify genomic regions associated with the trait. For this purpose, 7304 pigs from 11 boar families were analysed for associations between single nucleotide polymorphisms and ventro‐cranial chronic pleuritis. The pigs were genotyped by the use of the iSelect Custom 7 K porcine SNP Chip. Quantitative trait loci (QTL), significant at the chromosome‐wide level, were identified on Sus scrofa chromosomes (SSC) 2, 4, 11, 12 and 13 in four different boar families. The QTL on SSC 4 in family G was also significant at the genome‐wide threshold according to Bonferroni correction. We have identified a number of candidate genes, but the causative mutations still need to be identified. Markers closely associated with the resistance traits have a strong potential for use in breeding towards animals with improved characteristics concerning ventro‐cranial chronic pleuritis.  相似文献   

16.
In the mouse, homozygous animals for the high growth mutation show a 30–50% increase in growth without becoming obese. This region is homologous to the distal part of pig chromosome 5 (SSC5). A previous genome scan detected several quantitative trait loci (QTL) in this region for body composition and meat quality using a three generation Berkshire × Yorkshire resource family. In this study, the effects on swine growth, fat and meat quality traits of three genes previously identified within the mouse high growth region were analysed. The genes studied were CASP2 and RIPKI domain containing adaptor with death domain ( CRADD ), suppressor of cytokine signalling 2 ( SOCS2 ) and plexinC1 ( PLXNC1 ). In addition, the influence of two other genes located very close to this region, namely the plasma membrane calcium-transporting ATPase 1 ( ATP2B1 ) and dual specificity phosphatase 6 ( DUSP6 ) genes, was also investigated. Single nucleotide polymorphisms were identified and used to map these genes to the QTL region on SSC5. Results indicate significant associations between these genes and several phenotypic traits, including fat deposition and growth in pigs. The present study suggests associations of these genes with swine fat and growth related traits, but further studies are needed in order to clearly identify the genes involved in the regulation of the QTL located on SSC5.  相似文献   

17.
Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool‐based genome‐wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1. Statistical analysis revealed that both SNPs were significantly associated with C18:1 (p = .0080 and .0003), validating the quantitative trait loci (QTLs) detected in GWAS. We subsequently selected VNN1 and LYPLA1 genes as candidate genes from each region on BTA9 and BTA14, respectively. We sequenced full‐length coding sequence (CDS) of these genes in eight individuals and identified a nonsynonymous SNP T66M on VNN1 gene as a putative candidate polymorphism. The polymorphism was also significantly associated with C18:1, but the p value (p = .0162) was higher than the most significant SNP on BTA9, suggesting that it would not be responsible for the QTL. Although further investigation will be needed to determine the responsible gene and polymorphism, our findings would contribute to development of selective markers for fatty acid composition in the Japanese Black cattle of Hyogo.  相似文献   

18.

The aim of this work was to verify whether polymorphisms in candidate genes for litter size segregate in Italian Large White (ITLW) pigs. We genotyped 120 sows that belonged to six different farms for 10 single nucleotide polymorphisms (SNPs) of 10 different genes. Polymorphisms in the chosen genes had already been associated with litter-size traits in other pig populations and were candidates for function and/or chromosomal location. The results indicated that the CLGN, pDAZL, and RFN4 SNPs were not segregating in the genotyped samples. The remaining seven markers were polymorphic with minor allele frequencies ranging from 0.10 (AFP) to 0.48 (RBP4). Because of the observed genetic variabilities in the investigated loci, the polymorphisms in the AFP, BMPR1B, CXCL10, ESR2, GNRHR, MAN2B2, and RBP4 genes can be considered suitable markers for association studies with litter-size traits in ITLW pigs.

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19.
Natural infections with influenza viruses have been reported in a variety of animal species including humans, pigs, horses, sea mammals, mustelids and birds. Occasionally, devastating pandemics occur in domestic chickens (broiler and layers) and in humans. From November 2003 to March 2004 in many countries in Asia, there were outbreaks of H5N1 avian influenza virus, causing death of infected patients, and devastating the poultry industry. Some groups of Thai indigenous chickens survived and were therefore classified as resistant. These traits were related to immunogenetics, in particular, the major histocompatibility complex (MHC) class I and class II molecules. The chicken MHC class I were investigated as candidate genes for avian influenza virus disease resistance. Seven hundred and thirty Thai indigenous chickens from smallholder farms in the rural area of avian influenza virus disease outbreaks in the central part of Thailand were used in the present study. They were separated into two groups, 340 surviving chickens and 390 dead chickens (resistant and susceptible). Genomic DNA were precipitated from blood samples and feathers. The DNA were used to amplify the MHC class I gene. Data were analyzed using χ2 analysis to test significant differences of influences of MHC class I haplotypes on avian influenza virus disease traits. The results represented nine MHC class I haplotypes: A1, B12, B13, B15, B19, B21, B2, B6, and BA12, and included 10 of their heterozygotes. The homozygous B21 from these collected samples had a 100% survival rate and they were the major survival group. In addition, the heterozygous B21 also had a high survival rate because of co‐dominant expression of these genes. In contrast, the homozygous B13 had a 100% mortality rate and they were the major mortality group. These results confirmed that MHC class I haplotypes influence avian influenza virus disease‐resistant traits in Thai indigenous chicken. The MHC genes can be used as genetic markers to improve disease‐resistant traits in chicken.  相似文献   

20.
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