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1.
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.  相似文献   

2.
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   

3.
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   

4.
Records for yearling scrotal circumference (SC; n = 7,580), age at puberty in heifers (AP; n = 5,292), age at first calving (AFC; n = 4,835), and pregnancy, calving, or weaning status following the first breeding season (PR1, CR1, or WR1, respectively; n = 7,003) from 12 Bos taurus breeds collected at the Meat Animal Research Center (USDA) between 1978 and 1991 were used to estimate genetic parameters. Age at puberty (AP) was defined as age in days at first detected ovulatory estrus. Pregnancy (calving or weaning) status was scored as one for females conceiving (calving or weaning) given exposure during the breeding season and as zero otherwise. The final model for SC included fixed effects of age of dam at breeding (AD), year of breeding (Y), and breed (B) and age in days at measurement as a covariate. Fixed effects in models for AP and AFC were AD, Y, B, and month of birth. Fixed effects in models for PR1, CR1, and WR1 included AD, Y, and B. For all traits, random effects in the model were direct genetic, maternal genetic, maternal permanent environmental, and residual. Analyses for a three-trait animal model were carried out with SC, AP, and a third trait (the third trait was AFC, PR1, CR1, or WR1). A derivative-free restricted maximum likelihood algorithm was used to estimate the (co)variance components. Direct and maternal heritability estimates were 0.41 and 0.05 for SC; 0.16 and 0.03 for AP; 0.08 and 0.00 for AFC; 0.14 and 0.02 for PR1; 0.14 and 0.03 for CR1; and 0.12 and 0.01 for WR1. Genetic correlations between direct and maternal genetic effects within trait were -0.26, -0.63, -0.91, -0.79, -0.66, and -0.85 for SC, AP, AFC, PR1, CR1, and WR1, respectively. Direct genetic correlations between SC and AP and between those traits and AFC, PR1, CR1, and WR1 ranged from -0.15 (between SC and AP) to 0.23 (between AP and WR1). Estimates of heritability indicate that yearling SC should respond to direct selection better than AP, AFC, PR1, CR1, and WR1. Variation due to maternal genetic effects was small for all traits. No strong genetic correlations were detected between SC and female reproductive traits or between AP and the other female traits. These results suggest that genetic response in female reproductive traits through sire selection on yearling SC is not expected to be effective.  相似文献   

5.
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6.
单倍型标记与数量性状基因座(quantitative trait loci，QTL)之间具有较强的连锁不平衡(linkage disequilibrium，LD)关系，在基因定位和因果突变鉴定方面具有较高的应用价值。为了评估单倍型标记在基因组研究中的作用，本研究在华西牛资源群体中，选取该群体于2008—2021年间屠宰的共计1 478头平均月龄为24个月的个体进行研究，其中公牛1 333头，母牛145头。利用770K高密度芯片数据，基于LD阈值(r2>0.3)及固定单核苷酸多态(single nucleotide polymorphism,SNP)个数(5个连续SNP)两种方法进行单倍型构建，分别采用单位点SNP标记和两种单倍型标记共3种标记，基于GCTA的混合线性模型(mixed linear model,MLM)，开展宰前活重(LW)和屠宰率(DP)等屠宰性状的全基因组关联分析(genome-wide association study，GWAS)，定位影响屠宰性状的显著(P<0.05) SNPs、单倍型块和候选基因，同时比较3种标记的GWAS结果，评估3种标记的优劣。结果显示，3种标记在全基因组范围内共找到16个的显著SNPs及单倍型区域，主要分布于1、5、6、14、16、17和28号染色体上，同时鉴定到FAM184B、PPM1K、LCORL、RIMS2等10个与屠宰性状相关的候选基因，其中，基于SNP标记方法鉴定到的3个候选基因，在利用基于单倍型标记的方法中也鉴定到，且单倍型鉴定到的显著性位点或区域大多位于基因内部。在两种单倍型构建方法中，与基于固定SNP个数构建单倍型进行GWAS相比，基于LD阈值的构建方法鉴定到了更多候选基因。本研究结果表明，以单倍型开展GWAS可以综合考虑SNP位点间连锁关系，能较好地揭示复杂性状的遗传结构。  相似文献   

7.
The total meat yield in a beef cattle production cycle is economically very important and depends on the number of calves born per year or birth season, being directly related to reproductive potential. Accumulated Productivity (ACP) is an index that expresses a cow's capacity to give birth regularly at a young age and to wean animals of greater body weight. Using data from cattle participating in the “Program for Genetic Improvement of the Nelore Breed” (PMGRN — Nelore Brasil), bi-trait analyses were performed using the Restricted Maximum Likelihood method based on an ACP animal model and the following traits: age at first calving (AFC), female body weight adjusted for 365 (BW365) and 450 (BW450) days of age, and male scrotal circumference adjusted for 365 (SC365), 450 (SC450), 550 (SC550) and 730 (SC730) days of age. Median estimated ACP heritability was 0.19 and the genetic correlations with AFC, BW365, BW450, SC365, SC450, SC550 and SC730 were 0.33, 0.70, 0.65, 0.08, 0.07, 0.12 and 0.16, respectively. ACP increased and AFC decreased over time, revealing that the selection criteria genetically improved these traits. Selection based on ACP appears to favor the heaviest females at 365 and 450 days of age who showed better reproductive performance as regards AFC. Scrotal circumference was not genetically associated with ACP.  相似文献   

8.
Age at first calving (AFC) measures the entry of heifers into the beef cattle production system. This trait can be used as a selection criterion for earlier reproductive performance. Using data from Nelore cattle participating in the 'Program for Genetic Improvement of the Nelore Breed' (PMGRN-Nelore Brazil), bi-trait analyses were performed using the restricted maximum likelihood method, based on an AFC animal model and the following traits: female body weight adjusted to 365 (BW365) and 450 (BW450) days of age, and male scrotal circumference adjusted to 365 (SC365), 450 (SC450), 550 (SC550) and 730 (SC730) days of age. The heritability estimates for AFC ranged from 0.02 ± 0.02 to 0.04 ± 0.02. The estimates of additive direct heritabilities (with standard error) for BW365, BW450, SC365, SC450, SC550 and SC730 were 0.36 ± 0.07, 0.38 ± 0.07, 0.48 ± 0.07, 0.65 ± 0.07, 0.64 ± 0.07 and 0.42 ± 0.07, respectively, and the genetic correlations with AFC were −0.38, −0.33, 0.10, −0.13, −0.13 and 0.06, respectively. In the herds studied, selection for SC365, SC450, SC550 or SC730 should not cause genetic changes in AFC. Selection based on BW365 or BW450 would favor smaller AFC breeding values. However, the low magnitude of direct heritability estimates for AFC in these farms indicates that changes in phenotypical expression depend mostly on non-genetic factors.  相似文献   

9.
Data comprising 53,181 calving records were analyzed to estimate the genetic correlation between days to calving (DC), and days to first calving (DFC), and the following traits: scrotal circumference (SC), age at first calving (AFC), and weight adjusted for 550 d of age (W550) in a Nelore herd. (Co)variance components were estimated using the REML method fitting bivariate animal models. The fixed effects considered for DC were contemporary group, month of last calving, and age at breeding season (linear and quadratic effects). Contemporary groups were composed by herd, year, season, and management group at birth; herd and management group at weaning; herd, season, and management group at mating; and sex of calf and mating type (multiple sires, single sire, or AI). In DFC analysis, the same fixed effects were considered excluding the month of last calving. For DC, a repeatability animal model was applied. Noncalvers were not considered in analyses because an attempt to include them, attributing a penalty, did not improve the identification of genetic differences between animals. Heritability estimates ranged from 0.04 to 0.06 for DC, from 0.06 to 0.13 for DFC, from 0.42 to 0.44 for SC, from 0.06 to 0.08 for AFC, and was 0.30 for W550. The genetic correlation estimated between DC and SC was low and negative (-0.10), between DC and AFC was high and positive (0.76), and between DC and W550 was almost null (0.07). Similar results were found for genetic correlation estimates between DFC and SC (-0.14), AFC (0.94), and W550 (-0.02). The genetic correlation estimates indicate that the use of DC in the selection of beef cattle may promote favorable correlated responses to age at first mating and, consequently, higher gains in sexual precocity can be expected.  相似文献   

10.
In Brazil, water buffaloes have been used to produce milk for mozzarella cheese production. Consequently, the main selection criterion applied for the buffalo genetic improvement is the estimated mozzarella yield as a function of milk, fat and protein production. However, given the importance of reproductive traits in production systems, this study aimed to use techniques for identifying genomic regions that affect the age at first calving (AFC) and first calving interval (FCI) in buffalo cows and to select candidate genes for the identification of QTL and gene expression studies. The single-step GBLUP method was used for the identification of genomic regions. Windows of 1 Mb containing single-nucleotide polymorphisms were constructed and the 10 windows that explained the greatest proportion of genetic variance were considered candidate regions for each trait. Genes present into the selected windows were identified using the UOA_WB_1 assembly as the reference, and their ontology was defined with the Panther tool. Candidate regions for both traits were identified on BBU 3, 12, 21 and 22; for AFC, candidates were detected on BBU 6, 7, 8, 9 and 15 and for first calving interval on BBU 4, 14 and 19. This study identified regions with great contribution to the additive genetic variance of age at first calving and first calving interval in the population of buffalo cows studied. The ROCK2, PMVK, ADCY2, MAP2K6, BMP10 and GFPT1 genes are main candidates for reproductive traits in water dairy buffaloes, and these results may have future applications in animal breeding programs or in gene expression studies of the species.  相似文献   

11.
Field records from the American Angus Association were used to study the associations of sire marbling score EPD and sire weaning weight maternal (milk) EPD with age at first calving (AFC) and calving interval (CI). Cows were selected based on the accuracy of their sire's milk (> or =.7) or marbling (> or =.6) EPD. The data were screened using biological constraints, and regression models were used to identify records that were greater than 5 SD from the mean. The AFC was modeled for both milk and marbling data sets to account for effects of year, sire EPD, and their interaction. The CI was subdivided into first, second, and mature calving interval traits and modeled to account for state, year, calf sex, calf birth weight (BW), calf weaning weight (WW), sire EPD, and interactions of EPD with year and state. Derivative-free REML was used to estimate heritability and genetic correlations for AFC and CI. Sire milk EPD and marbling EPD were predictors of AFC (P < .001); however, pooled estimates were unreliable because of state x EPD interactions (P < .001). Increases in sire milk EPD resulted in reductions in AFC; however, there was no consistent pattern to effects of marbling EPD increases. Models accounted for < 8% of variation in AFC. Sire milk EPD was not a predictor of first, second, or mature CI (P > .1). Sire marbling score EPD was not a predictor of second, or mature CI (P > .1); however, it was associated (P = .059) with first CI, although regression estimates varied across states and prevented pooling. The BW, sex, and WW were predictors of CI (P < .001). Increases in BW resulted in longer mature CI, and mature CI decreased as WW increased. The AFC was heritable (.22), and CI traits had heritabilities ranging from .01 to .03. The AFC was genetically correlated with first CI (-.6) and mature CI (-.93). Genetic correlations between CI traits were uninterpretable because of low additive genetic variances. In conclusion, sire marbling score and milk EPD do not seem to be reliable predictors of AFC or CI. The BW and WW have significant but small effects on AFC and CI. Selection for AFC is possible, but earlier calving heifers may have longer calving intervals.  相似文献   

12.
试验旨在利用全基因组关联分析（GWAS）定位影响鸭胸肌肉色性状的候选基因及分子标记,探究肉色性状的遗传基础。本研究中,共测定了555只北京鸭×野鸭F2代资源群体的3种胸肌肉色性状（包括红度a*、黄度b*、亮度L*）。利用北京鸭×野鸭F2代资源群体胸肌肉色性状数据并结合全基因组重测序数据进行全基因组关联分析,检测影响胸肌肉色性状的相关基因及可能的因果变异位点。结果显示,肌肉亮度L*、红度a*、黄度b*均属于低遗传力性状,遗传力分别为0.23、0.12、0.13,且肌肉黄度b*变异系数较大（26.18%）。通过相关性分析可知,肌肉黄度与红度存在较强正表型相关（r=0.52）,肌纤维直径与肌肉黄度存在弱负相关性（r=-0.16）。利用混合线性模型进行GWAS,发现了1个SNP与肌肉黄度b*潜在显著关联（-log10 P=8.28）。对最高效应SNP进行连锁不平衡检验,发现42个SNPs与最高点SNP存在高相关性（r2>0.4）,这些SNPs位于9号染色体0.37~0.43 Mb之间,区间中共包含7个基因。通过转录组测序数据分析,发现只有5个基因在胸肌组织中表达。对这5个基因进行功能注释,确定硒蛋白T（SELENOT）基因为影响肌肉黄度的候选基因。该结果为解析鸭胸肌肉色性状和提高鸭肉品质的遗传改良提供重要参考。  相似文献   

13.
南阳牛生长性状相关基因组区域全基因组关联分析   总被引：1，自引：0，他引：1  
本研究旨在筛选和鉴定与南阳牛生长性状相关的基因组区域和候选基因,从而更好地了解牛生长性状的遗传机制。试验共采集71头南阳牛母牛血样并提取基因组DNA,利用SLAF-seq（specific-locus amplified fragment sequencing）技术获得全基因组SNP标记并对试验个体基因型进行分型。对每头个体初生重及不同月龄（6、12、18、24、36）的体重、体高、体斜长、胸围和坐骨端宽及每6个月体增重等生长性状进行全基因组关联分析;获得显著相关的基因组区域后,对其中基因进行功能注释以筛选候选基因。结果显示,共获得141 755个筛选后的SNPs,通过全基因组关联分析鉴定出5个分别与12月龄体重（8号染色体：17 320 634~17 347 720 bp）、12月龄胸围（2号染色体：15 063 190~15 155 309 bp）、24月龄体斜长（11号染色体：60 727 342~81 425 987 bp）、36月龄坐骨端宽（14号染色体：15 635 762~15 643 272 bp）和12~18月龄体增重（26号染色体：40 456 192~40 456 477 bp）等生长性状显著相关的基因组区域（LOD≥6.35）。通过对5个基因组区域内的186个基因进行功能注释,共筛选得到11号染色体上的8个基因（BMP10、IFT172、SDC1、TCF23、TRIM54、RAB1A、VPS54和GDF7）与骨生长、肌肉发育和生长调控有关,建议其可优先作为牛生长性状相关候选基因进行进一步验证。  相似文献   

14.
We performed a genome‐wide association study (GWAS) and candidate gene analysis to: (i) evaluate the effectiveness of the GWAS in our small population by performing GWAS for carcass weight (CW) and fatty acid composition; (ii) detect novel candidate regions affecting non‐CW carcass traits, chemical composition and sugar; and (iii) evaluate the association of the candidate genes previously detected in CW and fatty acid composition with other economically important traits. A total of 574 Japanese Black cattle and 40 657 Single nucleotide polymorphisms were used. In addition, candidate gene analyses were performed to evaluate the association of three CW‐related genes and two fatty acid‐related genes with carcass traits, fatty acid composition, chemical composition and sugar. The significant regions with the candidate genes were detected for CW and fatty acid composition, and these results showed that a significant region would be detectable despite the small sample size. The novel candidate regions were detected on BTA23 for crude protein and on BTA19 for fructose. CW‐related genes associated with the rib‐eye area and fatty acid composition were identified, and fatty acid‐related genes had no relationship with other traits. Moreover, the favorable allele of CW‐related genes had an unfavorable effect on fatty acid composition.  相似文献   

15.
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16.
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.  相似文献   

17.
The lipid content and fatty acid (FA) profile have an important impact in human health as well as in the technological transformation and nutritional and organoleptic quality of meat. A genome-wide association study (GWAS) on 144 backcross pigs (25% Iberian × 75% Landrace) was performed for 32 traits associated with intramuscular FA composition and indices of FA metabolism. The GWAS was carried out using Qxpak 5.0 and the genotyping information obtained from the Porcine SNP60K BeadChip (Illumina Inc., San Diego, CA). Signals of significant association considering a false- discovery rate (q-value < 0.05) were observed in 15 of the 32 analyzed traits, and a total of 813 trait-associated SNP (TAS), distributed in 43 chromosomal intervals on almost all autosomes, were annotated. According to the clustering analysis based on functional classification, several of the annotated genes are related to FA composition and lipid metabolism. Some interesting positional concordances among TAS and previously reported QTL for FA compositions and/or other lipid traits were also found. These common genomic regions for different traits suggest pleiotropic effects for FA composition and were found primarily on SSC4, SSC8, and SSC16. These results contribute to our understanding of the complex genetic basis of FA composition and FA metabolism.  相似文献   

18.
全基因组关联分析(GWAS)是近年兴起的用于分析复杂性状的重要研究方法。高通量测序技术的成熟发展使得基于全基因组测序技术和基因芯片技术的GWAS解析畜禽复杂性状成为可能,GWAS的运用对畜禽经济性状相关的SNP、QTL和候选功能基因研究起到关键作用。本文主要对GWAS的基本原理和方法、优劣势以及GWAS在畜禽生长发育相关性状中的应用现状进行综述,并对GWAS在今后畜禽育种中的应用前景进行展望,以期为GWAS在畜禽育种中的深入研究提供参考。  相似文献   

19.
应用常染色体上的标记基因研究能够加快数量性状的遗传进展。亲代由标记基因遗传给后代的加性遗传方差值可以用来测定标记基因这种效益。分别在个体水平上以及在复合连续平衡的分离群体水平上建立了标记基因加性遗传方差值的理论方程。这些方程包括与标记基因连锁的数量性状位点数、这些数量性状位点的效应值以及与标记基因有关的重组率。并就分离群体中标记基因加性遗传方差的期望值进行了推导。在分离群体的系谱选择方案中,常染色体上遗传方差中绝大部分与位于该染色体上的标记基因相关。对于牛的一个平均长度染色体来讲,这部分值大约是该染色体孟德尔分离方差值的40% 。标记基因的位置效应和干扰因素对这一期望值的影响是很小的,而染色体的长度对期望方差值影响很大。如果标记基因缺乏多态型以及染色体替代效应估计偏差会大大降低MAS的选择效果。常染色体上标记基因遗传方差期望值的大小表明:即使当标记基因处在一个非活动位点,在分离群体中,仍有较大的染色体替代效应存在。  相似文献   

20.
Progress of genome wide association study in domestic animals   总被引：1，自引：0，他引：1  
ABSTRACT: Domestic animals are invaluable resources for study of the molecular architecture of complex traits. Although the mapping of quantitative trait loci (QTL) responsible for economically important traits in domestic animals has achieved remarkable results in recent decades, not all of the genetic variation in the complex traits has been captured because of the low density of markers used in QTL mapping studies. The genome wide association study (GWAS), which utilizes high-density single-nucleotide polymorphism (SNP), provides a new way to tackle this issue. Encouraging achievements in dissection of the genetic mechanisms of complex diseases in humans have resulted from the use of GWAS. At present, GWAS has been applied to the field of domestic animal breeding and genetics, and some advances have been made. Many genes or markers that affect economic traits of interest in domestic animals have been identified. In this review, advances in the use of GWAS in domestic animals are described.  相似文献   

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