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1.
Objective of this study was to assess the association of SNP in the diacylglycerol O-acyltransferase 1 (DGAT1), thyroglobulin (TG), and micromolar calcium-activated neutral protease (CAPN1) genes with carcass composition and meat quality traits in Bos indicus cattle. A population of Brahman calves (n = 479) was developed in central Florida from 1996 to 2000. Traits analyzed were ADG, hip height, slaughter weight, fat thickness, HCW, marbling score, LM area, estimated KPH fat, yield grade, retail yield, sensory panel tenderness score, carcass hump height, and cooked meat tenderness measured as Warner-Bratzler shear force at 7, 14, and 21 d postmortem. Single nucleotide polymorphisms previously reported in the TG and DGAT1 genes were used as markers on chromosome 14. Two previously reported and two new SNP in the CAPN1 gene were used as markers on chromosome 29. One SNP in CAPN1 was uninformative, and another one was associated with tenderness score (P < 0.05), suggesting the presence of variation affecting meat tenderness. All three informative SNP at the CAPN1 gene were associated with hump height (P < 0.02). The TG marker was associated with fat thickness and LMA (P < 0.05), but not with marbling score. No significant associations of the SNP in the DGAT1 gene were observed for any trait. Allele frequencies of the SNP in TG and CAPN1 were different in this Brahman population than in reported allele frequencies in Bos taurus populations. The results suggest that the use of molecular marker information developed in Bos taurus populations to Bos indicus populations may require development of appropriate additional markers.  相似文献   

2.
Quantitative trait loci for growth traits in beef cattle have been previously reported and fine-mapped in three chromosomal regions of 0 to 30 cM, 55 to 70 cM, and 70 to 80 cM of bovine chromosome 5. In this study, we further examined the association between gene-specific single nucleotide polymorphisms (SNP) of two positional candidate genes, bovine myogenic factor 5 (myf5) and insulin-like growth factor-1 (igf1), in the QTL regions and the birth weight (BWT), preweaning average daily gain (PWADG), and average daily gain on feed (ADGF) in commercial lines of Bos taurus. The QTL regions for the growth traits identified using a haplotype association analysis, which included the gene-specific SNP markers for both genes in this study, were in agreement with previous studies. The gene-specific SNP marker association analysis indicated that the SNP in myf5 had a significant additive effect on PWADG in the M1 line of Beefbooster Inc. (P < 0.10), and a significant additive effect (P < 0.05) and a significant dominance effect (P < 0.10) on ADGF in the M3 line of Beefbooster Inc. When the data from the two commercial lines were pooled, the SNP in myf5 showed a significant association with PWADG (P < 0.10) and with ADGF (P < 0.05). The association between the SNP and BWT, however, did not reach a significance level in the M1 line, the M3 line, or across the lines. For igf1, no significant association between the SNP and the growth traits was detected in either the M1 line or the M3 line, whereas there was only a significant dominance effect (P < 0.10) on BWT detected for the SNP in igfl when the data from the two commercial lines were pooled. These results suggest that myf5 is a strong candidate gene that influences PWADG and ADGF in beef cattle. The SNP of igf1 may not be a causative or close to the causative mutation that affects the three growth traits in the populations of beef cattle examined in this study. Other SNP of igf1 and myf5 or other genes in their respective chromosomal regions, however, should also be studied.  相似文献   

3.
Backfat thickness is one of the major quantitative traits that affects carcass quality in beef cattle. In this study, we identified and fine-mapped QTL for backfat EBV on bovine chromosomes 2, 5, 6, 19, 21, and 23 using an identical-by-descent haplotype-sharing analysis in a commercial line of Bos taurus. Eleven haplotypes were found to have significant associations with backfat EBV at the comparison-wise P-value threshold, and one at the chromosome-wise P-value threshold on bovine chromosomes 5, 6, 19, 21, and 23. On average, the 12 significant haplotypes had an effect of 0.62 SD on backfat EBV, ranging from 0.38 SD to 1.33 SD. The 12 significant haplotypes spanned nine chromosomal regions, one on chromosome 5 (65.4 to 70.0 cM), three on 6 (8.2 to 11.8 cM, 63.6 to 68.1 cM, and 81.5 to 83.0 cM), three on 19 (4.8 to 15.9 cM, 39.4 to 46.5 cM, and 65.7 to 99.5 cM), one on 21 (46.1 to 53.1 cM), and one on 23 (45.1 to 50.9 cM). Among the nine chromosomal regions, six were new QTL regions and three showed remarkable agreement with QTL regions that were previously reported. Eight of the nine QTL regions were localized to less than or close to 10 cM in genetic distance. The results provide a useful reference for further positional candidate gene research and marker-assisted selection for backfat.  相似文献   

4.
Twinning in cattle is a complex trait that is associated with economic loss and health issues such as abortion, dystocia, and reduced calf survival. Twinning-rate QTL have been detected previously on BTA5 in the North American Holstein and Norwegian dairy cattle populations and in a USDA herd selected for high twinning rate. In previous work with the North American Holstein population, the strongest evidence for a QTL was obtained from analysis of an extended, multiple-generation family. Using additional animals, an increased density of SNP marker association tests, and a combined linkage and linkage disequilibrium mapping method, we refined the position of this QTL in the North American Holstein population. Two sets of twinning-rate predicted transmitting abilities estimated during 2 different time periods in the North American dairy cattle population were used to provide validation of results. A total of 106 SNP and 3 microsatellites were used to scan the genomic region between 5 and 80 Mb on BTA5. Combined linkage-linkage disequilibrium analysis identified significant evidence for QTL within the 25- to 35-Mb and 64- to 70-Mb regions of BTA5. The IGF-1 gene (IGF1) was examined as a positional candidate gene and an SNP in intron 2 of IGF1 was significantly associated with twinning rate by using both data sets (P = 0.003 and P = 1.05 x 10(-6)). Replication of this association in other cattle populations will be required to examine the extent of linkage disequilibrium with the underlying quantitative trait nucleotide across breeds.  相似文献   

5.
Previously, a quantitative trait locus (QTL) that affects body weight (BW) at 4-12 weeks of age and carcass weight at 12 weeks of age had been mapped on chicken chromosome 1. After including more markers and individuals, the confidence interval was narrowed down to approximately 5.5 Mbps and located this QTL near a microsatellite marker (ADL328). This QTL is the same as the QTL for 12 bone traits, including metatarsus length and metatarsus circumference at 4, 6, 8, 10 and 12 weeks of age and keel length and metatarsus claw weight at 12 weeks of age, that was identified using the same population. In the current study, 1010 individuals from the Northeast Agricultural University F(2) resource population were used and 14 single-nucleotide polymorphism (SNPs) around ADL328 were developed to construct haplotypes, and an association analysis was performed to fine-map the QTL. The haplotypes were constructed on the basis of a sliding 'window', with three SNP markers included in each 'window'. The association analysis results indicated that the haplotypes in 'windows' 6-12 were significantly associated with BW and bone traits and suggested that the QTL for BW and bone traits was located between SNP8 and SNP14 or was in linkage disequilibrium with this region. The interval from SNP8 to SNP14 was approximately 400 kbps. This region contained five RefSeq genes (RB1, P2RY5, FNDC3A, MLNR and CAB39L) on the University of California Santa Cruz website. The RB1 gene was selected as a candidate gene and five SNPs were identified in the gene. The association results indicated that the RB1 gene was a major gene for BW and bone traits. The SNPs g.39692 G>A and g.77260 A>G in RB1 gene might be two quantitative trait nucleotides for BW and bone traits.  相似文献   

6.
Multiple genomic scans have identified QTL for backfat deposition across the porcine genome. The objective of this study was to detect SNP and genomic regions associated with ultrasonic backfat. A total of 74 SNP across 5 chromosomes (SSC 1, 3, 7, 8, and 10) were selected based on their proximity to backfat QTL or to QTL for other traits of interest in the experimental population. Gilts were also genotyped for a SNP thought to influence backfat in the thyroxine-binding globulin gene (TBG) on SSC X. Genotypic data were collected on 298 gilts, divided between the F8 and F10 generations of the US Meat Animal Research Center Meishan resource population (composition, one-quarter Meishan). Backfat depths were recorded by ultrasound from 3 locations along the back at approximately 210 and 235 d of age in the F8 and F10 generations, respectively. Ultrasound measures were averaged for association analyses. Regressors for additive, dominant, and parent-of-origin effects of each SNP were calculated using genotypic probabilities computed by allelic peeling algorithms in GenoProb. The association model included the fixed effects of scan date and TBG genotype, the covariates of weight and SNP regressors, and random additive polygenic effects to account for genetic similarities between animals not explained by known genotypes. Variance components for polygenic effects and error were estimated using MTDFREML. Initially, each SNP was fitted (once with and once without parent-of-origin effects) separately due to potential multi-collinearity between regressions of closely linked markers. To form a final model, all significant SNP across chromosomes were included in a common model and were individually removed in successive iterations based on their significance. Across all analyses, TBG was significant, with an additive effect of approximately 1.2 to 1.6 mm of backfat. Three SNP on SSC3 remained in the final model even though few studies have identified QTL for backfat on this chromosome. Two of these SNP exhibited irregular parent-of-origin effects and may not have been detected in other genome scans. One significant SNP on SSC7 remained in the final, backward-selected model; the estimated effect of this marker was similar in magnitude and direction to previously identified QTL. This SNP can potentially be used to introgress the leaner Meishan allele into commercial swine populations.  相似文献   

7.
In dairy cattle, many studies have reported quantitative trait loci (QTL) on the centromeric end of chromosome 14 that affect milk production traits. One of the candidate genes in this QTL region – thyroglobulin (TG) – was previously found to be significantly associated with marbling in beef cattle. Thus, based on QTL studies in dairy cattle and because of possible effects of this gene on fat metabolism, we investigated the association of TG with milk yield and composition in Holstein dairy cattle. A total of 1279 bulls from the Cooperative Dairy DNA Repository Holstein population were genotyped for a single nucleotide polymorphism in TG used previously in beef cattle studies. Analysis of 29 sire families showed no significant association between TG variants and milk production traits. Within‐sire family analysis suggests that TG is neither the responsible gene nor a genetic marker in association with milk production traits.  相似文献   

8.
乙酰辅酯A∶二酰甘油酰基转移酶(DGAT1)是甘油三脂合成过程中唯一的关键酶,对动物机体脂肪代谢、沉积起重要作用,已成为研究奶牛泌乳性状和肉牛主要经济性状的重要候选基因之一。近年来,随着相关研究的不断深入,研究者普遍认为DGAT1基因对奶牛的产奶量、乳脂率、乳蛋白率、乳糖率、乳脂肪酸及空怀天数、输精次数、初配年龄等繁殖性状均有显著影响,且与肉牛体脂也存在相关性。作者主要介绍了DGAT1基因的遗传多态性及其与经济性状关联分析在中国各地区不同品种奶牛、肉牛、水牛和牦牛上的研究进展,指出该基因对奶牛的产奶性能及肉牛的肉质性状、生长性状具有重要的调控作用。但由于环境条件、品种及选育背景等因素影响,DGAT1基因遗传多态性对不同地区不同牛群体的经济性状影响不尽相同。因此,要将DGAT1基因实际应用在品种选育工作中还需明确该基因对研究群体的具体遗传效应,并结合其他候选基因进行综合分析。  相似文献   

9.
DGAT1 is a microsomal enzyme that catalyses the final step in triglycerides synthesis. DGAT1‐deficient mice are viable, lean, fertile and resistant to diet induced obesity. We have previously identified a quantitative trait loci (QTL) on chromosome 4 that affects fatty acid composition in an F2 cross between Iberian × Landrace. The human DGAT1 gene is located on chromosome 8q24.3, this region aligns to porcine chromosome 4, making the pig DGAT1 gene a suggestive positional candidate gene for the QTL. In this study, we sequenced 1679 bp of the mRNA from animals of five pig breeds (Iberian, Landrace, Large White, Piétrian and Meishan) to identify genetic variants. One of the polymorphisms found creates a polymorphic HinfI restriction site and it was genotyped by PCR‐RFLP in these five pig breeds. Allele A was not found in the analysed Iberian and Landrace populations, whereas Meishan population presents the highest frequency (35%). The DGAT1 gene was located by radiation hybrid mapping to the porcine chromosome 4, outside the confidence interval for the fatty acid composition QTL and excludes it as a positional candidate gene.  相似文献   

10.
Previous research has identified differences in carcass characteristics across SNP in the bovine leptin gene at slaughter, but before feedlot operators implement selection and sorting strategies, more information is needed to determine how carcass characteristics change over time. The objective of this study was to investigate the effect of 2 leptin SNP on growth curve parameters for BW and backfat. Two SNP (UASMS2 and R25C) were genotyped on 1,653 cross-bred steers and heifers in a commercial feedlot. Up to 4 serial measures of BW and ultrasound estimates of backfat thickness were taken for each animal from the time of placement on feed to slaughter. The measures were used to estimate growth models that describe changes in BW and backfat thickness as a function of days on feed. Data analysis was carried out by estimating nonlinear mixed models to determine the individual and joint effect of each SNP on growth curve parameters. Brody growth curves were fit to the BW data. Variations in the R25C SNP did not significantly affect growth parameters individually or in combination with the UASMS2 SNP. Variations in the UASMS2 SNP were significant in Brody growth curve parameters for BW growth (P < 0.001). The genotype UASMS2-CC was the heaviest at the beginning of the feeding period and exhibited the largest asymptotic mature BW, but UASMS2-TT cattle exhibited the fastest rate of BW growth. A modified power function was fit to the serial ultrasound backfat measures. Models that included the combined effect of the R25C and UASMS2 SNP provided the best fit to the data. Genotypes differed significantly in power function parameters for backfat growth (P < 0.001). The R25C-CC/UASMS2-TT cattle had the smallest backfat thickness at placement. The genotype R25C-CC/UASMS2-TT exhibited the fastest backfat growth rate, whereas backfat in R25C-CC/UASMS2-CC cattle grew at the slowest rate. The association between leptin genotype and growth in BW and backfat presents opportunities to identify genetically distinct cattle and to differentially optimize feeding times accordingly.  相似文献   

11.
The primary goal of this study was to detect and confirm QTL on SSC6 for growth and fatness traits in 2 experimental F(2) intercrosses: Iberian x Landrace (IB x LR) and Iberian x Meishan (IB x MS), which were used in this study for the first time in a QTL analysis related to productive traits. For this purpose, single- and joint-population analyses with single and bivariate trait models of both populations were performed. The presence of the SSC6 QTL for backfat thickness previously identified in the IB x LR cross was detected in this population with additional molecular information, but also was confirmed in the IB x MS cross. In addition, a QTL affecting BW was detected in both crosses in a similar position to the QTL detected for backfat thickness. This is the first study in which a QTL affecting BW is detected on SSC6 in the IB x LR cross, as well as in the IB x MS resource population. Furthermore, we analyzed a previously described nonsynonymous leptin receptor (LEPR) SNP located in exon 14 (c.2002C > T) for causality with respect to this QTL within both F(2) populations. Our results supported the previously reported association between LEPR alleles and backfat thickness in the IB x LR cross, and this association was also confirmed within the IB x MS cross. An association not reported before between LEPR alleles and BW was identified in both populations.  相似文献   

12.
Leptin produced by adipocytes acts through leptin receptors in the hypothalamus to control appetite and food intake and thus communicates information about degree of fatness. It is thought that a degree of body fat is required for initiation of puberty and maintenance of reproductive function in mammals. The objective of this study was to determine whether polymorphisms in the leptin (LEP), leptin receptor (LEPR), paired box 5 (PAX5), aldo-keto reductase (AKR), and pro-opiomelanocortin (POMC) genes were associated with age, leptin concentration, backfat as an indicator of body condition, or BW at puberty in 3 lines of gilts and to characterize genetic relationships among these traits. The first 2 lines, born in 2001, were formed by crossing maternal White Cross (Yorkshire x Maternal Landrace) gilts to Duroc (n = 210) or (lean) Landrace (n = 207) boars. The remaining line (n = 507), born in 2002, was formed by crossing progeny of the Duroc- and Landrace-sired lines. At first estrus, age, BW (BWP), and backfat (BFP) at puberty were recorded and blood was collected for leptin assays. Nine SNP were detected in candidate genes/regions: 1 in LEP, 3 in LEPR, 1 in PAX5, 2 in AKR, and 2 in POMC. Animals were genotyped for each of the SNP; genotypes were validated using GenoProb. The association model included fixed effects of farrowing group, covariates of SNP genotypic probabilities (from GenoProb), and random additive polygenic effects to account for genetic similarities between animals not explained by SNP. Variance components for polygenic effects and error were estimated using MTDFREML. Leptin concentrations were logarithmically transformed for data analysis. All 4 traits were moderately to highly heritable (0.38 to 0.48). Age and leptin at puberty had a significant (P < 0.01) genetic correlation at -0.63 +/- 0.097, and the genetic correlation between BWP and age at puberty was 0.65 +/- 0.083 (P < 0.01). Significant additive associations (a; P < 0.05) were detected at PAX5 for age at puberty (a = 3.2 d) and for BFP (a = 0.61 mm). One SNP in LEPR was associated with leptin concentration (a = 0.31 log units; P < 0.05). The associations from PAX5 correspond to a QTL peak for age at puberty detected on SSC1. Although not necessarily the causative mutation, this result implies that a QTL that can decrease age at puberty without increasing BFP and BWP at puberty may exist in this region in commercial pigs.  相似文献   

13.
Effects of DGAT1 variants on milk production traits in German cattle breeds   总被引：15，自引：0，他引：15  
Various QTL mapping experiments led to the detection of a QTL in the centromeric region of cattle chromosome 14 that had a major effect on the fat content of milk. Recently, the gene encoding diacylglycerol O-acyltransferase (DGAT1) was proposed to be a positional and functional candidate for this trait. This study investigated the effects of a nonconservative lysine to alanine (K232A) substitution in DGAT1, which very likely represents the causal mutation, on milk production traits. Existing granddaughter designs for Fleckvieh and German Holstein, the two major dairy/dual-purpose breeds in Germany, were used to estimate allele frequencies and gene substitution effects for milk, fat, and protein yield, as well as fat and protein content. A restriction fragment length polymorphism assay was applied to diagnose the K232A substitution in DGAT1. Estimates of the allele frequencies for the lysine-encoding variant were based on maternally inherited alleles in sons and amounted to 0.072 for Fleckvieh and 0.548 for German Holstein. Effects of DGAT1 variants on content traits were pronounced; estimates of the gene substitution effect for the lysine-encoding variant were 0.35 and 0.28% for fat content and 0.10 and 0.06% for protein content in Fleckvieh and German Holstein, respectively. Conversely, negative effects of the lysine variant of -242 to -180 kg for Fleckvieh and -260 to -320 kg for German Holstein were revealed for milk yield from first to third lactation, resulting in enhanced fat yield of 7.5 to 14.8 kg in Fleckvieh and 7.6 to 10.7 kg in German Holstein. For protein yield, however, mainly negative effects of -3.6 to 0.2 kg in Fleckvieh and -4.8 to -5.2 kg in German Holstein were observed. Pearson correlations between residuals of milk yield and content traits were decreased when omitting DGAT1 effects in the analysis, thereby indicating that DGAT1 contributes to negative correlations between these traits. Molecular tests allow for the direct selection among variants; however, the benefits of the alternative alleles depend on economic weights given to the different milk production traits in the breeding goal.  相似文献   

14.
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   

15.
The objective of this study was to identify single-nucleotide polymorphisms using a bovine chromosome 14 high-density SNP panel after accounting for the effect of DGAT1. Linkage disequilibrium information and sire heterozygosity were used to select markers for linkage analysis on bovine chromosome 14 for milk production traits in 321 Holstein animals. Results show putative milk peaks at 42 and 61 cM, both at p<0.10, a fat yield peak at 42 and 63 cM, both at p<0.05; a protein yield peak at 42 (p<0.01) and 84 cM (p<0.05); fat per cent peaks at 3 (p<0.01) and 29 cM (p<0.05), and a protein per cent peak at 4 cM (p<0.05). Once quantitative trait loci positions were established, allele substitution effects for all markers were evaluated using the same statistical model. Overlaying information between quantitative trait loci (QTL) and allele effect analysis enabled the identification (p<0.01) of 20 SNPs under the milk yield QTL, 2 under both of the fat yield peaks, 8 and 9 under the protein yield peaks, 2 and 6 for the fat per cent peaks and 5 for the protein per cent peak. One SNP in particular, ss61514555:A>C, showed association with 3 of the 5 traits: milk (p=1.59E-04), fat (p=6.88E-05) and protein yields (p=5.76E-05). Overall, combining information from linkage disequilibrium, sire heterozygosity and genetic knowledge of traits enabled the characterization of additional markers with significant associations with milk production traits.  相似文献   

16.
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   

17.
The c.1326T>G single nucleotide polymorphism (SNP) in the NCAPG gene, which leads to an amino acid change of Ile442 to Met442, was previously identified as a candidate causative variation for a bovine carcass weight quantitative trait loci (QTL) on chromosome 6, which was associated with linear skeletal measurement gains and daily body weight gain at puberty. Recently, we identified the stature quantitative trait nucleotides (QTNs) in the PLAG1‐CHCHD7 intergenic region as the causative variations for another carcass weight QTL on chromosome 14. This study aimed to compare the effects of the two QTL on growth and carcass traits using 768 Japanese Black steers from a progeny testing program and to determine whether a genetic interaction was present between them. The FJX_250879 SNP representing the stature QTL was associated with linear skeletal measurements and average daily body weight gain at early and late periods during adolescence. A genetic interaction between FJX_250879 and NCAPG c.1326T>G was detected only for body and rump lengths. Both were associated with increased carcass weight and Longissimus muscle area, and NCAPG c.1326T>G was also associated with reduced subcutaneous fat thickness and increased carcass yield estimate. These results will provide useful information to improve carcass weight in Japanese Black cattle.  相似文献   

18.
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19.
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   

20.
The detection and mapping of genetic markers linked to quantitative trait loci (QTL) can be utilized to enhance genetic improvement of livestock populations. With the completion of the bovine genome sequence assembly, single nucleotide polymorphisms (SNP) assays spanning the whole bovine genome and research work on large scale identification, validation and analysis of genotypic variation in cattle has become possible. The objective of the present study was to perform a whole genome scan to identify and map QTL affecting milk production traits and somatic cell scores using linkage disequilibrium (LD) regression and 1536 SNP markers. Three and 18 SNP were found to be associated with only milk yield (MY) at a genome and chromosome wise significance (p < 0.05) level respectively. Among the 21 significant SNP, 16 were in a region reported to have QTL for MY in other dairy cattle populations and while the rest five were new QTL finding. Four SNP out of 21 are significant for the milk production traits (MY, fat yield, protein yield (PY), and milk contents) in the present study. Six and nine SNP were associated with PY at a genome and chromosome wise significant (p < 0.05) level respectively. Three and 17 SNP were found to be associated with FY at a genome and chromosome wise significant (p < 0.05) level. Five and seven SNP were mapped with somatic cell score at a genome and chromosome wise significant (p < 0.05) level respectively. The results of this study have revealed QTL for MY, PY, protein percentage, FY, fat percentage, somatic cell score and persistency of milk in the Canadian dairy cattle population. The chromosome regions identified in this study should be further investigated to potentially identify the causative mutations underlying the QTL.  相似文献   

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