Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objec...Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.展开更多
为了筛选华西牛和雪龙黑牛背最长肌重量相关的遗传标记和候选基因,试验以1478头华西牛和452头雪龙黑牛为研究对象,对其背最长肌重量性状进行全基因组关联分析(genome-wide association study,GWAS),即测定其屠宰后背最长肌重量表型数据...为了筛选华西牛和雪龙黑牛背最长肌重量相关的遗传标记和候选基因,试验以1478头华西牛和452头雪龙黑牛为研究对象,对其背最长肌重量性状进行全基因组关联分析(genome-wide association study,GWAS),即测定其屠宰后背最长肌重量表型数据,利用Illumina Bovine-HD(770K)芯片对其基因组进行基因分型,采用FarmCPU模型和GEMMA模型对质控后的芯片数据进行GWAS,挖掘与华西牛和雪龙黑牛背最长肌重量显著相关的单核苷酸多态性(single nucleotide polymorphism,SNP)位点和候选基因。结果表明:华西牛与雪龙黑牛群体背最长肌重量表型性状均符合正态分布,且二者芯片数据经过质控后分别得到607198,511320个SNP位点,这些SNP位点在二者各个染色体上的分布比较均匀;利用FarmCPU模型在华西牛与雪龙黑牛群体分别检测到12个和9个与其背最长肌重量显著相关的SNP位点,且华西牛群体的显著SNP位点分别位于1,5,7,11,12,13,15,16,22,23号染色体上,鉴定到KCNAB1、PFN2、RNF13、TTLL1、MCAT、CREB3L3、ZBTB7A、MAP2K2、CAMKMT、ZC3H13、OPTN、MCM10、UCMA、OVOL2、PET117、KAT14、MAML2、HHAT、FHIT和LY86共20个候选基因;雪龙黑牛群体的SNP位点分别位于4,16,27号染色体上,鉴定到PCLO、DCTD、WWC2共3个候选基因;利用GEMMA模型在华西牛与雪龙黑牛群体中分别检测到6个与其背最长肌重量显著相关的SNP位点,其中华西牛群体的SNP位点位于13号染色体上,鉴定到GATA3、TAF3、ODAD2、SNX5、MGME1、OVOL2、KAT14、PET117共8个候选基因;雪龙黑牛群体的SNP位点位于1,4,5,25号染色体上,但未鉴定到有效的候选基因。说明在华西牛和雪龙黑牛群体中分别检测到的18个和15个SNP位点与注释到的25个和3个候选基因可作为改良牛背最长肌重量的新的分子标记和候选基因。展开更多
Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and ...Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and improve tenderness;however, there has been no direct correlation demonstrated between beef taste and oleic acid. To investigate genes affecting other fatty acids other than oleic acid, polymorphisms of the fatty acid desaturase 2 (FADS2) gene were genotyped and associations with fatty acid profile in JBK beef were investigated. Amplifications of 5’-flanking regions, 12 exons, and 3’-untranslated regions of the FADS2 gene in three Japanese and five Western cattle breeds via PCR, were amplified, sequenced and SNPs were identified using specific TaqMan genotyping assay. Fatty acid composition of intramuscular adipose tissue of the Trapezius muscle was analyzed in JBK steers. Six of the 15 identified SNPs are novel and have never been registered in any public bovine SNP database. A non-synonymous SNP (rs211580559;C > T;294 Ala > Val) in exon 7 was examined in order to evaluate its association with fatty acid profiles. The data showed that highly significant association existed between rs211580559 and C18:2 (n-6) composition, and accounted for 22.3% of the variation. There were no significant relationships between rs2115-80559 and the other fatty acids. It was concluded that rs211580559 of the FADS2 gene may be a useful selection marker for reducing unfavorable volatiles generated from linoleic acid in JBK beef during the cooking process.展开更多
文摘Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.
文摘Beef from Japanese Black cattle (JBK), is popular in Japan and valued for its highly marbled fat content. In JBK, genes affecting oleic acid content in meat have been studied mainly to lower the fat melting point and improve tenderness;however, there has been no direct correlation demonstrated between beef taste and oleic acid. To investigate genes affecting other fatty acids other than oleic acid, polymorphisms of the fatty acid desaturase 2 (FADS2) gene were genotyped and associations with fatty acid profile in JBK beef were investigated. Amplifications of 5’-flanking regions, 12 exons, and 3’-untranslated regions of the FADS2 gene in three Japanese and five Western cattle breeds via PCR, were amplified, sequenced and SNPs were identified using specific TaqMan genotyping assay. Fatty acid composition of intramuscular adipose tissue of the Trapezius muscle was analyzed in JBK steers. Six of the 15 identified SNPs are novel and have never been registered in any public bovine SNP database. A non-synonymous SNP (rs211580559;C > T;294 Ala > Val) in exon 7 was examined in order to evaluate its association with fatty acid profiles. The data showed that highly significant association existed between rs211580559 and C18:2 (n-6) composition, and accounted for 22.3% of the variation. There were no significant relationships between rs2115-80559 and the other fatty acids. It was concluded that rs211580559 of the FADS2 gene may be a useful selection marker for reducing unfavorable volatiles generated from linoleic acid in JBK beef during the cooking process.
