Genomic selection has been demonstrated as a powerful technology to revolutionize animal breeding. However, marker density and minor allele frequency can affect the predictive ability of genomic estimated breeding val...Genomic selection has been demonstrated as a powerful technology to revolutionize animal breeding. However, marker density and minor allele frequency can affect the predictive ability of genomic estimated breeding values （GEBVs）. To investigate the impact of marker density and minor allele frequency on predictive ability, we estimated GEBVs by constructing the different subsets of single nucleotide polymorphisms （SNPs） based on varying markers densities and minor allele frequency （MAF） for average daily gain （ADG）, live weight （LW） and carcass weight （CW） in 1 059 Chinese Simmental beef cattle. Two strategies were proposed for SNP selection to construct different marker densities： 1） select evenly-spaced SNPs （Strategy 1 ）, and 2） select SNPs with large effects estimated from BayesB （Strategy 2）. Furthermore, predictive ability was assessed in terms of the correlation between predicted genomic values and corrected phenotypes from 10-fold cross-validation. Predictive ability for ADG, LW and CW using autosomal SNPs were 0.13＋0.002, 0.21＋0.003 and 0.25＋0.003, respectively. In our study, the predictive ability increased dramatically as more SNPs were included in analysis until 200K for Strategy 1. Under Strategy 2, we found the predictive ability slightly increased when marker densities increased from 5K to 20K, which indicated the predictive ability of 20K （3% of 770K） SNPs with large effects was equal to the predictive ability of using all SNPs. For different MAF bins, we obtained the highest predictive ability for three traits with MAF bin 0.01-0.1. Our result suggested that designing a low-density chip by selecting low frequency markers with large SNP effects sizes should be helpful for commercial application in Chinese Simmental cattle.展开更多
In this study,the effects of two types of premixed materials with different combinations of trace elements on the production performance and antioxidant capacity of simmental beef cattle were examined.Fifteen healthy ...In this study,the effects of two types of premixed materials with different combinations of trace elements on the production performance and antioxidant capacity of simmental beef cattle were examined.Fifteen healthy simmental beef cattle of similar weight(approximately 330 kg),the same age(12 months),without castration,and a good physique were divided into three groups,with five beef cattle in each group.Food of Group Ⅰ beef cattle was supplemented with a commercially marketed 5% compound trace element premixture for fine beef cattle.Food of Group Ⅱ beef cattle was supplemented with a 5% compound microelement premixture for beef cattle that was designed to address local nutrient deficiencies and surpluses.In the blank control group,the beef cattle were not fed a premixture.The pretest period was 15 days,and the test period was divided into prefattening(45 days)and postfattening(45 days)stages.Body weight and body size indices were recorded at 1,2 and 3 months,and blood samples were collected regularly.In Group Ⅰ,the daily weight gain increased significantly by 15.7% compared with that of the control group.The largest daily weight gain was in Group Ⅱ,which increased by 31.6% compared with that in the control.During the test period of 90 days,the body size indices of the three different groups increased in different months,with significant increases in the indices for both test groups compared with those of the control.In Group Ⅰ,the activity of CP,the total activity of SOD and Cu-Zn-SOD increased significantly(p<0.05)compared with those in the control group,with a highly significant increase observed in GSH-PX activity(p<0.01).In Group Ⅱ,the increases in the activity of CP and the total activity of SOD and Cu-Zn-SOD were highly significant compared with those in the control group(p<0.01).In addition,a significant increase was observed in GSH-PX activity(p<0.05).Based on pretest results,the concentrations of Cu,Zn,Mo,Mn,Se and Co in the blood of experimental beef cattle were lower than those of the normal range.After feeding for 90 days,the concentrations of Cu,Zn,Mo,Mn,Se and Co in the blood of Groups Ⅰ and Ⅱ were significantly higher than those in the control group(p<0.05).The concentrations of elements in the blood of Group Ⅱ were close to the appropriate levels.Thus,the effects of the specifically designed compound microelement premixture on the prevention of nutrient imbalances and control of beef cattle nutrition metabolism and the production of fattened beef cattle were significant.展开更多
基金supported by the National Natural Science Foundation of China(31201782,31672384 and 31372294)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(ASTIPIAS03)+3 种基金the Cattle Breeding Innovative Research Team of Chinese Academy of Agricultural Sciences(cxgc-ias-03)the Key Technology R&D Program of China during the 12th Five-Year Plan period(2011BAD28B04)the National High Technology Research and Development Program of China(863 Program 2013AA102505-4)the Beijing Natural Science Foundation,China(6154032)
文摘Genomic selection has been demonstrated as a powerful technology to revolutionize animal breeding. However, marker density and minor allele frequency can affect the predictive ability of genomic estimated breeding values （GEBVs）. To investigate the impact of marker density and minor allele frequency on predictive ability, we estimated GEBVs by constructing the different subsets of single nucleotide polymorphisms （SNPs） based on varying markers densities and minor allele frequency （MAF） for average daily gain （ADG）, live weight （LW） and carcass weight （CW） in 1 059 Chinese Simmental beef cattle. Two strategies were proposed for SNP selection to construct different marker densities： 1） select evenly-spaced SNPs （Strategy 1 ）, and 2） select SNPs with large effects estimated from BayesB （Strategy 2）. Furthermore, predictive ability was assessed in terms of the correlation between predicted genomic values and corrected phenotypes from 10-fold cross-validation. Predictive ability for ADG, LW and CW using autosomal SNPs were 0.13＋0.002, 0.21＋0.003 and 0.25＋0.003, respectively. In our study, the predictive ability increased dramatically as more SNPs were included in analysis until 200K for Strategy 1. Under Strategy 2, we found the predictive ability slightly increased when marker densities increased from 5K to 20K, which indicated the predictive ability of 20K （3% of 770K） SNPs with large effects was equal to the predictive ability of using all SNPs. For different MAF bins, we obtained the highest predictive ability for three traits with MAF bin 0.01-0.1. Our result suggested that designing a low-density chip by selecting low frequency markers with large SNP effects sizes should be helpful for commercial application in Chinese Simmental cattle.
基金Supported by the National Science and Technology Support Program Project(2011BAD47B04)
文摘In this study,the effects of two types of premixed materials with different combinations of trace elements on the production performance and antioxidant capacity of simmental beef cattle were examined.Fifteen healthy simmental beef cattle of similar weight(approximately 330 kg),the same age(12 months),without castration,and a good physique were divided into three groups,with five beef cattle in each group.Food of Group Ⅰ beef cattle was supplemented with a commercially marketed 5% compound trace element premixture for fine beef cattle.Food of Group Ⅱ beef cattle was supplemented with a 5% compound microelement premixture for beef cattle that was designed to address local nutrient deficiencies and surpluses.In the blank control group,the beef cattle were not fed a premixture.The pretest period was 15 days,and the test period was divided into prefattening(45 days)and postfattening(45 days)stages.Body weight and body size indices were recorded at 1,2 and 3 months,and blood samples were collected regularly.In Group Ⅰ,the daily weight gain increased significantly by 15.7% compared with that of the control group.The largest daily weight gain was in Group Ⅱ,which increased by 31.6% compared with that in the control.During the test period of 90 days,the body size indices of the three different groups increased in different months,with significant increases in the indices for both test groups compared with those of the control.In Group Ⅰ,the activity of CP,the total activity of SOD and Cu-Zn-SOD increased significantly(p<0.05)compared with those in the control group,with a highly significant increase observed in GSH-PX activity(p<0.01).In Group Ⅱ,the increases in the activity of CP and the total activity of SOD and Cu-Zn-SOD were highly significant compared with those in the control group(p<0.01).In addition,a significant increase was observed in GSH-PX activity(p<0.05).Based on pretest results,the concentrations of Cu,Zn,Mo,Mn,Se and Co in the blood of experimental beef cattle were lower than those of the normal range.After feeding for 90 days,the concentrations of Cu,Zn,Mo,Mn,Se and Co in the blood of Groups Ⅰ and Ⅱ were significantly higher than those in the control group(p<0.05).The concentrations of elements in the blood of Group Ⅱ were close to the appropriate levels.Thus,the effects of the specifically designed compound microelement premixture on the prevention of nutrient imbalances and control of beef cattle nutrition metabolism and the production of fattened beef cattle were significant.
