山羊基因组选择的展望
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摘要
基因组选择作为一种现代的育种手段,可以改善家畜的生产性能,缩短世代间隔,有效实现畜禽的早期选择。随着数量遗传学的发展、分子标记技术的提高、QTL技术的进步和GWAS的深入研究,为山羊基因组选择奠定了基础。本文综述了基因组选择的理论、方法和影响基因组选择准确性的关键因素,总结了山羊基因组的研究进展,为实现山羊基因组选择提供一定的借鉴,可以有效加快其育种效率。
As a modern breeding technology, genomic selection can improve production performance, shorten generation gap and realize early selection of animal effectively. With the development of quantitative genetics, improvement of molecular marker technology, progress of QTL technology and the in-depth study of GWAS, it laid the foundation for genome selection in goats. In this review, the theory and method of genome selection and key factors affecting the accuracy of genome selection are demonstrated. Additionally, research progress of goat genome is summarized. All of these will be helpful for realizing genomic selection in goat and improving breeding efficiency.
As a modern breeding technology, genomic selection can improve production performance, shorten generation gap and realize early selection of animal effectively. With the development of quantitative genetics, improvement of molecular marker technology, progress of QTL technology and the in-depth study of GWAS, it laid the foundation for genome selection in goats. In this review, the theory and method of genome selection and key factors affecting the accuracy of genome selection are demonstrated. Additionally, research progress of goat genome is summarized. All of these will be helpful for realizing genomic selection in goat and improving breeding efficiency.
引文
[1] 张沅. 家畜育种学[M].北京:中国农业出版社, 2001.
[2]刘志娟, 石双, 和杜富林, 羊绒业可持续发展面临的问题及对策——以鄂尔多斯市鄂托克旗为例[J]. 内蒙古农业大学学报(社会科学版), 2014. 16(6):32-36.
[3]Li X,Su R,Wan W,et al.Identification of selection signals by large-scale whole-genome resequencing of cashmere goats[J].Scientific Reports,2017,7(1):15142.
[4]Thepparat M, Boonkum W, Duangjinda M, et al. Genetic evaluation using random regression models with different covariance functions for test-day milk yield in an admixture population of Thailand goats[J]. Animal Science Journal, 2015, 86(7):655-660.
[5]杨晓虹, 道尔吉,李金泉, 等. 影响内蒙古白绒山羊性状的非遗传因素分析[J]. 内蒙古农业大学学报(自然科学版),2003. 24(4): 44-50.
[6]Mia M M, Khandoker M A M Y, Husain S S, et al. Genetic evaluation of growth traits of Black Bengal goat[J]. Iranian Journal of Applied Animal Science, 2013(2):845-852.
[7]Rashidi A, Sheikhahmadi M, Rostamzadeh J, et al. Genetic and phenotypic parameter estimates of body weight at different ages and yearling fleece weight in Markhoz goats[J]. Asian-Australasian journal of animal sciences, 2008, 21(10):1395-1403.
[8]Visser C, Snyman M A, Marlek?ster E V, et al. Genetic parameters for physical and quality traits of mohair in South African Angora goats[J]. Small Ruminant Research, 2009, 87(1):27-32.
[9]魏永龙. 白绒山羊生长性状遗传评估模型及遗传参数估计的研究[D].呼和浩特:内蒙古农业大学, 2014.
[10]张文. 内蒙古绒山羊毛被生长规律的研究[D].呼和浩特:内蒙古农业大学, 2011.
[11]李学武, 王瑞军, 王志英,等. 内蒙古绒山羊不同毛被类型遗传参数估计及遗传进展研究[J]. 中国农业大学学报,2018,23(4):53-59.
[12]王志英. 内蒙古绒山羊绒毛品质性状早期选择原理与方法的研究[D]. 内蒙古农业大学, 2016.
[13]Hayes B J, Bowman P J, Chamberlain A J, et al. Invited review: Genomic selection in dairy cattle: progress and challenges[J]. Journal of Dairy Science, 2009, 92(2):433-443.
[14]Meuwissen T H, Hayes B J, Goddard M E. Prediction of total genetic value using genome-wide dense marker maps[J]. Genetics, 2001, 157(4):1819-29.
[15]Meuwissen T, Goddard M. Accurate prediction of genetic values for complex traits by whole-genome resequencing[J]. Genetics, 2010, 185(2):623-631.
[16]Nirea K G, Meuwissen T H E. Improving production efficiency in the presence of genotype by environment interactions in pig genomic selection breeding programmes[J]. Journal of Animal Breeding & Genetics, 2016, 134(2).
[17]Calenge F, Legarra A, Beaumont C. Genomic selection for carrier-state resistance in chicken commercial lines[J]. Bmc Proceedings, 2011, 5(4):1-3.
[18]Verbyla K L, Hayes B J, Bowman P J, et al. Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle[J]. Genetics Research, 2009, 91(5):307-311.
[19]Dong Y, Xie M, Jiang Y, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)[J]. Nature Biotechnology, 2013, 31(2):135-141.
[20]Carillier C, Larroque H, Palhière I, et al. A first step toward genomic selection in the multi-breed French dairy goat population[J]. Journal of Dairy Science, 2013, 96(11):7294-7305.
[21]Tosser-Klopp G, Bardou P, Bouchez O, et al. Design and characterization of a 52K SNP chip for goats[J]. Plos One, 2014, 9(1):e86227.
[22]JIN Mei,GUO ChunLi,HU Jinghui,et al.Correlation Analysis of Economic Traits in Liaoning New Breed of Cashmere Goats Using Microsatellite DNA Markers[J].Acta Genetica Sinica,2006,33(3):230-235.
[23]Naicy T, Venkatachalapathy R T, Aravindakshan T V, et al. Relative abundance of tissue mRNA and association of the single nucleotide polymorphism of the goat NGF gene with prolificacy[J]. Animal Reproduction Science, 2016, 173:42-48.
[24]Mucha S, Mrode R, Coffey M, et al. Genome-wide association study of conformation and milk yield in mixed-breed dairy goats[J]. Journal of Dairy Science, 2018, 101(3):2213.
[25]Hayes B J, Bowman P J, Chamberlain A J, et al. Invited review: Genomic selection in dairy cattle: progress and challenges[J]. Journal of Dairy Science, 2009, 92(2):433-443.
[26]Powell J E, Visscher P M, Goddard M E. Reconciling the analysis of IBD and IBS in complex trait studies[J]. Nature Reviews Genetics, 2010, 11(11):800.
[27]Vanraden, P.M. and R. Wiggans, GENETICS AND BREEDING Productive Life Evaluations: Calculation, Accuracy, and Economic Value[J]. Journal of Dairy Science, 2008. 78(3):631-8.
[28]Piepho H P, Ogutu J O, Schulzstreeck T, et al. Efficient Computation of Ridge-Regression Best Linear Unbiased Prediction in Genomic Selection in Plant Breeding[J]. Crop Science, 2012, 52(3):1093.
[29]Wang C, Ding X, Liu J, et al. [Bayesian methods for genomic breeding value estimation][J]. Hereditas, 2014, 36(2):111.
[30]Meuwissen Theo H E, Solberg T R, Ross S, et al. A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value[J]. Genetics Selection Evolution,2009,41(1):2-2.
[31]Habier D. Extension of the bayesian alphabet for genomic selection[J]. Bmc Bioinformatics, 2011, 12(1):186.
[32]Moala, F.A., P.L. Ramos, and J.A. Achcar, Bayesian Inference for Two-Parameter Gamma Distribution Assuming Different Noninformative Priors[J]. Revista Colombiana De Estadistica, 2013.36(2):317-318.
[33]Park, T. and G. Casella, The Bayesian Lasso[J]. Publications of the American Statistical Association, 2008. 103(482):681-686.
[34]Br·ndum R F, Su G, Lund M S, et al. Genome position specific priors for genomic prediction[J]. Bmc Genomics, 2012, 13(1):543.
[35]Hozé C, Fritz S, Phocas F, et al. Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population[J]. Journal of Dairy Science, 2014, 97(6):3918-3929.
[36]Liu Z, Seefried F R, Reinhardt F, et al. Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction[J]. Genetics Selection Evolution, 2011, 43(1):19-19.
[37]吴晓平. 基于SNP芯片和全测序数据的奶牛全基因组关联分析和基因组选择研究[D].北京:中国农业大学, 2014.
[38]Muir W M. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters[J]. Journal of Animal Breeding and Genetics, 2015, 124(6):342-355.
[39]Goddard M. Genomic selection: prediction of accuracy and maximisation of long term response[J]. Genetica, 2009, 136(2):245-257.
[40]Habier D, Tetens J, Seefried F R, et al. The impact of genetic relationship information on genomic breeding values in German Holstein cattle[J]. Genetics Selection Evolution, 2010, 42(1):5-5.
[41]Berry D P, Mcclure M C, Mullen M P. Within‐ and across‐breed imputation of high‐density genotypes in dairy and beef cattle from medium-and low-density genotypes[J]. Journal of Animal Breeding & Genetics, 2014, 131(3):165-172.
[42]Calus M P, Meuwissen T H, de Roos A P, et al. Accuracy of genomic selection using different methods to define haplotypes[J]. Genetics, 2008, 178(1):553.
[43]Calus Mario P L, Meuwissen Theo H E, Windig J J, et al. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values[J]. Genetics Selection Evolution, 2009, 41(1):11-11.
[44]Villumsen T M, Janss L, Lund M S. The importance of haplotype length and heritability using genomic selection in dairy cattle[J]. Journal of Animal Breeding & Genetics, 2015, 126(1):3-13.
[45]Kolbehdari D, Schaeffer L R, Robinson J A. Estimation of genome-wide haplotype effects in half-sib designs[J]. Journal of Animal Breeding & Genetics, 2015, 124(6):356-361.
[46]Cleveland M A, Hickey J M, Forni S. A common dataset for genomic analysis of livestock populations[J]. G3 (Bethesda, Md.), 2012, 2(4):429.
[47]Su G, Guldbrandtsen B, Gregersen V R, et al. Preliminary investigation on reliability of genomic estimated breeding values in the Danish Holstein population[J]. Journal of Dairy Science, 2010, 93(3):1175-1183.
[48]Akanno E C, Schenkel F S, Sargolzaei M, et al. Persistency of accuracy of genomic breeding values for different simulated pig breeding programs in developing countries[J]. Journal of Animal Breeding and Genetics, 2015, 131(5):367-378.
[49]王延晖. 基于加性显性模型的基因组选择应用于西门塔尔牛的初步研究[D].北京:中国农业科学院, 2014.
[50]Moser G, Tier B, Crump R E, et al. A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers[J]. Genetics Selection Evolution,2009, 41(1):56.
[51]Clark S A, Hickey J M, Werf J H V D. Different models of genetic variation and their effect on genomic evaluation[J]. Genetics Selection Evolution,2011, 43(1):18-18.
[52]Colombani C, Legarra A, Fritz S, et al. Application of Bayesian least absolute shrinkage and selection operator (LASSO) and BayesCπ methods for genomic selection in French Holstein and Montbéliarde breeds[J]. Journal of Dairy Science, 2013, 96(1):575-591.
[53]Qiao X, Su R, Wang Y, et al. Genome-wide Target Enrichment-aided Chip Design: a 66 KSNP Chip for Cashmere Goat[J]. Sci Rep, 2017,7(1):8621.
[54]Bickhart D M, Rosen B D, Koren S, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome[J]. Nature Genetics,2017,49(4):643-650.
[55]Benjelloun B, Alberto F J, Streeter I, et al. Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data[J]. Frontiers in Genetics, 2015, 6:107.
[2]刘志娟, 石双, 和杜富林, 羊绒业可持续发展面临的问题及对策——以鄂尔多斯市鄂托克旗为例[J]. 内蒙古农业大学学报(社会科学版), 2014. 16(6):32-36.
[3]Li X,Su R,Wan W,et al.Identification of selection signals by large-scale whole-genome resequencing of cashmere goats[J].Scientific Reports,2017,7(1):15142.
[4]Thepparat M, Boonkum W, Duangjinda M, et al. Genetic evaluation using random regression models with different covariance functions for test-day milk yield in an admixture population of Thailand goats[J]. Animal Science Journal, 2015, 86(7):655-660.
[5]杨晓虹, 道尔吉,李金泉, 等. 影响内蒙古白绒山羊性状的非遗传因素分析[J]. 内蒙古农业大学学报(自然科学版),2003. 24(4): 44-50.
[6]Mia M M, Khandoker M A M Y, Husain S S, et al. Genetic evaluation of growth traits of Black Bengal goat[J]. Iranian Journal of Applied Animal Science, 2013(2):845-852.
[7]Rashidi A, Sheikhahmadi M, Rostamzadeh J, et al. Genetic and phenotypic parameter estimates of body weight at different ages and yearling fleece weight in Markhoz goats[J]. Asian-Australasian journal of animal sciences, 2008, 21(10):1395-1403.
[8]Visser C, Snyman M A, Marlek?ster E V, et al. Genetic parameters for physical and quality traits of mohair in South African Angora goats[J]. Small Ruminant Research, 2009, 87(1):27-32.
[9]魏永龙. 白绒山羊生长性状遗传评估模型及遗传参数估计的研究[D].呼和浩特:内蒙古农业大学, 2014.
[10]张文. 内蒙古绒山羊毛被生长规律的研究[D].呼和浩特:内蒙古农业大学, 2011.
[11]李学武, 王瑞军, 王志英,等. 内蒙古绒山羊不同毛被类型遗传参数估计及遗传进展研究[J]. 中国农业大学学报,2018,23(4):53-59.
[12]王志英. 内蒙古绒山羊绒毛品质性状早期选择原理与方法的研究[D]. 内蒙古农业大学, 2016.
[13]Hayes B J, Bowman P J, Chamberlain A J, et al. Invited review: Genomic selection in dairy cattle: progress and challenges[J]. Journal of Dairy Science, 2009, 92(2):433-443.
[14]Meuwissen T H, Hayes B J, Goddard M E. Prediction of total genetic value using genome-wide dense marker maps[J]. Genetics, 2001, 157(4):1819-29.
[15]Meuwissen T, Goddard M. Accurate prediction of genetic values for complex traits by whole-genome resequencing[J]. Genetics, 2010, 185(2):623-631.
[16]Nirea K G, Meuwissen T H E. Improving production efficiency in the presence of genotype by environment interactions in pig genomic selection breeding programmes[J]. Journal of Animal Breeding & Genetics, 2016, 134(2).
[17]Calenge F, Legarra A, Beaumont C. Genomic selection for carrier-state resistance in chicken commercial lines[J]. Bmc Proceedings, 2011, 5(4):1-3.
[18]Verbyla K L, Hayes B J, Bowman P J, et al. Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle[J]. Genetics Research, 2009, 91(5):307-311.
[19]Dong Y, Xie M, Jiang Y, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)[J]. Nature Biotechnology, 2013, 31(2):135-141.
[20]Carillier C, Larroque H, Palhière I, et al. A first step toward genomic selection in the multi-breed French dairy goat population[J]. Journal of Dairy Science, 2013, 96(11):7294-7305.
[21]Tosser-Klopp G, Bardou P, Bouchez O, et al. Design and characterization of a 52K SNP chip for goats[J]. Plos One, 2014, 9(1):e86227.
[22]JIN Mei,GUO ChunLi,HU Jinghui,et al.Correlation Analysis of Economic Traits in Liaoning New Breed of Cashmere Goats Using Microsatellite DNA Markers[J].Acta Genetica Sinica,2006,33(3):230-235.
[23]Naicy T, Venkatachalapathy R T, Aravindakshan T V, et al. Relative abundance of tissue mRNA and association of the single nucleotide polymorphism of the goat NGF gene with prolificacy[J]. Animal Reproduction Science, 2016, 173:42-48.
[24]Mucha S, Mrode R, Coffey M, et al. Genome-wide association study of conformation and milk yield in mixed-breed dairy goats[J]. Journal of Dairy Science, 2018, 101(3):2213.
[25]Hayes B J, Bowman P J, Chamberlain A J, et al. Invited review: Genomic selection in dairy cattle: progress and challenges[J]. Journal of Dairy Science, 2009, 92(2):433-443.
[26]Powell J E, Visscher P M, Goddard M E. Reconciling the analysis of IBD and IBS in complex trait studies[J]. Nature Reviews Genetics, 2010, 11(11):800.
[27]Vanraden, P.M. and R. Wiggans, GENETICS AND BREEDING Productive Life Evaluations: Calculation, Accuracy, and Economic Value[J]. Journal of Dairy Science, 2008. 78(3):631-8.
[28]Piepho H P, Ogutu J O, Schulzstreeck T, et al. Efficient Computation of Ridge-Regression Best Linear Unbiased Prediction in Genomic Selection in Plant Breeding[J]. Crop Science, 2012, 52(3):1093.
[29]Wang C, Ding X, Liu J, et al. [Bayesian methods for genomic breeding value estimation][J]. Hereditas, 2014, 36(2):111.
[30]Meuwissen Theo H E, Solberg T R, Ross S, et al. A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value[J]. Genetics Selection Evolution,2009,41(1):2-2.
[31]Habier D. Extension of the bayesian alphabet for genomic selection[J]. Bmc Bioinformatics, 2011, 12(1):186.
[32]Moala, F.A., P.L. Ramos, and J.A. Achcar, Bayesian Inference for Two-Parameter Gamma Distribution Assuming Different Noninformative Priors[J]. Revista Colombiana De Estadistica, 2013.36(2):317-318.
[33]Park, T. and G. Casella, The Bayesian Lasso[J]. Publications of the American Statistical Association, 2008. 103(482):681-686.
[34]Br·ndum R F, Su G, Lund M S, et al. Genome position specific priors for genomic prediction[J]. Bmc Genomics, 2012, 13(1):543.
[35]Hozé C, Fritz S, Phocas F, et al. Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population[J]. Journal of Dairy Science, 2014, 97(6):3918-3929.
[36]Liu Z, Seefried F R, Reinhardt F, et al. Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction[J]. Genetics Selection Evolution, 2011, 43(1):19-19.
[37]吴晓平. 基于SNP芯片和全测序数据的奶牛全基因组关联分析和基因组选择研究[D].北京:中国农业大学, 2014.
[38]Muir W M. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters[J]. Journal of Animal Breeding and Genetics, 2015, 124(6):342-355.
[39]Goddard M. Genomic selection: prediction of accuracy and maximisation of long term response[J]. Genetica, 2009, 136(2):245-257.
[40]Habier D, Tetens J, Seefried F R, et al. The impact of genetic relationship information on genomic breeding values in German Holstein cattle[J]. Genetics Selection Evolution, 2010, 42(1):5-5.
[41]Berry D P, Mcclure M C, Mullen M P. Within‐ and across‐breed imputation of high‐density genotypes in dairy and beef cattle from medium-and low-density genotypes[J]. Journal of Animal Breeding & Genetics, 2014, 131(3):165-172.
[42]Calus M P, Meuwissen T H, de Roos A P, et al. Accuracy of genomic selection using different methods to define haplotypes[J]. Genetics, 2008, 178(1):553.
[43]Calus Mario P L, Meuwissen Theo H E, Windig J J, et al. Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values[J]. Genetics Selection Evolution, 2009, 41(1):11-11.
[44]Villumsen T M, Janss L, Lund M S. The importance of haplotype length and heritability using genomic selection in dairy cattle[J]. Journal of Animal Breeding & Genetics, 2015, 126(1):3-13.
[45]Kolbehdari D, Schaeffer L R, Robinson J A. Estimation of genome-wide haplotype effects in half-sib designs[J]. Journal of Animal Breeding & Genetics, 2015, 124(6):356-361.
[46]Cleveland M A, Hickey J M, Forni S. A common dataset for genomic analysis of livestock populations[J]. G3 (Bethesda, Md.), 2012, 2(4):429.
[47]Su G, Guldbrandtsen B, Gregersen V R, et al. Preliminary investigation on reliability of genomic estimated breeding values in the Danish Holstein population[J]. Journal of Dairy Science, 2010, 93(3):1175-1183.
[48]Akanno E C, Schenkel F S, Sargolzaei M, et al. Persistency of accuracy of genomic breeding values for different simulated pig breeding programs in developing countries[J]. Journal of Animal Breeding and Genetics, 2015, 131(5):367-378.
[49]王延晖. 基于加性显性模型的基因组选择应用于西门塔尔牛的初步研究[D].北京:中国农业科学院, 2014.
[50]Moser G, Tier B, Crump R E, et al. A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers[J]. Genetics Selection Evolution,2009, 41(1):56.
[51]Clark S A, Hickey J M, Werf J H V D. Different models of genetic variation and their effect on genomic evaluation[J]. Genetics Selection Evolution,2011, 43(1):18-18.
[52]Colombani C, Legarra A, Fritz S, et al. Application of Bayesian least absolute shrinkage and selection operator (LASSO) and BayesCπ methods for genomic selection in French Holstein and Montbéliarde breeds[J]. Journal of Dairy Science, 2013, 96(1):575-591.
[53]Qiao X, Su R, Wang Y, et al. Genome-wide Target Enrichment-aided Chip Design: a 66 KSNP Chip for Cashmere Goat[J]. Sci Rep, 2017,7(1):8621.
[54]Bickhart D M, Rosen B D, Koren S, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome[J]. Nature Genetics,2017,49(4):643-650.
[55]Benjelloun B, Alberto F J, Streeter I, et al. Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data[J]. Frontiers in Genetics, 2015, 6:107.