The application of genomic selection in pig cross breeding
Received date: 2019-08-28
Revised date: 2020-02-08
Online published: 2020-02-19
Supported by
the National Key Research and Development(2017YFD0501504);the National Key Research and Development(2016YFD0501308);Special Fund for the Industrial Technology System Construction of Modern Agriculture(CARS-36)
Genomic selection is a form of marker-assisted selection in which genetic markers covering the entire genome are used so that all quantitative trait loci are in linkage disequilibrium with at least one marker. Genomic selection improves the efficiency and accuracy of breeding and it is widely used in purebred breeding across many animal species. However, some studies indicate that the accuracy of genome selection in cross breeding needs to be improved,especially in cross population. As one of the most extensive breeding methods employed in the swine industry, cross breeding has significant, potential research and economic value to further improve its performance by combining with genomic selection. In this review, we summarize the application of genomic selection in pigs, and elucidate the genomic selection deficiencies in breeding hybrid pigs. This review will also provide valuable insights for the future application and improvement of genomic selection in pig cross breeding.
Key words： genomic selection; swine; cross breeding; statistical genetics
Anqi Yang, Bin Chen, Maoliang Ran, Guangmin Yang, Cheng Zeng . The application of genomic selection in pig cross breeding[J]. Hereditas(Beijing), 2020 , 42(2) : 145 -152 . DOI: 10.16288/j.yczz.19-253
| [1] | Goddard ME, Hayes BJ . Genomic selection. J Anim Breed Genet, 2007,124(6):323-330. |
| [2] | Li HD, Bao ZM, Sun XW . Genomic selection and its application. Hereditas(Beijing), 2011,33(12):1308-1316. |
| [2] | 李恒德, 包振民, 孙效文 . 基因组选择及其应用. 遗传, 2011,33(12):1308-1316. |
| [3] | Toosi A, Fernando RL, Dekkers JC . Genomic selection in admixed and crossbred populations. J Anim Sci, 2010,88(1):32-46. |
| [4] | Berry DP, Kearney F, Harris BL . Genomic selection in Ireland. Interbull Bull, 2009,39:29-29. |
| [5] | VanRaden PM, Van Tassell CP, Wiggans GR, Sonstegard TS, Schnabel RD, Taylor JF, Schenkel FS . Invited review: reliability of genomic predictions for North American Holstein bulls. J Dairy Sci, 2009,92(1):16-24. |
| [6] | Tao ZY, Xue PP, Zhang XY, Sui J, Chen J, Zhao B, Wu ZL, Hu JH . Research progress on the technology of swine crossbreeding. J Dom Anim Ecol, 2019,40(4):81-84. |
| [6] | 陶泽宇, 薛盼盼, 张潇筠, 隋洁, 陈剑, 赵博, 吴忠利, 胡建宏 . 猪杂交改良研究进展. 家畜生态学报, 2019,40(4):81-84. |
| [7] | Yang SB, Li XL, Li K, Fan B, Tang ZL . A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds. BMC Genet, 2014,15:7. |
| [8] | Chen L, Tian SL, Jin L, Guo ZY, Zhu D, Lan J, Che TD, Tang QZ, Chen SQ, Zhang L, Zhang TH, Liu ZH, Wang JY, Li MZ . Genome-wide analysis reveals selection for Chinese Rongchang pigs. Front Agr Sci Eng, 2017,4(3):319-326. |
| [9] | Goff SA . A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding. New Phytol, 2011,189(4):923-937. |
| [10] | Peter V, Ricardo PW, Colin W, Chris H . Impact of biotechnology on (cross) breeding programmes in pigs. Livest Prod Sci, 2000,65(1-2):57-70. |
| [11] | Chen ZJ . Genomic and epigenetic insights into the molecular bases of heterosis. Nat Rev Genet, 2013,14(7):471-482. |
| [12] | Wellmann R . Optimum contribution selection for animal breeding and conservation: the R package optiSel. BMC Bioinformatics, 2019,20(1):25. |
| [13] | Fujii J, Otsu K , Zorzato F, de Leon S, Khanna VK, Weiler JE, O'Brien PJ, MacLennan DH. Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia. Science, 1991,253(5018):448-451. |
| [14] | Geldermann H . Investigations on inheritance of quantitative characters in animals by gene markers I. Methods. Theor Appl Genet, 1975,46(7):319-330. |
| [15] | Rothschild M, Jacobson C, Vaske D, Tuggle C, Wang L, Short T, Eckardt G, Sasaki S, Vincent A , McLaren D, Southwood O, van der Steen H, Mileham A, Plastow G. The estrogen receptor locus is associated with a major gene influencing litter size in pigs. Proc Natl Acad Sci USA, 1996,93(1):201-205. |
| [16] | Tsuruta S, Misztal I, Strandén I . Use of the preconditioned conjugate gradient algorithm as a generic solver for mixed-model equations in animal breeding applications. J Anim Sci, 2001,79(5):1166-1172. |
| [17] | Meuwissen TH, Hayes BJ, Goddard ME . Prediction of total genetic value using genome-wide dense marker maps. Genetics, 2001,157(4):1819-1829. |
| [18] | Ernst CW, Steibel JP . Molecular advances in QTL discovery and application in pig breeding. Trends Genet, 2013,29(4):215-224. |
| [19] | Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME . Invited review: Genomic selection in dairy cattle: progress and challenges. J Dairy Sci, 2009,92(2):433-443. |
| [20] | Yin LL, Ma YL, Xiang T, Zhu MJ, Yu M, Li XY, Liu XL, Zhao SH . The progress and prospect of genomic selection models. Acta Veter Zoot Sin, 2019,50(2):233-242. |
| [20] | 尹立林, 马云龙, 项韬, 朱猛进, 余梅, 李新云, 刘小磊, 赵书红 . 全基因组选择模型研究进展及展望. 畜牧兽医学报, 2019,50(2):233-242. |
| [21] | VanRaden PM . Efficient methods to compute genomic predictions. J Dairy Sci, 2008,91(11):4414-4423. |
| [22] | Misztal I, Legarra A . Invited review: efficient computation strategies in genomic selection. Animal, 2017,11(5):731-736. |
| [23] | Calus MPL . Genomic breeding value prediction: methods and procedures. Animal, 2010,4(2):157-164. |
| [24] | Gianola D, de los Campos G, Hill WG, Manfredi E, Fernando R . Additive genetic variability and the Bayesian alphabet. Genetics, 2009,183(1):347-363. |
| [25] | Yi NJ, Xu SZ . Bayesian LASSO for quantitative trait loci mapping. Genetics, 2008,179(2):1045-1055. |
| [26] | Habier D, Fernando RL, Kizilkaya K, Garrick DJ . Extension of the Bayesian alphabet for genomic selection. BMC Bioinformatics, 2011,12(1):186. |
| [27] | Wang CL, Ding XD, Liu JF, Yin ZJ, Zhang Q . Bayesian methods for genomic breeding value estimation. Hereditas(Beijing), 2014,36(2):111-118. |
| [27] | 王重龙, 丁向东, 刘剑锋, 殷宗俊, 张勤 . 基因组育种值估计的贝叶斯方法研究进展. 遗传, 2014,36(2):111-118. |
| [28] | Wray NR, Wijmenga C, Sullivan PF, Yang J, Visscher PM . Common disease is more complex than implied by the core gene omnigenic model. Cell, 2018,173(7):1573-1580. |
| [29] | Legarra A, Aguilar I, Misztal I . A relationship matrix including full pedigree and genomic information. J Dairy Sci, 2009,92(9):4656-4663. |
| [30] | Aguilar I, Misztal I, Johnson DL, Legarra A, Tsuruta S, Lawlor TJ . Hot topic: A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score. J Dairy Sci, 2010,93(2):743-752. |
| [31] | Tan C, Bian C, Yang D, Li N, Wu ZF, Hu XX . Application of genomic selection in farm animal breeding. Hereditas (Beijing), 2017,39(11):1033-1045. |
| [31] | 谈成, 边成, 杨达, 李宁, 吴珍芳, 胡晓湘 . 基因组选择技术在农业动物育种中的应用. 遗传, 2017,39(11):1033-1045. |
| [32] | Samore AB, Fontanesi L . Genomic selection in pigs: state of the art and perspectives. Italian J Anim Sci, 2016,15(2):211-232. |
| [33] | Sonesson AK, Gjerde B, Meuwissen THE . Truncation selection for BLUP-EBV and phenotypic values in fish breeding schemes. Aquaculture, 2005,243(1-4):61-68. |
| [34] | Cleveland MA, Davis SF, Garrick DJ, Deeb JN . Prediction of genomic breeding values in a commercial pig population. Proc 9th WCGALP, 2010,266. |
| [35] | Forni S, Aguilar I, Misztal I . Different genomic relationship matrices for single-step analysis using phenotypic, pedigree and genomic information. Genet Sel Evol, 2011,43(1):1. |
| [36] | Jafarikia M, Sullivan B . Genomics tools for improving health and production performance of Canadian Pigs. Proc 10th WCGALP, 2014, 611-618. |
| [37] | Tusell L, Pérez-Rodriguez P, Forni S, Wu XL, Gianola D . Genome-enabled methods for predicting litter size in pigs: a comparison. Animal, 2013,7(11):1739-1749. |
| [38] | Guo X, Christensen OF, Ostersen T, Wang Y, Lund MS, Su G . Improving genetic evaluation of litter size and piglet mortality for both genotyped and nongenotyped individuals using a single-step method. J Anim Sci, 2015,93(2):503-512. |
| [39] | Zhang JX, Tang SQ, Song HL, GAO H, Jiang Y, Jiang YF, Mi SR, Meng QL, Yu Fan, Xiao W, Yun P, Zhang Q, Ding XD . Joint genomic selection of Yorkshire in Beijing. Sci Agr Sin, 2019,52(12):2161-2170. |
| [39] | 张金鑫, 唐韶青, 宋海亮, 高虹, 蒋尧, 江一凡, 弥世荣, 孟庆利, 于凡, 肖炜, 云鹏, 张勤, 丁向东 . 北京地区大白猪基因组联合育种研究. 中国农业科学, 2019,52(12):2161-2170. |
| [40] | Tribout T, Larzul C, Phocas F . Efficiency of genomic selection in a purebred pig male line. J Anim Sci, 2012,90(12):4164-4176. |
| [41] | Akanno EC, Schenkel FS, Sargolzaei M, Friendship RM, Robinson JAB . Opportunities for genome-wide selection for pig breeding in developing countries. J Anim Sci, 2013,91(10):4617-4627. |
| [42] | Jiao S, Maltecca K, Gray KA, Cassady JP . Feed intake, average daily gain, feed efficiency, and real-time ultrasound traits in Duroc pigs: II. Genomewide association. J Anim Sci, 2014,92(7):2846-2860. |
| [43] | Do DN, Janss LLG, Jensen J, Kadarmi HN . SNP annotation-based whole genomic prediction and selection: an application to feed efficiency and its component traits in pigs. J Animal Sci, 2015,93(5):2056-2063. |
| [44] | Ou Z, Tempelman RJ, Steibel JP, Ernst CW, Bates RO, Bello NM . Genomic prediction accounting for residual heteroskedasticity. G3 (Bethesda), 2015,6(1):1-13. |
| [45] | Tribout T, Bidanel JP, Phocas F, Schwob S, Guillaume F, Larzul C . La sélection génomique: principe et perspectives d’utilisation pour l’amélioration des populations porcines. J Rec Porc Fr, 2011: 13-25. |
| [46] | Dekkers JCM . Marker-assisted selection for commercial crossbred performance. J Anim Sci, 2007,85(9):2104-2114. |
| [47] | Xiang T, Nielsen B, Su G, Legarra A, Christensen OF . Application of single-step genomic evaluation for crossbred performance in pig. J Anim Sci, 2016,94(3):936-948. |
| [48] | Christensen OF, Madsen P, Nielsen B, Su G . Genomic evaluation of both purebred and crossbred performances. Genet Sel Evol, 2014,46(1):23. |
| [49] | Hidalgo AM, Bastiaansen JWM, Lopes MS, Harlizius B, Groenen MAM, Koning DJD . Accuracy of predicted genomic breeding values in purebred and crossbred pigs. G3 (Bethesda), 2015,5(8):1575-1583. |
| [50] | Zhang SW. Creating a new method of local famous pig breeding & Xiangsha pig synthetic line was approving. Hunan Daily, 2019-7-7(2). |
| [50] | 张尚武 . 开创地方名猪保种新模式湘沙猪配套系通过专家现场评审. 湖南日报, 2019-7-7(2). |
| [51] | Wu MS, Liu TM, Peng YL, Chen B, Zuo XH, Luo QH, Xiang YJ, Tang GQ, Liu W, Li L . Experiment on two-way cross of Shazilin pig with Berkshire and Hampshire. Acta Ecol Anim Dom, 2011,32(3):22-24, 108. |
| [51] | 吴买生, 刘天明, 彭英林, 陈斌, 左晓红, 罗强华, 向拥军, 唐国其, 刘伟, 李论 . 沙子岭猪与巴克夏、汉普夏猪的二元杂交试验. 家畜生态学报, 2011,32(3):22-24, 108. |
| [52] | Wang C . Inheritance of two-end black colour and genome- wide analysis of selective regions in Tongcheng pigs [Dissertation]. Huazhong Agricultural University, 2014. |
| [52] | 汪超 . 通城猪两头乌毛色遗传规律研究及其全基因组选择区域分析[学位论文]. 华中农业大学, 2014. |
| [53] | Veroneze R, Bastiaansen JWM, Knol EF, Guimar?es SEF, Silva FF, Harlizius BB, Lopes MS, Lopes PS . Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations. BMC Genet, 2014,15(1):126. |
| [54] | Birchler JA, Yao H, Chudalayandi S, Vaiman D, Veitia RA . Heterosis. Plant Cell, 2010,22(7):2105-2112. |
| [55] | Pérez-Rodríguez P, Gianola D, Weigel KA, Rosa G . J, Crossa J. Technical Note: An R package for fitting Bayesian regularized neural networks with applications in animal breeding. J Anim Sci, 2013,91(8):3522-3531. |
| [56] | ?zesmi U, Tan CO , ?zesmi, SL, Robertson RJ. Generalizability of artificial neural network models in ecological applications: Predicting nest occurrence and breeding success of the red-winged blackbird Agelaius phoeniceus. Ecolog Mod, 2006,195(1):94-104. |
| [57] | Akdemir D, Sánchez JI . Efficient breeding by genomic mating. Front Genet, 2016,7:210. |
/
| 〈 |
|
〉 |
www.chinagene.cn
备案号：京ICP备09063187号
