Acta Veterinaria et Zootechnica Sinica ›› 2024, Vol. 55 ›› Issue (1): 1-10.doi: 10.11843/j.issn.0366-6964.2024.01.001
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WANG Yuanqing, WANG Jing, ZHU Bo, CHEN Yan, XU Lingyang, WANG Zezhao, ZHANG Lupei, GAO Huijiang, LI Junya*, GAO Xue*
Received:
2023-08-16
Online:
2024-01-23
Published:
2024-01-24
CLC Number:
WANG Yuanqing, WANG Jing, ZHU Bo, CHEN Yan, XU Lingyang, WANG Zezhao, ZHANG Lupei, GAO Huijiang, LI Junya, GAO Xue. Genomic Mating Research and Its Application in Livestock and Poultry[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 1-10.
[1] | 张 沅.家畜育种学[M].北京:中国农业出版杜, 2001.ZHANG Y.Animal breeding science[M].Beijing:China Agriculture Press, 2001.(in Chinese) |
[2] | 张 勤.遗传评估与种猪选留[J].北方牧业, 2018(11):13-14.ZHANG Q.Genetic evaluation and selection of breeding stock[J].Northern Animal Husbandry, 2018(11):13-14.(in Chinese) |
[3] | HENDERSON C R.Best linear unbiased estimation and prediction under a selection model[J].Biometrics, 1975, 31(2):423-447. |
[4] | JANSEN G B, WILTON J W.Selecting mating pairs with linear programming techniques[J].J Dairy Sci, 1985, 68(5):1302-1305. |
[5] | WILTON J W, MORRIS C A, LEIGH A O, et al.A linear programming model for beef cattle production[J].Can J Anim Sci, 1974, 54(4):693-707. |
[6] | WEIGEL K A, LIN S W.Use of computerized mate selection programs to control inbreeding of Holstein and Jersey cattle in the next generation[J].J Dairy Sci, 2000, 83(4):822-828. |
[7] | WOOLLIAMS J A, THOMSON R.A theory of genetic contributions[C]//Proceedings of the 5th World Congress on Genetics Applied to Livestock Production.Guelph:Organising Committee, 1994:127-134. |
[8] | LINDGREN D, MATHESON A C.An algorithm for increasing the genetic quality of seed from seed orchards by using the better clones in higher proportions[J].Silvae Genet, 1986, 35(5-6):173-177. |
[9] | CABALLERO A, SANTIAGO E, TORO M A.Systems of mating to reduce inbreeding in selected populations[J].Anim Sci, 1996, 62(3):431-442. |
[10] | MEUWISSEN T.Operation of conservation schemes[M]//OLDENBROEK K.Proceedings of the Utilisation and Conservation of Farm Animal Genetic Resources.Wageningen:Wagenin gen Academic Publishers, 2007:167-193. |
[11] | WOOLLIAMS J A, PONG-WONG R, VILLANUEVA B.Strategic optimisation of short-and long-term gain and inbreeding in MAS and non-MAS schemes[C]//Proceedings of the 7th World Congress on Genetics Applied to Livestock Production.Montpellier:Institut National de la Recherche Agronomique (INRA), 2002:155-162. |
[12] | KINGHORN B P, SHEPHERD R K.Mate selection for the tactical implementation of breeding programs[J].Proc Advancem Anim Breed Genet, 1999, 13:130-133. |
[13] | KINGHORN B P.An algorithm for efficient constrained mate selection[J].Genet Sel Evol, 2011, 43(1):4. |
[14] | MEUWISSEN T H E.Maximizing the response of selection with a predefined rate of inbreeding[J].J Anim Sci, 1997, 75(4):934-940. |
[15] | WRAY N R, GODDARD M E.Increasing long-term response to selection[J].Genet Sel Evol, 1994, 26(5):431. |
[16] | GRUNDY B, VILLANUEVA B, WOOLLIAMS J A.Dynamic selection procedures for constrained inbreeding and their consequences for pedigree development[J].Genet Res, 1998, 72(2):159-168. |
[17] | MEUWISSEN T H E.Accuracy of breeding values of ‘unrelated’ individuals predicted by dense SNP genotyping[J]. Genet Sel Evol, 2009, 41(1):35. |
[18] | SØRENSEN A C, BERG P, WOOLLIAMS J A.The advantage of factorial mating under selection is uncovered by deterministically predicted rates of inbreeding[J].Genet Sel Evol, 2005, 37(1):57. |
[19] | OGAWA S, SATOH M.Genetic contributions of genes on sex chromosomes and mitochondrial DNA in a pedigreed population[J].Diversity, 2022, 14(2):142. |
[20] | LIU H, HENRYON M, SØRENSEN A C.Mating strategies with genomic information reduce rates of inbreeding in animal breeding schemes without compromising genetic gain[J].Animal, 2017, 11(4):547-555. |
[21] | SONESSON A K, WOOLLIAMS J A, MEUWISSEN T H E.Genomic selection requires genomic control of inbreeding[J].Genet Sel Evol, 2012, 44(1):27. |
[22] | HENRYON M, LIU H M, BERG P, et al.Pedigree relationships to control inbreeding in optimum-contribution selection realise more genetic gain than genomic relationships[J].Genet Sel Evol, 2019, 51(1):39. |
[23] | HJORTØ L, HENRYON M, LIU H M, et al.Pre-selection against a lethal recessive allele in breeding schemes with optimum-contribution selection or truncation selection[J].Genet Sel Evol, 2021, 53(1):75. |
[24] | LEGARRA A, AGUILAR I, MISZTAL I. A relationship matrix including full pedigree and genomic information[J]. J Dairy Sci, 2009, 92(9):4656-4663. |
[25] | MEUWISSEN T H E, HAYES B J, GODDARD M E.Prediction of total genetic value using genome-wide dense marker maps[J].Genetics, 2001, 157(4):1819-1829. |
[26] | VANRADEN P M.Efficient methods to compute genomic predictions[J].J Dairy Sci, 2008, 91(11):4414-4423. |
[27] | VANRADEN P M, VAN TASSELL C P, WIGGANS G R, et al.Invited review:Reliability of genomic predictions for North American Holstein bulls[J].J Dairy Sci, 2009, 92(1):16-24. |
[28] | TESSEMA B B, LIU H M, SØRENSEN A C, et al.Strategies using genomic selection to increase genetic gain in breeding programs for wheat[J].Front Genet, 2020, 11:578123. |
[29] | HABIER D, FERNANDO R L, KIZILKAYA K, et al.Extension of the Bayesian alphabet for genomic selection[J].BMC Bioinf, 2011, 12(1):186. |
[30] | HAYES B J, BOWMAN P J, CHAMBERLAIN A J, et al.Invited review:Genomic selection in dairy cattle:Progress and challenges[J].J Dairy Sci, 2009, 92(2):433-443. |
[31] | MAKANJUOLA B O, MIGLIOR F, ABDALLA E A, et al.Effect of genomic selection on rate of inbreeding and coancestry and effective population size of Holstein and Jersey cattle populations[J].J Dairy Sci, 2020, 103(6):5183-5199. |
[32] | SENO L D O, GUIDOLIN D G F, ASPILCUETA-BORQUIS R R, et al.Genomic selection in dairy cattle simulated populations[J].J Dairy Res, 2018, 85(2):125-132. |
[33] | LILLEHAMMER M, MEUWISSEN T H E, SONESSON A K.A comparison of dairy cattle breeding designs that use genomic selection[J].J Dairy Sci, 2011, 94(1):493-500. |
[34] | GUO X, CHRISTENSEN O F, OSTERSEN T, et al.Improving genetic evaluation of litter size and piglet mortality for both genotyped and nongenotyped individuals using a single-step method[J].J Anim Sci, 2015, 93(2):503-512. |
[35] | PRYCE J E, GODDARD M E, RAADSMA H W, et al.Deterministic models of breeding scheme designs that incorporate genomic selection[J].J Dairy Sci, 2010, 93(11):5455-5466. |
[36] | SAMORō A B, BUTTAZZONI L, GALLO M, et al.Genomic selection in a pig population including information from slaughtered full sibs of boars within a sib-testing program[J].Animal, 2015, 9(5):750-759. |
[37] | AKDEMIR D, SÁNCHEZ J I.Efficient breeding by genomic mating[J].Front Genet, 2016, 7:210. |
[38] | 高振东, 何 俊.基因组选配:基因组时代的高效育种[J].黑龙江畜牧兽医, 2020(24):61-64, 175.GAO Z D, HE J.Genomic Mating:efficient breeding in the genome era[J].Heilongjiang Animal Science and Veterinary Medicine, 2020(24):61-64, 175.(in Chinese) |
[39] | 何 俊, LOPES F B, 吴晓林.动物基因组选配方法与应用[J].遗传, 2019, 41(6):486-493.HE J, LOPES F B, WU X L.Methods and applications of animal genomic mating[J].Hereditas (Beijing), 2019, 41(6):486-493.(in Chinese) |
[40] | ZHANG P F, QIU X T, WANG L X, et al.Progress in genomic mating in domestic animals[J].ANIMALS, 2022, 12(18):2306. |
[41] | HOWARD D M, PONG-WONG R, KNAP P W, et al.Selective advantage of implementing optimal contributions selection and timescales for the convergence of long-term genetic contributions[J].Genet Sel Evol, 2018, 50(1):24. |
[42] | HAMILTON M G.Optimal contribution selection in highly fecund species with overlapping generations[J].J Hered, 2020, 111(7):646-651. |
[43] | SÁNCHEZ-MOLANO E, PONG-WONG R, BANOS G.Genomic-based optimum contribution in conservation and genetic improvement programs with antagonistic fitness and productivity traits[J].Front Genet, 2016, 7:25. |
[44] | LI M H, STRANDÉN I, TIIRIKKA T, et al.A comparison of approaches to estimate the inbreeding coefficient and pairwise relatedness using genomic and pedigree data in a sheep population[J].PLoS One, 2011, 6(11):e26256. |
[45] | LOPES M S, SILVA F F, HARLIZIUS B, et al.Improved estimation of inbreeding and kinship in pigs using optimized SNP panels[J].BMC Genet, 2013, 14:92. |
[46] | 杨湛澄, 黄河天, 闫青霞, 等.利用高密度SNP标记分析中国荷斯坦牛基因组近交[J].遗传, 2017, 39(1):41-47.YANG Z C, HUANG H T, YAN Q X, et al.Estimation of genomic inbreeding coefficients based on high-density SNP markers in Chinese Holstein cattle[J].Hereditas (Beijing), 2017, 39(1):41-47.(in Chinese) |
[47] | KARDOS M, LUIKART G, ALLENDORF F W.Measuring individual inbreeding in the age of genomics:marker-based measures are better than pedigrees[J].Heredity (Edinb), 2015, 115(1):63-72. |
[48] | CLARK S A, KINGHORN B P, HICKEY J M, et al.The effect of genomic information on optimal contribution selection in livestock breeding programs[J].Genet Sel Evol, 2013, 45:44. |
[49] | PRYCE J E, HAYES B J, GODDARD M E.Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information[J].J Dairy Sci, 2012, 95(1):377-388. |
[50] | CARTHY T R, MCCARTHY J, BERRY D P.A mating advice system in dairy cattle incorporating genomic information[J].J Dairy Sci, 2019, 102(9):8210-8220. |
[51] | HENRYON M, SØRENSEN A C, BERG P.Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection[J].Animal, 2009, 3(10):1339-1346. |
[52] | HE J, WU X L, ZENG Q H, et al.Genomic mating as sustainable breeding for Chinese indigenous Ningxiang pigs[J].PLoS One, 2020, 15(8):e0236629. |
[53] | SCHIERENBECK S, PIMENTEL E C G, TIETZE M, et al.Controlling inbreeding and maximizing genetic gain using semi-definite programming with pedigree-based and genomic relationships[J].J Dairy Sci, 2011, 94(12):6143-6152. |
[54] | BÉRODIER M, BERG P, MEUWISSEN T, et al.Improved dairy cattle mating plans at herd level using genomic information[J].Animal, 2021, 15(1):100016. |
[55] | BENGTSSON C, STÅLHAMMAR H, THOMASEN J R, et al.Mating allocations in Nordic Red Dairy Cattle using genomic information[J].J Dairy Sci, 2022, 105(2):1281-1297. |
[56] | GANTEIL A, POOK T, RODRIGUEZ-RAMILO S T, et al.Comparison of breeding strategies for the creation of a synthetic pig line[Z].bioRxiv, 2021, doi:10.1101/2021.09.22.461330. |
[57] | TANG Z S, YIN L L, YIN D, et al.Development and application of an efficient genomic mating method to maximize the production performances of three-way crossbred pigs[J].Brief Bioinform, 2023, 24(1):bbac587. |
[58] | 张鹏飞, 何 俊, 王立贤, 等.基于基因组和系谱信息的不同选配方案效果模拟研究[J].畜牧兽医学报, 2022, 53(10):3448-3458.ZHANG P F, HE J, WANG L X, et al.Simulation study on the effects of different mating schemes based on genomic and pedigree information[J].Acta Veterinaria et Zootechnica Sinica, 2022, 53(10):3448-3458.(in Chinese) |
[59] | ZHAO F P, ZHANG P F, WANG X Q, et al.Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement[J].J Anim Sci Biotechnol, 2023, 14(1):87. |
[60] | SUN C, VANRADEN P M, O'CONNELL J R, et al.Mating programs including genomic relationships and dominance effects[J].J Dairy Sci, 2013, 96(12):8014-8023. |
[61] | GONZÁLEZ-DIÉGUEZ D, TUSELL L, CARILLIER-JACQUIN C, et al.SNP-based mate allocation strategies to maximize total genetic value in pigs[J].Genet Sel Evol, 2019, 51(1):55. |
[62] | 李佳芮.整合非加性效应的生猪基因组选配[D].北京:中国农业大学, 2023.LI J R.Research on pig genomic allocation strategy of integrating non-additive effects[D].Beijing:China Agricultural University, 2023.(in Chinese) |
[63] | ALILOO H, PRYCE J E, GONZÁLEZ-RECIO O, et al.Including nonadditive genetic effects in mating programs to maximize dairy farm profitability[J].J Dairy Sci, 2017, 100(2):1203-1222. |
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