利用后裔测定验证大白猪基因组选择实施效果研究

doi:10.11843/j.issn.0366-6964.2020.10.005

摘要/Abstract

摘要： 旨在通过测定基因组选择选留的大白公猪的后裔生产性能，探究基因组选择实际育种效果。本研究选用913头大白猪构建参考群体，利用ssGBLUP对新出生的823头大白公猪在去势前进行第一次基因组评估，待生产性能测定后进行第二次基因组评估，最终选留10头性能差异显著的公猪留种，比较其后代生长性状表型和育种值及综合选择指数差异。结果表明，两次基因组遗传评估，达100 kg体重日龄、100 kg活体背膘厚和总产仔数3个性状基因组育种值（GEBV）估计准确性分别由0.56、0.67和0.64提高至0.73、0.73和0.67，两次基因组选择基因组母系指数相关系数为0.82，表明在去势前进行公猪基因组选择具有较高的准确性，可实现种猪早期选择。根据各性状GEBV和基因组母系指数，10头公猪被划分为高、低生产性能组，后裔测定成绩表明，两组公猪后代100 kg体重日龄表型均值之差为2.58 d，育种值之差为3.08 d，100 kg活体背膘厚表型均值之差为1.15 mm，育种值之差为1.03 mm，综合母系指数均值之差为9.3，除后代100 kg体重日龄表型均值之差外，其他差异均达到极显著水平。本研究证明，在基因组评估中具有显著差异的公猪其后代在表型值和育种值等方面均存在显著差异，通过基因组选择能够挑选出优秀种公猪，可将其遗传优势传递给后代。

关键词: 基因组选择, 大白猪, 后裔测定, 准确性

Abstract: This study aimed to evaluate the actual genetic improvement effect of genomic selection in Large White boars through progeny testing in production performance. Nine hundred and thirteen Large White pigs were used to construct a reference group, and 823 new-born Large White boars were used to implement the first genomic selection through ssGBLUP before castration. The second genomic selection were carried out after performance testing, then 10 boars with significant difference in production performance were selected and their offsprings were compared in phenotypic values, estimated breeding values of growth traits and selection index. The results showed that the accuracies of genomic prediction on age at 100 kg body weight, 100 kg backfat thickness and total number born increased from 0.56, 0.67 and 0.64 in the first genomic selection to 0.73, 0.73 and 0.67 in the second genomic selection, respectively. The correlation coefficient of maternal selection index between the two genomic selection before castration and after performance testing was 0.82, which indicated that the first genomic selection before castration was accurate enough to make early selection on boars. According to the genomic breeding values and maternal selection index of 10 selected boars, two groups with high and low production performance were set up. The progeny testing showed that the difference of average phenotypic value between groups was 2.58 days, and the difference of average evaluated breeding value(EBV) between groups was 3.08 days in age at 100 kg body weight, those were 1.15 mm and 1.03 mm in 100 kg backfat thickness, respectively, and the difference in the mean of the comprehensive maternal index was 9.3, all the differences(except age at 100 kg body weight) were extremely significant. This study prove that the offspring of boars with significant differences in genomic evaluation have significant differences in phenotypic values and breeding values, which indicate that, through genomic selection, excellent breeding boars can be selected and their genetic superiority can be passed to their offsprings.

Key words: genomic selection, Large White pig, progeny testing, accuracy

中图分类号:

S828.2

周子文, 付璐, 孟庆利, 周海深, 张勤, 丁向东. 利用后裔测定验证大白猪基因组选择实施效果研究[J]. 畜牧兽医学报, 2020, 51(10): 2367-2377.

ZHOU Ziwen, FU Lu, MENG Qingli, ZHOU Haishen, ZHANG Qin, DING Xiangdong. Using Progeny Testing to Evaluate the Efficiency of Genomic Selection in Large White Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(10): 2367-2377.

参考文献 41

[1]	HENDERSON C R.Applications of linear models in animal breeding[M].Guelph:University of Guelph,1984.
[2]	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.
[3]	ZHANG Z,ZHANG Q,DING X D.Advances in genomic selection in domestic animals[J].Chin Sci Bull,2011,56(25):2655-2663.
[4]	SAMORÈ A B,FONTANESI L.Genomic selection in pigs:state of the art and perspectives[J].Ital J Anim Sci,2016,15(2):211-232.
[5]	HAYES B J,LEWIN H A,GODDARD M E.The future of livestock breeding:genomic selection for efficiency,reduced emissions intensity,and adaptation[J].Trends Genet,2013,29(4):206-214.
[6]	GARCÍA-RUIZ A,COLE J B,VANRADEN P M,et al.Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection[J].Proc Natl Acad Sci U S A,2016,113(28):E3995-E4004.
[7]	IBÑEZ-ESCRICHE N,FORNI S,NOGUERA J L,et al.Genomic information in pig breeding:Science meets industry needs[J].Livest Sci,2014,166:94-100.
[8]	POLLAK E J,BENNETT G L,SNELLING W M,et al.Genomics and the global beef cattle industry[J].Anim Prod Sci,2012, 52(3):92-99.
[9]	DUCHEMIN S I,COLOMBANI C,LEGARRA A,et al.Genomic selection in the French Lacaune dairy sheep breed[J].J Dairy Sci,2012,95(5):2723-2733.
[10]	张统雨,魏霞,张勤,等.基因组选择在羊育种中的应用研究进展[J].畜牧兽医学报,2018,49(12):2535-2542.ZHANG T Y,WEI X,ZHANG Q,et al.Progress on application of genomic selection in sheep and goat breeding[J].Acta Veterinaria et Zootechnica Sinica,2018,49(12):2535-2542.(in Chinese)
[11]	PREISINGER R.Genome-wide selection in poultry[J].Anim Prod Sci,2012,52(3):121-125.
[12]	LIU T F,QU H,LUO C L,et al.Accuracy of genomic prediction for growth and carcass traits in Chinese triple-yellow chickens[J].BMC Genet,2014,15(1):110.
[13]	CROSSA J E,DE LOS CAMPOS G,PÉREZ P,et al.Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers[J].Genetics,2010,186(2):713-724.
[14]	张金鑫,唐韶青,宋海亮,等.北京地区大白猪基因组联合育种研究[J].中国农业科学,2019,52(12):2161-2170.ZHANG J X,TANG S Q,SONG H L,et al.Joint genomic selection of yorkshire in Beijing[J].Scientia Agricultura Sinica,2019,52(12):2161-2170.(in Chinese)
[15]	ZHANG Z,ZHANG H,PAN R Y,et al.Genetic parameters and trends for production and reproduction traits of a Landrace herd in China[J].J Integr Agric,2016,15(5):1069-1075.
[16]	王晨,秦珂,薛明,等.全基因组选择在猪育种中的应用[J].畜牧兽医学报,2016,47(1):1-9.WANG C,QIN K,XUE M,et al.Application of genomic selection in swine breeding[J].Acta Veterinaria et Zootechnica Sinica,2016,47(1):1-9.(in Chinese)
[17]	SONG H L,ZHANG J,JIANG Y,et al.Genomic prediction for growth and reproduction traits in pig using an admixed reference population[J].J Anim Sci,2017,95(8):3415-3424.
[18]	TOOSI A,FERNANDO R L,DEKKERS J C M.Genomic selection in admixed and crossbred popu-lations[J].J Anim Sci, 2010, 88(1):32-46.
[19]	CHANG C C,CHOW C C,TELLIER L C,et al.Second-generation PLINK:rising to the challenge of larger and richer datasets[J]. Gigascience,2015,4(1):7.
[20]	BROWNING B L,BROWNING S R.A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals[J].Am J Hum Genet,2009,84(2):210-223.
[21]	张勤,丁向东,陈瑶生.种猪遗传评估技术研发与评估系统应用[J].中国畜牧杂志,2015,51(8):61-65,84.ZHANG Q,DING X D,CHEN Y S.Development and application of swine genetic evaluation system in China[J].Chinese Chinese Journal of Animal Science,2015,51(8):61-65,84.(in Chinese)
[22]	LEGARRA A,AGUILAR I,MISZTAL I.A relation-ship matrix including full pedigree and genomic information[J].J Dairy Sci,2009,92(9):4656-4663.
[23]	CHEN Z Q,BAISON J,PAN J,et al.Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in Norway spruce[J].BMC Genomics,2018,19(1):946.
[24]	SONG H L,ZHANG J X,ZHANG Q,et al.Using different single-step strategies to improve the efficiency of genomic prediction on body measurement traits in pig[J].Front Genet,2019,9:730.
[25]	PSZCZOLA M,STRABEL T,MULDER H A,et al.Reliability of direct genomic values for animals with different relationships within and to the reference population[J].J Dairy Sci,2012,95(1):389-400.
[26]	ZHANG H H,YIN L L,WANG M Y,et al.Factors affecting the accuracy of genomic selection for agricultural economic traits in maize,cattle,and pig populations[J].Front Genet,2019,10:189.
[27]	杜环利,尚伟伟,周振金,等.去势对公猪生长性能和胴体品质的影响[J].畜牧与兽医,2014,46(6):27-32.DU H L,SHANG W W,ZHOU Z J,et al.Effects of castration on growth performance and carcass qualities in the boar[J].Animal Husbandry & Veterinary Medicine,2014,46(6):27-32.(in Chinese)
[28]	蔡兆伟,陈民利,张立凡,等.去势对猪脂肪沉积及其关键基因表达的影响[J].农业生物技术学报,2013,21(10):1203-1209.CAI Z W,CHEN M L,ZHANG L F,et al.Effects of castration on fat deposition and its related gene expression in adipose tissues of male pigs (Sus scrofa)[J].Journal of Agricultural Biotechnology,2013,21(10):1203-1209.(in Chinese)
[29]	GODDARD M E,HAYES B J.Genomic selection[J].J Anim Breed Genet,2007,124(6):323-330.
[30]	GODDARD M.Genomic selection:prediction of accuracy and maximisation of long term response[J].Genetica, 2009, 136(2):245-257.
[31]	ZHANG Z,ZHANG Q,DING X D.Advances in genomic selection in domestic animals[J].Chin Sci Bull,2011,56(25):2655.
[32]	YI N J,XU S Z.Bayesian LASSO for quantitative trait loci mapping[J].Genetics,2008,179(2):1045-1055.
[33]	CALUS M P L.Genomic breeding value prediction:methods and procedures[J].Animal,2010,4(2):157-164.
[34]	GIANOLA D,DE LOS CAMPOS G,HILL W G,et al.Additive genetic variability and the Bayesian alphabet[J]. Genetics, 2009,183(1):347-363.
[35]	HABIER D,FERNANDO R L,KIZILKAYA K,et al.Extension of the Bayesian alphabet for genomic selection[J].BMC Bioinformatics,2011,12(1):186.
[36]	VANRADEN P M.Efficient methods to compute genomic predictions[J].J Dairy Sci,2008,91(11):4414-4423.
[37]	HABIER D,FERNANDO R L,DEKKERS J C M.The impact of genetic relationship information on genome-assisted breeding values[J].Genetics,2007,177(4):2389-2397.
[38]	ZHANG J,SONG H L,ZHANG Q,et al.Assessment of relationships between pigs based on pedigree and genomic information[J]. Animal,2020,14(4):697-705.
[39]	SONG H L,LI L,ZHANG Q C,et al.Accuracy and bias of genomic prediction with different de-regression methods[J]. Animal, 2018,12(6):1111-1117.
[40]	王欣.基因组选择方法的比较与多变量GBLUP模型研究[D].扬州:扬州大学,2017.WANG X.Comparisons of genomic selection methods and studies of multivariate GBLUP models[D].Yangzhou:Yangzhou University,2017.(in Chinese)
[41]	彭潇,尹立林,梅全顺,等.猪主要经济性状的基因组选择研究[J].畜牧兽医学报,2019,50(2):439-445.PENG X,YIN L L,MEI Q S,et al.A study of genome selection based on the porcine major economic traits[J].Acta Veterinaria et Zootechnica Sinica,2019,50(2):439-445.(in Chinese)