[1] |
WIGGANS G R, VANRADEN P M, COOPER T A.The genomic evaluation system in the United States:past, present, future[J].J Dairy Sci, 2011, 94(6):3202-3211.
|
[2] |
WEISHAAR R, WELLMANN R, CAMARINHA-SILVA A, et al.Selecting the hologenome to breed for an improved feed efficiency in pigs-a novel selection index[J].J Anim Breed Genet, 2020, 137(1):14-22.
|
[3] |
GAO N, TENG J Y, PAN R Y, et al.Accuracy of whole genome prediction with single-step GBLUP in a Chinese yellow-feathered chicken population[J].Livest Sci, 2019, 230:103817.
|
[4] |
ZENGER K R, KHATKAR M S, JONES D B, et al.Genomic selection in aquaculture:application, limitations and opportunities with special reference to marine shrimp and pearl oysters[J].Front Genet, 2019, 9:693.
|
[5] |
DAETWYLER H D, VILLANUEVA B, WOOLLIAMS J A.Accuracy of predicting the genetic risk of disease using a genome-wide approach[J].PLoS One, 2008, 3(10):e3395.
|
[6] |
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.
|
[7] |
DAS S, FORER L, SCHÖNHERR S, et al.Next-generation genotype imputation service and methods[J].Nat Genet, 2016, 48(10):1284-1287.
|
[8] |
SOLLERO B P, HOWARD J T, SPANGLER M L.The impact of reducing the frequency of animals genotyped at higher density on imputation and prediction accuracies using ssGBLUP1[J].J Anim Sci, 2019, 97(7):2780-2792.
|
[9] |
FERNANDES JÚNIOR G A, CARVALHEIRO R, DE OLIVEIRA H N, et al.Imputation accuracy to whole-genome sequence in Nellore cattle[J].Genet Sel Evol, 2021, 53(1):27.
|
[10] |
VAN BINSBERGEN R, BINK M C, CALUS M P, et al.Accuracy of imputation to whole-genome sequence data in Holstein Friesian cattle[J].Genet Sel Evol, 2014, 46(1):41.
|
[11] |
VAN DEN BERG S, VANDENPLAS J, VAN EEUWIJK F A, et al.Imputation to whole-genome sequence using multiple pig populations and its use in genome-wide association studies[J].Genet Sel Evol, 2019, 51(1):2.
|
[12] |
YE S, YUAN X, HUANG S, et al.Comparison of genotype imputation strategies using a combined reference panel for chicken population[J].Animal, 2019, 13(6):1119-1126.
|
[13] |
VANRADEN P M.Symposium review:how to implement genomic selection[J].J Dairy Sci, 2020, 103(6):5291-5301.
|
[14] |
RUBINACCI S, DELANEAU O, MARCHINI J.Genotype imputation using the positional burrows wheeler transform[J].PLoS Genet, 2020, 16(11):e1009049.
|
[15] |
ROS-FREIXEDES R, WHALEN A, GORJANC G, et al.Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling[J].Genet Sel Evol, 2020, 52(1):18.
|
[16] |
YE S P, YUAN X L, LIN X R, et al.Imputation from SNP chip to sequence:a case study in a Chinese indigenous chicken population[J].J Anim Sci Biotechnol, 2018, 9:30.
|
[17] |
SARGOLZAEI M, CHESNAIS J P, SCHENKEL F S.A new approach for efficient genotype imputation using information from relatives[J].BMC Genomics, 2014, 15(1):478.
|
[18] |
YU X J, WOOLLIAMS J A, MEUWISSEN T H.Prioritizing animals for dense genotyping in order to impute missing genotypes of sparsely genotyped animals[J].Genet Sel Evol, 2014, 46(1):46.
|
[19] |
DRUET T, MACLEOD I M, HAYES B J.Toward genomic prediction from whole-genome sequence data:impact of sequencing design on genotype imputation and accuracy of predictions[J].Heredity (Edinb), 2014, 112(1):39-47.
|
[20] |
PURCELL S, NEALE B, TODD-BROWN K, et al.PLINK:a tool set for whole-genome association and population-based linkage analyses[J].Am J Hum Genet, 2007, 81(3):559-575.
|
[21] |
BROWNING S R, BROWNING B L.Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering[J].Am J Hum Genet, 2007, 81(5):1084-1097.
|
[22] |
R Core Team.R:a language and environment for statistical computing[R].Vienna, Austria:R Foundation for Statistical Computing, 2020.
|
[23] |
BROWNING B L, ZHOU Y, BROWNING S R.A one-penny imputed genome from next-generation reference panels[J].Am J Hum Genet, 2018, 103(3):338-348.
|
[24] |
ENDELMAN J B.Ridge regression and other kernels for genomic selection with R package rrBLUP[J].Plant Genome, 2011, 4(3):250-255.
|
[25] |
POOK T, MAYER M, GEIBEL J, et al.Improving imputation quality in BEAGLE for crop and livestock data[J].G3(Bethesda), 2020, 10(1):177-188.
|
[26] |
WHALEN A, HICKEY J M.AlphaImpute2:fast and accurate pedigree and population based imputation for hundreds of thousands of individuals in livestock populations[J/OL].bioRxiv, 2020, doi:10.1101/2020.09.16.299677.
|
[27] |
HOWIE B N, DONNELLY P, MARCHINI J.A flexible and accurate genotype imputation method for the next generation of genome-wide association studies[J].PLoS Genet, 2009, 5(6):e1000529.
|
[28] |
LIU E Y, LI M Y, WANG W, et al.MaCH-admix:genotype imputation for admixed populations[J].Genet Epidemiol, 2013, 37(1):25-37.
|
[29] |
WANG X, SU G S, HAO D, et al.Comparisons of improved genomic predictions generated by different imputation methods for genotyping by sequencing data in livestock populations[J].J Anim Sci Biotechnol, 2020, 11:3.
|
[30] |
PAUSCH H, AIGNER B, EMMERLING R, et al.Imputation of high-density genotypes in the Fleckvieh cattle population[J].Genet Sel Evol, 2013, 45(1):3.
|
[31] |
TSAIRIDOU S, HAMILTON A, ROBLEDO D, et al.Optimizing low-cost genotyping and imputation strategies for genomic selection in atlantic salmon[J].G3(Bethesda), 2020, 10(2):581-590.
|
[32] |
BICKHART D M, HUTCHISON J L, NULL D J, et al.Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes[J].J Dairy Sci, 2016, 99(7):5526-5534.
|
[33] |
LEGARRA A, AGUILAR I, MISZTAL I.A relationship matrix including full pedigree and genomic information[J].J Dairy Sci, 2009, 92(9):4656-4663.
|
[34] |
MEUWISSEN T H E, LUAN T, WOOLLIAMS J A.The unified approach to the use of genomic and pedigree information in genomic evaluations revisited[J].J Anim Breed Genet, 2011, 128(6):429-439.
|
[35] |
WANG H Y, WOODWARD B, BAUCK S, et al.Imputation of missing SNP genotypes using low density panels[J].Livest Sci, 2012, 146(1):80-83.
|
[36] |
GHOREISHIFAR S M, MORADI-SHAHRBABAK H, MORADI-SHAHRBABAK M, et al.Accuracy of imputation of single-nucleotide polymorphism marker genotypes for water buffaloes (Bubalus bubalis) using different reference population sizes and imputation tools[J].Livest Sci, 2018, 216:174-182.
|
[37] |
BUTTY A M, SARGOLZAEI M, MIGLIOR F, et al.Optimizing selection of the reference population for genotype imputation from array to sequence variants[J].Front Genet, 2019, 10:510.
|
[38] |
邓天宇, 杜立新, 王立贤, 等.基因型填充策略研究[J].畜牧兽医学报, 2020, 51(9):2068-2078.DENG T Y, DU L X, WANG L X, et al.Study on the strategies of genotype imputation[J].Acta Veterinaria et Zootechnica Sinica, 2020, 51(9):2068-2078.(in Chinese)
|
[39] |
YANG W Q, YANG Y B, ZHAO C C, et al.Animal-ImputeDB:a comprehensive database with multiple animal reference panels for genotype imputation[J].Nucleic Acids Res, 2020, 48(D1):D659-D667.
|
[40] |
GAO Y J, YANG Z Q, YANG W Q, et al.Plant-ImputeDB:an integrated multiple plant reference panel database for genotype imputation[J].Nucleic Acids Res, 2021, 49(D1):D1480-D1488.
|