References
- ADEYINKA I.A., ONI O.O., NWAGU B.I., ADEYINKA F.D., 2006 - Genetic parameter estimates of body weights of naked neck broiler chickens. International Journal of Poultry Science 5(6), 589-592.
- AGUILAR I., MISZTAL I., TSURUTA S., WIGGANS G.R., LAWLOR T.J., 2011- Multiple trait genomic evaluation of conception rate in Holsteins. Journal of Dairy Science 94(5), 2621-2624.
- BERMANN M., LEGARRA A., HOLLIFIELD M.K., MASUDA Y., LOURENCO D., MISZTAL I., 2021- Validation of single‐step GBLUP genomic predictions from threshold models using the linear regression method: An application in chicken mortality. Journal of Animal Breeding and Genetics 138(1), 4-13.
- BRADBURY P.J., ZHANG Z., KROON D. E., CASSTEVENS T.M., RAMDOSS Y., BUCKLER E.S., 2007 - TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19), 2633-2635.
- CHANG C.C., CHOW C.C., TELLIER L.C., VATTIKUTI S., PURCELL S.M., LEE J.J., 2015 -Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4(1), s13742-015.
- CHEN C.Y., MISZTAL I., AGUILAR I., TSURUTA S., MEUWISSEN T.H.E., AGGREY S.E., MUIR W.M., 2011 - Genome-wide marker-assisted selection combining all pedigree phenotypic information with genotypic data in one step: an example using broiler chickens. Journal of Animal Science 89(1), 23-28.
- CHRISTENSEN O.F., MADSEN P., NIELSEN B., OSTERSEN T, SU G., 2012 - Single-step methods for genomic evaluation in pigs. Animal 6(10), 1565-1571.
- CLARK S.A., HICKEY J.M., VANDERWERF J.H., 2011 - Different models of genetic variation and their effect on genomic evaluation. Genetics Selection Evolution 43(1), 1-9.
- DRUET T., MACLEOD I.M., HAYES B.J., 2014 - Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions. Heredity 112(1), 39-47.
- GODDARD M.E, HAYES B.J., 2009 - Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Reviews Genetics 10(6), 381-391.
- HABIER D., FERNANDO R.L., DEKKERS J.C., 2009 - Genomic selection using low-density marker panels. Genetics 182(1), 343-353.
- LEGARRA A., AGUILAR I., MISZTAL I., 2009 - A relationship matrix including full pedigree and genomic information. Journal of Dairy Science 92(9), 4656-4663.
- LI B., ZHANG N., WANG Y.G., GEORGE A.W., REVERTER A., LI Y., 2018 - Genomic prediction of breeding values using a subset of SNPs identified by three machine learning methods. Frontiers in Genetics 9, 237.
- LI X., WANG S., HUANG J., LI L., ZHANG Q, DING X., 2014 - Improving the accuracy of genomic prediction in Chinese Holstein cattle by using one-step blending. Genetics Selection Evolution 46(1), 1-5.
- LIU R., SUN Y., ZHAO G., WANG H., ZHENG M., LI P., WEN J., 2015 - Identification of loci and genes for growth related traits from a genome-wide association study in a slow× fast-growing broiler chicken cross. Genes and Genomics 37(10), 829-836.
- LOURENCO D.A.L., MISZTAL I., TSURUTA S., AGUILAR I., EZRA E., RON M., WELLER J.I., 2014 - Methods for genomic evaluation of a relatively small genotyped dairy population and effect of genotyped cow information in multiparity analyses. Journal of Dairy Science 97(3), 1742-1752.
- LOURENCO D., LEGARRA A., TSURUTA S., MASUDA Y., AGUILAR I., MISZTAL I., 2020-Single-step genomic evaluations from theory to practice: using SNP chips and sequence data in BLUPF90. Genes 11(7), 790.
- LUO W., LUO C., WANG M., GUO L., CHEN X., LI Z., NIE Q., 2020 - Genome diversity of Chinese indigenous chicken and the selective signatures in Chinese gamecock chicken. Scientific Reports 10(1), 1-14.
- MACLEOD I.M., HAYES B.J., GODDARD M.E., 2014 - The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data. Genetics 198(4), 1671-1684.
- MEBRATIE W., SHIRALI M., MADSEN P., SAPP R.L., HAWKEN R., JENSEN J., 2017 - The effect of selection and sex on genetic parameters of body weight at different ages in a commercial broiler chicken population. Livestock Science 204, 78-87.
- MEUWISSEN T.H., HAYES B.J., GODDARD M., 2001 - Prediction of total genetic value using genome-wide dense marker maps. Genetics 157(4), 1819-1829.
- MEUWISSEN T., GODDARD M., 2010 - Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics 185(2), 623-631.
- MEUWISSEN T., HAYES B., GODDARD M., 2016 - Genomic selection: A paradigm shift in animal breeding. Animal Frontiers 6(1), 6-14.
- MIGNON-GRASTEAU S., 1999 - Genetic parameters of growth curve parameters in male and female chickens. British Poultry Science 40(1), 44-51.
- MISZTAL I., TSURUTA S., LOURENCO D., AGUILAR I., LEGARRA A., VITEZICA Z., 2014 -Manual for BLUPF90 Family of Programs. Athens: University of Georgia.
- MISZTAL I., TSURUTA S., STRABEL T., AUVRAY B., DRUET T., LEE D., 2002 - “BLUPF90 and related programs (BGF90),” in Proceedings of the 7th world Congress on Genetics Applied to Livestock Production, Montpellier, 743-744.
- MRODE R., OJANGO J. M., OKEYO A.M., MWACHARO J. M., 2019 - Genomic selection and use of molecular tools in breeding programs for indigenous and crossbred cattle in developing countries: Current status and future prospects. Frontiers in Genetics 694.
- OGAWA S., MATSUDA H., TANIGUCHI Y., WATANABE T., NISHIMURA S., SUGIMOTO Y., IWAISAKI H., 2014 - Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle. BMC Genetics 15(1), 1-13.
- PURCELL S., NEALE B., TODD-BROWN K., THOMAS L., FERREIRA M.A., BENDER D., SHAM P.C., 2007 - PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics 81(3), 559-575.
- R CORE TEAM., 2013 - R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing.
- ROLF M.M., TAYLOR J.F., SCHNABEL R.D., MCKAY S.D., MCCLURE M.C., NORTHCUTT S.L., WEABER R.L., 2010- Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle. BMC Genetics 11(1), 1-10.
- SALEK ARDESTANI S., JAFARIKIA M., SARGOLZAEI M., SULLIVAN B., MIAR Y., 2021 -Genomic prediction of average daily gain, back-fat thickness, and loin muscle depth using different genomic tools in Canadian swine populations. Frontiers in Genetics 12, 735.
- SALVIAN M., MOREIRA G.C.M., REIS A.P., DAURIA B.D., PILONETTO F., GERVÁSIO I.C., MOURÃO G.B., 2020 - Estimation of breeding values using different densities of Snp to inform Kinship in broiler chickens. https://doi.org/10.21203/rs.3.rs-32429/v1
- SILVA R.M.O., FRAGOMENI B.O., LOURENCO D.A.L., MAGALHÃES A.F.B., IRANO N., CARVALHEIRO R., ALBUQUERQUE L.G., 2016 - Accuracies of genomic prediction of feed efficiency traits using different prediction and validation methods in an experimental Nelore cattle population. Journal of Animal Science 94(9), 3613-3623.
- SIMEONE R., MISZTAL I., AGUILAR I., VITEZICA Z.G., 2012 - Evaluation of a multi‐line broiler chicken population using a single‐step genomic evaluation procedure. Journal of Animal Breeding and Genetics 129(1), 3-10.
- SONG H., ZHANG J., JIANG Y., GAO H., TANG S., MI S., DING X., 2017 - Genomic prediction for growth and reproduction traits in pig using an admixed reference population. Journal of Animal Science 95(8), 3415-3424.
- SONG H., ZHANG J., ZHANG Q., DING X., 2019 - Using different single-step strategies to improve the efficiency of genomic prediction on body measurement traits in pig. Frontiers in Genetics 9, 730.
- SU G., BRØNDUM R.F., MA P., GULDBRANDTSEN B., AAMAND G.P., LUND M.S., 2012 -Comparison of genomic predictions using medium-density (~54,000) and high-density (~777,000) single nucleotide polymorphism marker panels in Nordic Holstein and Red Dairy Cattle populations. Journal of Dairy Science 95(8), 4657-4665.
- SUN Y., ZHAO G., LIU R., ZHENG M., HU Y., WU D., WEN J., 2013 - The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study. BMC Genomics 14(1), 1-11.
- VANRADEN P.M., 2007 - Efficient estimation of breeding values from dense genomic data. Journal of Dairy Science 90, 374-375.
- VANRADEN P.M., TOOKER M.E., O’CONNELL J.R., COLE J.B., BICKHART D.M., 2017 -Selecting sequence variants to improve genomic predictions for dairy cattle. Genetics Selection Evolution 49(1), 1-12.
- VANRADEN P.M., VAN TASSELL C.P., WIGGANS G.R., SONSTEGARD T.S., SCHNABEL R.D., TAYLOR J.F., SCHENKEL F.S., 2009 - Invited review: Reliability of genomic predictions for North American Holstein bulls. Journal of Dairy Science 92(1), 16-24.
- WANG D., SUN Y., STANG P., BERLIN J. A., WILCOX M.A., LI Q., 2009 - December. Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: principal-component analysis versus multidimensional scaling. BMC Proceedings 3(7), 1-6.
- WELLMANN R., PREUß S., THOLEN E., HEINKEL J., WIMMERS K., BENNEWITZ J., 2013 -Genomic selection using low density marker panels with application to a sire line in pigs. Genetics Selection Evolution 45(1), 1-11.
- WIMMER V., ALBRECHT T., AUINGER H.J., SCHÖN C.C., 2012 - synbreed: a framework for the analysis of genomic prediction data using R. Bioinformatics 28(15), 2086-2087.
- YAN G., QIAO R., ZHANG F., XIN W., XIAO S., HUANG T., HUANG L., 2017 - Imputation-based whole-genome sequence association study rediscovered the missing QTL for lumbar number in Sutai pigs. Scientific Reports 7(1), 1-10.
- ZHANG C., KEMP R. A., STOTHARD P., WANG Z., BODDICKER N., KRIVUSHIN K., PLASTOW G., 2018 - Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants. Genetics Selection Evolution 50(1), 1-13.