Comparison of accuracy of genomic evaluation of body weight and average daily gain using different SNP densities in the F2 population of broiler chickens
References
- ADEYINKA I.A., ONI O.O., NWAGU B.I., F. D. 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.
- ASADOLLAHI H., VAEZ TORSHIZI R., EHSANI A., MASOUDI A.A., 2022 - An association of CEP78, MEF2C, VPS13A and ARRDC3 genes with survivability to heat stress in an F2 chicken population. Journal of Animal Breeding and Genetics 139(5), 574-582.
- 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 Genomics 37(10), 829-836.
- LOURENCO D. MISZTAL A. L., 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., AGGREY S.E., MUIR W.M., 2013 - Experiences with a single-step genome evaluation. Poultry Science 92(9), 2530-2534.
- MISZTAL I., TSURUTA S., LOURENCO D., AGUILAR I., LEGARRA A., Z. VITEZICA., 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. 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. DigitalCommons@University of Nebraska - Lincoln
- 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., J. WEN., 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 - Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: principal-component analysis versus multidimensional scaling. BMC Proceedings - BioMed Central 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.
DOI: https://doi.org/10.2478/aspr-2025-0021 | Journal eISSN: 2300-8342
Language: English
Page range: 301 - 316
Accepted on: Jun 16, 2025
Published on: Oct 7, 2025
Published by: Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences
In partnership with: Paradigm Publishing Services
Publication frequency: 4 times per year
Related subjects:
© 2025 Hamed Asadollahi, Saeid Ansari Mahyari, Rasoul Vaez Torshizi, Hossein Emrani, Alireza Ehsani, published by Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.