D.J.A. Santos*,†,1, J.B. Cole‡, T.J. Lawlor, Jr.,,§ P.M. VanRaden,‡ H. Tonhati†, and L. Ma*,1
*Department of Animal and Avian Sciences, University of Maryland, College Park, 20742
†Departamento de Zootecinia, Universidade Estadual Paulista, Jaboticabal, 14884-900, Brazil
‡Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD 20705-2350
§Holstein Association USA, Brattleboro, VT 05302-0808
1Corresponding author: D.J.A. Santos and Li Ma
2018 J. Dairy Sci. (?)
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The variance of gametic diversity (σ2gamete) can be a useful tool to find individuals that are more likely to produce progeny with extreme breeding values. The aim of this study is to show how to obtain this variance for individuals in routine genomic evaluations, as well as to use this variance as a selection criterion in conjunction with breeding values to improve genetic gains. An analytical approach was employed to obtain the gametic variance from the sum of binomial variances of individual QTL across the genome. Simulation was then used to verify the predictability of the σ2gamete in many scenarios. For genomic evaluation, genomic BLUP (GBLUP) and Bayesian least absolute shrinkage and selection operator (BLASSO) models were compared, with BLASSO having better performance for estimating σ2gamete. Results suggested that markers with low minor allele frequency (MAF), as well as the covariance between markers, should be included in the estimation. Compared to sequence data, SNP data are sufficient for estimating σ2gamete. To incorporate σ2gamete into selective breeding, we proposed a new index, the relative predicted transmitting ability (RPTA), which allows a better use of the genetic potential of individuals than traditional PTA. The RPTA is easy to obtain and apply in existing genomic evaluations. In addition, the confidence levels of this index can be adjusted by the number of progeny per parent, making it suitable for dairy cattle breeding. We also applied σ2gamete to the U.S. genomic evaluations for Holstein and Jersey. The DGAT1 gene had a strong effect on the prediction of σ2gamete for several dairy traits, biasing the distributions of this parameter in both cattle breeds. Population-level inbreeding had a small impact on gametic variability, with greater effects for traits affected by many genes. In conclusion, σ2gamete, a potentially important parameter in selective breeding programs, is easy to compute and useful for both improving genetic gains and control of genetic diversity.
Keywords: Mendelian sampling, heterozygosity, selective breeding, dairy cattle