title: The Prediction of the Expected Current Selection Coefficient of Single Nucleotide Polymorphism Associated with Holstein Milk Yield, Fat and Protein Contents.
abstract: Milk-related traits (milk yield, fat and protein) have been crucial to selection of Holstein. It is essential to find the current selection trends of Holstein. Despite this, uncovering the current trends of selection have been ignored in previous studies. We suggest a new formula to detect the current selection trends based on single nucleotide polymorphisms (SNP). This suggestion is based on the best linear unbiased prediction (BLUP) and the Fisher's fundamental theorem of natural selection both of which are trait-dependent. Fisher's theorem links the additive genetic variance to the selection coefficient. For Holstein milk production traits, we estimated the additive genetic variance using SNP effect from BLUP and selection coefficients based on genetic variance to search highly selective SNPs. Through these processes, we identified significantly selective SNPs. The number of genes containing highly selective SNPs with p-value <0.01 (nearly top 1% SNPs) in all traits and p-value <0.001 (nearly top 0.1%) in any traits was 14. They are phosphodiesterase 4B (PDE4B), serine/threonine kinase 40 (STK40), collagen, type XI, alpha 1 (COL11A1), ephrin-A1 (EFNA1), netrin 4 (NTN4), neuron specific gene family member 1 (NSG1), estrogen receptor 1 (ESR1), neurexin 3 (NRXN3), spectrin, beta, non-erythrocytic 1 (SPTBN1), ADP-ribosylation factor interacting protein 1 (ARFIP1), mutL homolog 1 (MLH1), transmembrane channel-like 7 (TMC7), carboxypeptidase X, member 2 (CPXM2) and ADAM metallopeptidase domain 12 (ADAM12). These genes may be important for future artificial selection trends. Also, we found that the SNP effect predicted from BLUP was the key factor to determine the expected current selection coefficient of SNP. Under Hardy-Weinberg equilibrium of SNP markers in current generation, the selection coefficient is equivalent to 2*SNP effect.
authors.affiliation: Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747, Korea.
authors.forename: Young-Sup
authors.initials: YS
authors.lastname: Lee
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea .
authors.forename: Donghyun
authors.initials: D
authors.lastname: Shin
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea .
authors.forename: Wonseok
authors.initials: W
authors.lastname: Lee
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea .
authors.forename: Mengistie
authors.initials: M
authors.lastname: Taye
authors.affiliation: National Livestock Research Institute, Cheonan 330-801, Korea .
authors.forename: Kwanghyun
authors.initials: K
authors.lastname: Cho
authors.affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea .
authors.forename: Kyoung-Do
authors.initials: KD
authors.lastname: Park
authors.affiliation: Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747, Korea ; Department of Agricultural Biotechnology, Animal Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea .
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
keywords: Best Linear Unbiased Prediction [BLUP]; Expected Current Relative Selection Coefficient; Fisher’s Fundamental Theorem of Natural Selection; Holstein; Milk Production Trait; Single Nucleotide Polymorphism-Genomic Best Linear Unbiased Prediction [SNP-GBLUP]