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Effect of allele frequencies, effect sizes and number of markers on prediction of quantitative traits in chickens
Author(s) -
AbdollahiArpanahi R.,
NejatiJavaremi A.,
Pakdel A.,
MoradiShahrbabak M.,
Morota G.,
Valente B.D.,
Kranis A.,
Rosa G.J.M.,
Gianola D.
Publication year - 2014
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12075
Subject(s) - single nucleotide polymorphism , snp , biology , minor allele frequency , allele frequency , genetics , best linear unbiased prediction , allele , selection (genetic algorithm) , genotype , gene , computer science , artificial intelligence
Summary The objective was to assess goodness of fit and predictive ability of subsets of single nucleotide polymorphism ( SNP ) markers constructed based on minor allele frequency ( MAF ), effect sizes and varying marker density. Target traits were body weight ( BW ), ultrasound measurement of breast muscle ( BM ) and hen house egg production ( HHP ) in broiler chickens. We used a 600 K Affymetrix platform with 1352 birds genotyped. The prediction method was genomic best linear unbiased prediction ( GBLUP ) with 354 564 single nucleotide polymorphisms ( SNP s) used to derive a genomic relationship matrix ( G ). Predictive ability was assessed as the correlation between predicted genomic values and corrected phenotypes from a threefold cross‐validation. Predictive ability was 0.27 ± 0.002 for BW , 0.33 ± 0.001 for BM and 0.20 ± 0.002 for HHP . For the three traits studied, predictive ability decreased when SNP s with a higher MAF were used to construct G . Selection of the 20% SNP s with the largest absolute effect sizes induced a predictive ability equal to that from fitting all markers together. When density of markers increased from 5 K to 20 K, predictive ability enhanced slightly. These results provide evidence that designing a low‐density chip using low‐frequency markers with large effect sizes may be useful for commercial usage.