02612naa a2200277 a 450000100080000000500110000800800410001902400270006010000210008724501340010826000090024250005000025152013160075165300120206765300120207965300180209165300230210965300200213270000200215270000190217270000170219170000190220870000160222770000160224377300750225910579022019-10-15       2017    bl uuuu     u00u1 u    #d7 a10.1111/jbg.122882DOI1 aLOURENCO, D.A.L.  aImplications of SNP weighting on single-step genomic predictions for different reference population sizes.h[electronic resource]  c2017  aArticle history: Received: 28 February 2017 / Accepted: 19 July 2017. This study was partially funded by the American Angus Association (St. Joseph, MO), Zoetis (Kalamazoo, MI) and by Agriculture and Food Research Initiative Competitive Grants no. 2015-67015-22936 from the US Department of Agriculture's National Institute of Food and Agriculture. We gratefully acknowledge the very helpful comments by the two anonymous reviewers, and we thank Andra H. Nelson for assisting with data analysis.  aABSTRACT. We investigated the importance of SNP weighting in populations with 2,000 to 25,000 genotyped animals. Populations were simulated with two effective sizes (20 or 100) and three numbers of QTL (10, 50 or 500). Pedigree information was available for six generations; phenotypes were recorded for the four middle generations. Animals from the last three generations were genotyped for 45,000 SNP. Single-step genomic BLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) were used to estimate genomic EBV using a genomic relationship matrix (G). The WssGBLUP performed better in small genotyped populations; however, any advantage for WssGBLUP was reduced or eliminated when more animals were genotyped. WssGBLUP had greater resolution for genome-wide association (GWA) as did increasing the number of genotyped animals. For few QTL, accuracy was greater for WssGBLUP than ssGBLUP; however, for many QTL, accuracy was the same for both methods. The largest genotyped set was used to assess the dimensionality of genomic information (number of effective SNP). The number of effective SNP was considerably less in weighted G than in unweighted G. Once the number of independent SNP is well represented in the genotyped population, the impact of SNP weighting becomes less important.  © 2017 Blackwell Verlag GmbH  aACCURAY  aBAYES B  aSNP WEIGHTING  aVARIABLE SELECTION  aWEIGTED SSGBLUP1 aFRAGOMENI, B.O.1 aBRADFORD, H.L.1 aMENEZES I.R.1 aFERRAZ, J.B.S.1 aAGUILAR, I.1 aMISZTAL, I.  tJournal of Animal Breeding and Genetics, 2017gv. 134 (6), p. 463-471.