the effect of using approximate gametic variance covariance matrices on marker assisted selection by blup使用近似的影响配子的方差协方差矩阵blup分子标记辅助选择.pdf

Genet. Sel. Evol. 36 (2004) 29–48 29 c INRA, EDP Sciences, 2004 DOI: 10.1051/gse:2003049 Original article The effect of using approximate gametic variance covariance matrices on marker assisted selection by BLUP Liviu R. Ta∗ , Rohan L. Fa,b , Jack C.M. Da,b , ´ c d Soledad A. F , Bernt G a Department of Animal Science, Iowa State University, Ames, IA 50011, USA b Lawrence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA c Department of Statistics, The Ohio State University, Columbus, OH 43210, USA d Danish Institute of Animal Science, Foulum, Denmark (Received 19 September 2002; accepted 13 May 2003) Abstract – Under additive inheritance, the Henderson mixed model equations (HMME) pro- vide an efficient approach to obtaining genetic evaluations by marker assisted best linear un- biased prediction (MABLUP) given pedigree relationships, trait and marker data. For large pedigrees with many missing markers, however, it is not feasible to calculate the exact gametic variance covariance matrix required to construct HMME. The objective of this study was to investigate the consequences of using approximate gametic variance covariance matrices on re- sponse to selection by MABLUP. Two methods were used to generate approximate variance covariance matrices. The first method (Method A) completely discards the marker informa- tion for individuals with an unknown linkage phase between two flanking markers. The second method (Method B) makes use of the marker information at only the most polymorphic marker locus