Computer simulation of marker-assisted selection utilizing linkage disequilibrium

Abstract

The value of marker-assisted selection (MAS) using linkage disequilibrium between genetic markers and quantitative trait loci (QTL) was examined. To simulate the disequilibrium, four base populations were created, F2, F5, F10 and F20, by random mating from a cross between two inbred lines. Selections were on breeding values estimated from: (1) marker QTL (MQTL) associations (MAS); (2) conventional best linear unbiased prediction (BLUP) methods; and (3) a combination of 1 and 2 (COMB). Alternative cases were studied by varying the parameters (heritability, initial linkage disequilibrium, and distribution of QTL effects). A genome with 100 QTL and 100 markers randomly (but equally) spread over 20 chromosomes, each 100 centiMorgans (cM) in length, was generated. Linkage disequilibrium (over 30 replicates) of QTLs with their nearest marker averaged 0.153, 0.104, 0.068, and 0.047 for the four base populations, and fell to 0.035, 0.025, 0.021, and 0.018, respectively, after ten generations of MAS selection (heritability 0.25). The initial linkage disequilibrium had the greatest effect on the genetic gain by MAS with the responses for the base populations F2>F5>F10>F20. Genetic gains by conventional BLUP selection were usually greater than by MAS. However, MAS contributed to the combined selection (COMB) to give appreciably higher genetic responses. Hybridization of selected lines after several generations of selection contributed little to generating further linkage disequilibrium. Detection of markers closer to the QTL will increase the linkage disequilibrium available for selection. Eventually with very close linkage each QTL allele can be uniquely identified in selection, and selection will then be equivalent to selection on the QTLs themselves.