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Benefits from marker-assisted selection under an additive polygenic genetic model¹

B. Villanueva^*,2, R. Pong-Wong, J. Fernández and M. A. Toro

^* Scottish Agricultural College, Edinburgh EH9 3JG, U.K.; and Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, U.K.; and and INIA, 28040 Madrid, Spain

² Correspondence: Sustainable Livestock Systems Group, SAC, Bush Estate, Penicuik, Midlothian EH26 0PH, Scotland, U.K. (phone: +44-131-535-3224; fax: +44-131-535 3121; e-mail: beatriz.villanueva{at}sac.ac.uk).

This study investigated, through stochastic computer simulation, the extra gains expected from marker-assisted selection (MAS) in an infinitesimal model with linkage. The trait under selection was assumed to be controlled by 2,000 loci of additive small effect and evenly distributed in c chromosomes of one Morgan each (and c = 5, 10, 20, or 30). This approach differs from previous studies on the benefits of MAS that have considered mixed inheritance models. Marker information was used together with pedigree information to compute the relationship matrix used in BLUP genetic evaluations. The MAS schemes were compared with schemes where genetic evaluations were performed using standard BLUP (i.e., the relationship matrix is obtained using pedigree information only). When the number of markers was large enough (approximately one marker every 10 cM), there were increases in the accuracy of selection with MAS, and this led to extra gains compared with standard BLUP for all genome sizes considered. The benefit from MAS increased over generations. At the last generation of selection (Generation 10), the response from MAS was 11, 9, 7, and 5% greater than with standard BLUP for genomes with 5, 10, 20, and 30 chromosomes, respectively. Thus, although small, gains from MAS were nonetheless detectable for genome sizes typical of livestock populations.

Key Words: BLUP Genetic Evaluation • Additive Relationship Matrix • Marker-Assisted Selection

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