Comparison of multiple-trait genetic evaluation accuracy using region marker relationships with traditional best linear unbiased prediction (BLUP)

Abstract

Accuracy of multiple-trait genetic evaluation based on allelic relationships with traditional best linear unbiased prediction (BLUP) was compared through computer simulation. Firstly, a base population (N = 100) was simulated; the population was half male/half female. After  reaching linkage disequilibrium between marker and QTL, phenotypic and genotypic records were simulated for the last generation. For each  animal in the base population, three chromosomes (each one Morgan in  length) was created; on each chromosome, 200 markers and 50 QTLs were randomly located. Mutation rate in each generation was 2.5 × 10^-5. Total allelic relationships consider variety of genetic relationships  among relatives and employ information of non-relatives as well. In  evaluation using total allelic relationships, three separate allelic matrixes were required. To form such matrixes, firstly, marker effects were estimated for each trait using mixed model of BLUP. Then, based on these effects, particular markers of each trait as well as common  markers among two traits were determined and used to form allelic  relationship matrixes. Correlation between actual and estimated  breeding values in the last generation was evaluated based on 10 iterations. Statistical comparison was performed using t-student test. A significant difference was observed between evaluation accuracy of  studied two methods.

Keywords: Marker, allelic relationships, multiple-trait evaluation