Genet. Sel. Evol. 40 (2008) 79-89
DOI: 10.1051/gse:2007038

Genes influencing milk production traits predominantly affect one of four biological pathways

Amanda Jane Chamberlain, Helen Clare McPartlan and Michael Edward Goddard

Animal Genetics and Genomics Platform, Department of Primary Industries, Victoria, Australia

(Received 14 December 2006; accepted 24 July 2007 ; published online 21 December 2007)

Abstract - In this study we introduce a method that accounts for false positive and false negative results in attempting to estimate the true proportion of quantitative trait loci that affect two different traits. This method was applied to data from a genome scan that was used to detect QTL for three independent milk production traits, Australian Selection Index (ASI), protein percentage (P%) and fat percentage corrected for protein percentage (F% - P%). These four different scenarios are attributed to four biological pathways: QTL that (1) increase or decrease total mammary gland production (affecting ASI only); (2) increase or decrease lactose synthesis resulting in the volume of milk being changed but without a change in protein or fat yield (affecting P% only); (3) increase or decrease protein synthesis while milk volume remains relatively constant (affecting ASI and P% in the same direction); (4) increase or decrease fat synthesis while the volume of milk remains relatively constant (affecting F% - P% only). The results indicate that of the positions that detected a gene, most affected one trait and not the others, though a small proportion (2.8%) affected ASI and P% in the same direction.

Key words: bivariate analysis / independent traits / pleiotropy / genome scan / false discovery rate

Correspondence and reprints: amanda.chamberlain@dpi.vic.gov.au

© INRA, EDP Sciences 2008