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Open Access

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

  • Amanda Jane Chamberlain1Email author,
  • Helen Clare McPartlan1 and
  • Michael Edward Goddard1
Genetics Selection Evolution200840:79

Received: 14 December 2006

Accepted: 24 July 2007

Published: 15 January 2008


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.


bivariate analysisindependent traitspleiotropygenome scanfalse discovery rate

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Authors’ Affiliations

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


© INRA, EDP Sciences 2008