A Global Search Reveals Epistatic Interaction Between QTL for Early Growth in the Chicken

Abstract

We have identified quantitative trait loci (QTL) explaining a large proportion of the variation in body weights at different ages and growth between chronological ages in an F 2 intercross between red junglefowl and White Leghorn chickens. QTL were mapped using forward selection for loci with significant marginal genetic effects and with a simultaneous search for epistatic QTL pairs. We found 22 significant loci contributing to these traits, nine of these were only found by the simultaneous two-dimensional search, which demonstrates the power of this approach for detecting loci affecting complex traits. We have also estimated the relative contribution of additive, dominance, and epistasis effects to growth and the contribution of epistasis was more pronounced prior to 46 days of age, whereas additive genetic effects explained the major portion of the genetic variance later in life. Several of the detected loci affected either early or late growth but not both. Very few loci affected the entire growth process, which points out that early and late growth, at least to some extent, have different genetic regulation.

Controlling false positives in the mapping of epistatic QTL

“…Our observations are roughly in line with earlier studies: four interaction-only pairs detected from an F 2 mouse population (size is 510, 166 females) explained about 36% of the total variation in litter size (that is h epi 2 ¼ 9% on average) (Peripato et al, 2004); most epistatic pairs detected for obesity-related traits using 513 F 2 mice had a h epi 2 42% despite the relatively relaxed thresholds that were used (Stylianou et al, 2006). Increasing the population size is a good option to increase power (Carlborg et al, 2003;Ma et al, 2009). For example, according to our additional simulation results (Supplementary Figure S1), when increasing the population size from 540 to 840, scenarios with 2.5% h epi 2 at least doubled the power, and scenarios with 5.0% h epi 2 at the population size of 840 had power comparable to those with a h epi 2 of 7.5% at the size of 540.…”

Identification of quantitative trait loci associated with bone traits and body weight in an F2 resource population of chickens

“…A number of QTL mapping studies have been performed on crosses between genetically and phenotypically divergent lines of chickens. These studies have focused on identifying QTL responsible for body weight [39,46,47,51,52,55], feed-efficiency [57], growth [7,20,27,55,57,62], carcass characteristics [12,23,24,56], and egg traits [27,39,44,54,59]. Other researchers have investigated specific candidate genes potentially associated with variation in traits relating to bone integrity [31,61].…”

Review: How to improve genomic predictions in small dairy cattle populations

“…In this case the effect of a particular QTN depends on the frequency of genes it interacts with (e.g. Carlborg et al, 2003;Huang et al, 2012). As these could have very different frequencies among breeds it results in breed-specific effects.…”