Genetic mapping of quantitative trait loci affecting susceptibility to Marek's disease virus induced tumors in F2 intercross chickens

High resolution mapping and identification of new quantitative trait loci (QTL) affecting susceptibility to Marek's disease

Marek's disease (MD) is a lymphoproliferative disease of chickens that costs the poultry industry approximately $1 billion annually. Genetic resistance to MD is gaining increased attention to augment vaccinal control as disease outbreaks occur more frequently. Previously, analysis of a 272 F2 White Leghorn resource population measured for many MD traits and genotyped for 78 microsatellite markers revealed two and four quantitative trait loci (QTL) with significant and suggestive association, respectively, to one or more MD associated traits. Additional genetic markers have since been scored on the MD resource population to increase QTL resolution and genome coverage. Saturation of four of the QTL regions with 17 markers revealed five new QTL while 32 markers extended the genome coverage by 400 + CM and uncovered three more QTL. QTL analysis by single-point and interval mapping algorithms agreed well when marker saturation was approximately 20 CM or less. Currently 127 genetic markers cover approximately 68% of the genome that contain up to 14 MD QTL associated to one or more MD trait; seven at the significant level and seven at the suggestive level. Individually each QTL accounts for 2-10% of the variation and, in general, resistance was dominant although the resistant allele may come from either parental line. This study suggests that a limited number of genomic regions play a major role in the genetic control of MD resistance. Markers linked to these loci may be useful for selection of MD resistant stock by the poultry industry following verification of the association within their breeding populations.

Application of AFLP markers to genome mapping in poultry

The amplified fragment length polymorphism (AFLP) technique has been used to enhance marker density in the East Lansing reference chicken genome map, using a backcross family derived from a Red Jungle Fowl by White Leghorn mating with White Leghorn as the recurrent parent. To date, 204 AFLP markers have been added, expanding overall map coverage by about 25%. To the limits of our resolution, AFLP markers are distributed relatively evenly across the EL reference map. AFLP are about 60% as frequent in a cross within White Leghorns (line 7(2) x 6(3)) in comparison to the more divergent reference map population. Based on apparent identity of size, about 40% of the 7(2) x 6(3) cross AFLP fragments were also polymorphic in the reference map cross. Primer pairs in which one primer contains 3' extensions of three selective nucleotides and the other has two selective nucleotides successfully generated AFLP from chicken DNA, but such pairs appeared to amplify only a subset of those fragments to which they have an exact sequence match. Three different restriction enzymes with 4 bp recognition sites (TaqI, HinP1I and MspI) were found to work well with EcoRI as the rarer of the two AFLP restriction enzymes used, with HinP1I being the most effective of the three. AFLP markers are likely to provide an economical method with which to enhance framework linkage maps of chicken and probably other avian genomes.

Whole genome scan in chickens for quantitative trait loci affecting growth and feed efficiency

A feed efficiency experiment was conducted in a population consisting of progeny from 10 full sib families of a cross between two broiler lines. Microsatellite genotypes were determined on Generation (G) 1 and 2. In G3, BW at 23 and 48 d and feed intake were measured and were used to calculate growth between 23 and 48 d, feed intake adjusted for BW, and feed efficiency. Average adjusted progeny trait values were calculated for G2 animals after adjusting phenotypic observations on offspring for fixed effects, covariables, maternal genetic effects, the additive genetic contribution of the mate, and heterogeneity between sexes and were used as dependent variable in the quantitative trait loci (QTL) analysis. A full sib interval mapping approach was applied using genotypes from 420 markers on 27 autosomal linkage groups. Four QTL exceeded significance thresholds. The most significant QTL was located on Chromosome 1 at 235 cM and had a 4% genomewise significance for feed intake between 23 and 48 d. Furthermore, this QTL exceeded suggestive linkage for growth between 23 and 48 d and BW at 48 d. A second QTL was located on linkage group WAU26 at 16 cM and showed suggestive linkage for feed intake between 23 and 48 d. On Chromosome 4, at 147 cM a third QTL, which had an effect on both feed intake traits, was found. Finally, a fourth QTL, which affected feed intake adjusted for BW, was located on Chromosome 2 at 41 cM.