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Background: The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference genome, we set-up an analysis pipeline based on a short read de novo sequence assembler and a program designed to identify variation within short reads. To illustrate the potential of this technique, we present the results obtained with a randomly sheared, enzymatically generated, 2-3 kbp genome fraction of six pooled Meleagris gallopavo (turkey) individuals.

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.

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A cross between 2 genetically different outcross broiler dam lines, originating from the White Plymouth Rock breed, was used to produce a large 3-generation broiler population. This population was used to detect and localize QTL affecting fatness in chicken. Twenty full-sib birds in generation 1 and 456 full-sib birds in generation 2 were typed for microsatellite markers, and phenotypic observations were collected for 3 groups of generation 3 birds (approximately 1,800 birds per group). Body weight, abdominal fat weight, and percentage abdominal fat was recorded at the age of 7, 9, and 10 wk. To study the presence of QTL, an across-family weighted regression interval mapping approach was used in a full-sib QTL analysis. Genotypes from 410 markers mapped on 25 chromosomes were available. For the 3 traits, 26 QTL were found for 18 regions on 12 chromosomes. Two genomewise significant QTL (P < 0.05) were detected, one for percentage abdominal fat at the age of 10 wk on chicken chromosome 1 at 241 cM (MCW0058 to MCW0101) with a test statistic of 2.75 and the other for BW at the age of 10 wk on chicken chromosome 13 at 9 cM (MCW0322 to MCW0110) with a test statistic of 2.77. Significance levels were obtained using the permutation test. Multiple suggestive QTL were found on chromosomes 1, 2, 4, 13, 15, and 18, whereas chromosomes 3, 7, 10, 11, 14, and 27 had a single suggestive QTL.