Whole genome resequencing of 125 chicken and two pooled populations including red jungle fowl and multiple populations of commercial broilers and layers

We carried out whole genome resequencing of 125 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus).Three groups of birds were included in the study (1) red jungle fowls (Gallus gallus gallus, RJFs), (2) broilers (BRs) and (3) layers (LRs) (Table 1). The RJFs were sampled from two geographical origins in Thailand (RJFt) and India (RJFi). The RJFt consisted of 25 DNA samples collected within a European collaborative research project AVIANDIV (https://www.tzv.fal.de/). RJFt was randomly down-sampled from ~150 RJFs caught in northern Thailand in 1997 and maintained since with random mating over four flocks; given the place and date, the RJFt samples likely have seen some contamination from domestic or feral populations prior to collection (Peterson & Brisbin 1998). The DNA samples from RJFt were collected in 1999. For further information on the behaviour and morphology of these birds we refer to the AVIANDIV project webpage. The RJFi population involved 10 individuals of the Richardson line, originating from RJF caught in India in the 1960´s. This population has been extensively studied (Brisbin et al., 2002; Brisbin & Peterson 2007; Condon 2012), and appears to have been established from a wild population prior to major genetic contamination of red jungle fowl populations, such that it may represent a unique RJF line that is at least largely free of influence from domestic stocks. The second and third group of birds represent commercial chicken, comprising three broiler and three layer populations, respectively. The broilers (BRs) were represented by 20 DNA samples of each of two lines (BRA and BRB) established independently and previously collected as part of the AVIANDIV project. BRA was a sire line belonging to the company Indian River International (Texas) established in 1980 and closed since with a breeding population size of >10,000 birds. BRB was another sire line originally from France, developed in 1970 with a breeding population size varying between 10,000 to 70,000. The broiler group further involved a pooled sample of 25 birds from AVIANDIV's broiler sire line D, hereafter denoted BRpD. This is a sire line originally from UK, established in 1974 and closed since with unknown population size. In the layer group (LRs), data from 25 birds each from purebred white (WL) and brown (BL) egg laying populations, sequenced in the frame of SYNBREED project (http://www.synbreed.tum.de/index.php?id=2), were included. WL and BL birds represent parental lines of the LOHMANN Tierzucht GmbH that are originally established from White Leghorn and Rhode Island Red, respectively. Moreover, we used pooled sequence data of 48 birds from Rhode Island White (RWp), a crossbred layer population collected by the AVIANDIV project.Sequencing libraries of 300 – 500 bp fragments were constructed for each individual sample using Illumina Nextera Library preparation kits. Sequencing of RJFt, BRA and BRB was conducted using an Illumina HiSeq 2500 machine and 2x126 bp paired-end reads were generated. RJFi, WL and BL along with the three DNA pools (RWp, BRpB and BRpD) were sequenced with 2x101 bp paired-end reads (see Table 1). The paired-end reads from individuals along with reads from pools were mapped against the reference genome assembly Galgal5 using the Burrows-Wheeler aligner (bwa-0.7.13). Duplicate reads were masked during pre-processing using the Picard tool set (version 2.2.0) and base quality scores were recalibrated using GATK 3.7 BaseRecalibrator.