The data and methods used have been described previously [54 (link)]. Briefly, two quail lines were used, divergently selected on their sociability [19 (link)]: high social (HSR) and low social (LSR) reinstatement behaviour. A total of 10 individuals from generation 50 of each quail line were sequenced after equimolar DNA pooling. Sequencing was performed (paired-ends, 100 bp) on a HiSeq 2000 sequencer (Illumina), using one lane per line (TruSeq sbs kit version 3). The reads (190,159,084 and 230,805,732 reads, respectively, for the HSR and LSR lines) were mapped to the CoJa2.2 genome assembly using BWA [112 (link)], with the mem algorithm. Data are publicly available under SRA accession number SRP047364. Within each line, the frequency of the reference allele was estimated for all SNPs covered by at least 5 reads, using Pool-HMM [113 (link)]. This analysis provided 13,506,139 SNPs with allele frequency estimates in the two lines. FLK values [55 (link)] were computed for all these SNPs, and the local score method [54 (link)] was applied to the p value on single-marker tests.
Other organizations :
Génétique Physiologie et Systèmes d'Elevage, Université de Toulouse, École Nationale Vétérinaire de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, University of Queensland, St. Jude Children's Research Hospital, Centre Val de Loire, Institut Pasteur, James S. McDonnell Foundation, Inserm, Sorbonne Université, Laboratoire de Biologie du Développement, Centre National de la Recherche Scientifique, Children's Hospital of Los Angeles, University of Southern California, Physiologie de la Reproduction et des Comportements, Université de Tours, University of Manchester, AgroParisTech, Université Paris-Saclay, Tokyo University of Agriculture and Technology, Nagoya University, University of Missouri
Selection on sociability: high social (HSR) and low social (LSR) reinstatement behaviour
dependent variables
Allele frequency estimates for 13,506,139 SNPs
FLK values computed for all SNPs
Local score method applied to p-value on single-marker tests
control variables
Individuals from generation 50 of each quail line
Equimolar DNA pooling of 10 individuals from each line
Sequencing performed using paired-ends, 100 bp on a HiSeq 2000 sequencer (Illumina), using one lane per line (TruSeq sbs kit version 3)
Reads mapped to the CoJa2.2 genome assembly using BWA, with the mem algorithm
SNPs covered by at least 5 reads were used for allele frequency estimation using Pool-HMM
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