Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail

Abstract

BackgroundAs for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of a QTL for a fear-related behaviour, namely tonic immobility, previously localized on Coturnix japonica chromosome 1. To this aim, two reduced representations of the genome were analysed through high-throughput 454 sequencing: AFLP (Amplified Fragment Length Polymorphism) fragments as representatives of genomic DNA, and EST (Expressed Sequence Tag) as representatives of the transcriptome.ResultsThe sequencing runs produced 399,189 and 1,106,762 sequence reads from cDNA and genomic fragments, respectively. They covered over 434 Mb of sequence in total and allowed us to detect 17,433 putative SNP. Among them, 384 were used to genotype two Advanced Intercross Lines (AIL) obtained from three quail lines differing for duration of tonic immobility. Despite the absence of genotyping for founder individuals in the analysis, the previously identified candidate region on chromosome 1 was refined and led to the identification of a candidate gene.ConclusionsThese data confirm the efficiency of transcript and AFLP-sequencing for SNP discovery in a non-model species, and its application to the fine mapping of a complex trait. Our results reveal a significant association of duration of tonic immobility with a genomic region comprising the DMD (dystrophin) gene. Further characterization of this candidate gene is needed to decipher its putative role in tonic immobility in Coturnix.

Genetical Genomics of Tonic Immobility in the Chicken

“…Targeted resequencing of the QTL region corroborated the previous results and highlighted PRDX4 and ACOT9 as likely candidate genes [26]. In addition, PRDX4 and ACOT9 were both present in a candidate QTL interval for tonic immobility in the quail selected lines [27].…”

Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

“…QTL analysis can increase the selection response in breeding programs by investigating genotype and phenotype relationships using marker-assisted selection (MAS) [ 2 , 3 ]. Several DNA markers, such as single nucleotide polymorphisms (SNPs) [ 4 ], restriction fragment length polymorphisms [ 5 ], amplified fragment length polymorphisms (AFLPs) [ 6 ], and simple sequence length polymorphisms (or microsatellite) [ 7 ], have been used to identify the chromosomal positions of loci. Among these markers, SNPs play a crucial role in genetics, biomedicine, ecology, and evolutionary studies [ 8 , 9 , 10 , 11 ].…”

“…Compared with chickens, few studies have performed QTL analysis on the Japanese quail, and the genome of this species has been poorly explored [ 31 ]. The first studies reported on the genetic and QTL analyses of the Japanese quail involved the identification of panels of markers [ 32 , 33 ], construction of genetic maps using AFLP [ 34 ] and microsatellite [ 35 ], complete sequencing of the mitochondrial genome [ 36 ], detection of QTL for growth-performance and meat-quality traits [ 37 ], determination of egg-laying curve [ 38 ], and analyses of carcass traits, internal organs [ 39 ], and fearfulness-related traits [ 6 , 40 ]. The construction of genetic maps and QTL analysis in poultry have mostly focused on chickens rather than Japanese quails.…”

“…Summary of QTL detected for egg-related traits. Subscript letters are first and second egg laying stages; 1 peak position; 2 physical position of the marker; 3 genome-wide significant and suggestive QTL (** significant at 1% and * 5% level, † suggestive at 10% level); 4 confidence interval at 1.8-LOD drop-off; 5 phenotypic variance explained by QTL;6 additive effect of the QTL; 7 dominant effect of the QTL; 8 the degree of dominance; 9 parental allele.…”

Age-Dependent Change in the Morphology of Nucleoli and Methylation of Genes of the Nucleolar Organizer Region in Japanese Quail (<I>Coturnix japonica</I>) Model (Temminck and Schlegel, 1849) (Galliformes: Aves)

“…It is also the basic model in studies of embryology and development and in research on viruses and cancer. Another species of bird which is increasingly serving as a model species, replacing Gallus domesticus, is the Japanese quail (Coturnix japonica), for which the mitochondrial genome (NISHIBORI et al 2002) and nuclear genome (FRÉSARD et al 2012) have been sequenced. Quails are rapidly-maturing organisms with rapid turnover of generations.…”