Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica)

Abstract

SummaryA large F2 cross with 920 Japanese quail was used to map QTL for phosphorus utilization, calcium utilization, feed per gain and body weight gain. In addition, four bone ash traits were included, because it is known that they are genetically correlated with the focal trait of phosphorus utilization. Trait recording was done at the juvenile stage of the birds. The individuals were genotyped genome‐wide for about 4k SNPs and a linkage map constructed, which agreed well with the reference genome. QTL linkage mapping was performed using multimarker regression analysis in a line cross model. Single marker association mapping was done within the mapped QTL regions. The results revealed several genome‐wide significant QTL. For the focal trait phosphorus utilization, a QTL on chromosome CJA3 could be detected by linkage mapping, which was substantiated by the results of the SNP association mapping. Four candidate genes were identified for this QTL, which should be investigated in future functional studies. Some overlap of QTL regions for different traits was detected, which is in agreement with the corresponding genetic correlations. It seems that all traits investigated are polygenic in nature with some significant QTL and probably many other small‐effect QTL that were not detectable in this study.

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

“…For clarity, only the first 23 Coturnix japonica chromosomes (CJA) are shown within the plots, since no significant peaks were observed for the other chromosomes. As described in Vollmar et al [18], none of the genotyped SNPs were located on CJA16. Six QTL with genome-wide significance thresholds of 5 and 10% were found across all genera (Table 3).…”

“…In previous studies, we investigated the impact of host genetics [15,18,23] and of the composition of the ileum microbiota [16,17] on PU and related traits in Japanese quail. To complement these studies, here we modeled the microbiota composition as a host trait and investigated how the microbiota composition and the host genome can predict the four host phenotypic traits considered in this study.…”

“…DNA preparation, 4k SNP genotyping, and construction of a genome-wide linkage map are described in detail by Vollmar et al [18]. In brief, all birds were genotyped for 5388 SNPs and the following criteria were applied to filter the genotypes: SNPs with one or more conflicting genotypes between parent and offspring, a minor allele frequency (MAF) ≤ 0.03, a SNP call frequency ≤ 0.9, and a cluster separation ≤ 0.4 were removed.…”

“…Subsequently, we used the same dataset to map quantitative trait loci (QTL) for PU in the quail genome. The quails were genotyped with 4k single nucleotide polymorphisms (SNPs) and several significant QTL were identified [18].…”

“…Using the same quail dataset as in our previous studies [17,18], the aim of the current study was to analyze the impact of host genetics on composition of the ileum microbiota and the relationship of ileal bacterial genera with PU and related traits, i.e. body weight gain (BWG), feed intake (FI) and feed per gain (F:G).…”