Deciphering mechanisms underlying the genetic variation of general production and liver quality traits in the overfed mule duck by pQTL analyses

Abstract

BackgroundThe aim of this study was to analyse the mechanisms that underlie phenotypic quantitative trait loci (QTL) in overfed mule ducks by identifying co-localized proteomic QTL (pQTL). The QTL design consisted of three families of common ducks that were progeny-tested by using 294 male mule ducks. This population of common ducks was genotyped using a genetic map that included 334 genetic markers located across 28 APL chromosomes (APL for Anas platyrhynchos). Mule ducks were phenotyped for 49 traits related to growth, metabolism, overfeeding ability and meat and fatty liver quality, and 326 soluble fatty liver proteins were quantified.ResultsOne hundred and seventy-six pQTL and 80 phenotypic QTL were detected at the 5% chromosome-wide significance threshold. The great majority of the identified pQTL were trans-acting and localized on a chromosome other than that carrying the coding gene. The most significant pQTL (1% genome-wide significance) were found for alpha-enolase on APL18 and fatty acid synthase on APL24. Some proteins were associated with numerous pQTL (for example, 17 and 14 pQTL were detected for alpha-enolase and apolipoprotein A1, respectively) and pQTL hotspots were observed on some chromosomes (APL18, 24, 25 and 29). We detected 66 co-localized phenotypic QTL and pQTL for which the significance of the two-trait QTL (2t-QTL) analysis was higher than that of the strongest QTL using a single-trait approach. Among these, 16 2t-QTL were pleiotropic. For example, on APL15, melting rate and abundance of two alpha-enolase spots appeared to be impacted by a single locus that is involved in the glycolytic process. On APLZ, we identified a pleiotropic QTL that modified both the blood level of glucose at the beginning of the force-feeding period and the concentration of glutamate dehydrogenase, which, in humans, is involved in increased glucose absorption by the liver when the glutamate dehydrogenase 1 gene is mutated.ConclusionsWe identified pleiotropic loci that affect metabolic pathways linked to glycolysis or lipogenesis, and in the end to fatty liver quality. Further investigation, via transcriptomics and metabolomics approaches, is required to confirm the biomarkers that were found to impact the genetic variability of these phenotypic traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0313-6) contains supplementary material, which is available to authorized users.

Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2

“…We detected large number of eQTLs significantly associated with gene expression. However, associations were weaker for pQTLs, possibly because the genetic basis underlying protein expression involves more complex regulation than mRNA abundance [71] , [72] , [73] . Our study provides evidence supporting the roles of SNPs associated with BADH2 expression in 2AP variation in fragrant rice.…”

Population analysis of the Korean native duck using whole-genome sequencing data

“…One is the KD genes which contain loci where only KD has nsSNPs (but can have loci with nsSNPs only found in other breeds), and another is the KD-specific genes which have loci with nsSNPs only found in KD. Among the 3062 KD genes, the PNPLA8 gene is involved in energy mobilization and lipid storage in adipocyte tissue [ 27 ], and the ENO1 gene plays a role in the glycolysis pathway as an enzyme which is related to fatty acid synthesis [ 28 ]. Although no significantly enriched function has been identified in the 103 KD-specific genes, these genes may underlie a difference between KD and other breeds.…”