QTL analysis of clinical-chemical traits in an F₂intercross between Landrace and Korean native pigs

Abstract

Clinical-chemical traits are essential when examining the health status of individuals. The aim of this study was to identify quantitative trait loci (QTL) and the associated positional candidate genes affecting clinical-chemical traits in a reciprocal F(2) intercross between Landrace and Korean native pigs. Following an overnight fast, 25 serum phenotypes related to clinical-chemical traits (e.g., hepatic function parameters, renal function parameters, electrolyte, lipids) were measured in >970 F(2) progeny. All experimental samples were subjected to genotyping analysis using 165 microsatellite markers located across the genome. We identified eleven genome-wide significant QTL in six chromosomal regions (SSC 2, 7, 8, 13, 14, and 15) and 59 suggestive QTL in 17 chromosomal regions (SSC 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, and 18). We also observed significant effects of reciprocal crosses on some of the traits, which would seem to result from maternal effect, QTL on sex chromosomes, imprinted genes, or genetic difference in mitochondrial DNA. The role of genomic imprinting in clinical-chemical traits also was investigated. Genome-wide analysis revealed a significant evidence for an imprinted QTL in SSC4 affecting serum amylase levels. Additionally, a series of bivariate linkage analysis provided strong evidence that QTL in SSC 2, 13, 15, and 18 have a pleiotropic effect on clinical-chemical traits. In conclusion, our study detected both novel and previously reported QTL influencing clinical-chemical traits in pigs. The identified QTL together with the positional candidate genes identified here could play an important role in elucidating the genetic structure of clinical-chemical phenotype variation in humans and swine.

Estimation of Genetic Parameters for Serum Clinical-Chemical Traits in Korean Native Chickens

“…However, Glu was found to be very low heritable, with heri- (Yoo et al, 2012). The estimated heritabilities ranged from 40.1% (GOT) to 96.8% (T-Cho and HDL-c), which were higher than those estimated in this study.…”

Genetic variants of major genes contributing to phosphate and calcium homeostasis and their association with serum parameters in pigs

“…Secondly, blood sample collection is minimally invasive. Recently, high heritability estimates for serum P, Ca, and ALP concentrations were revealed by microsatellite analysis of an F2 intercross between Landrace and Korean native pigs (Yoo et al 2012 ), indicating a prominent role of genetics in the variability of these parameters. There are a few studies addressing the genetic background of serum parameter in pigs, particularly with regard to the health status of animals (Reiner et al 2008 ; Yoo et al 2012 ; Bovo et al 2016 ).…”

A genome-wide association analysis for porcine serum lipid traits reveals the existence of age-specific genetic determinants

“…The existence of a genetic determinant for serum lipids on SSC13 is supported by results from previous genome scans, where QTL for CHOL (SSC13, 212 Mb approx.) and LDL (SSC13, 194 Mb) were detected by Yoo et al [8] and Uddin et al [7], respectively.…”

“…There is substantial evidence that additive variance for serum lipid levels exists in swine populations, with heritability estimates that range between 0.2-0.4 [4]. Besides, several porcine serum lipid QTL have been detected with the aid of microsatellite markers [5–8] and, more recently, it was reported the first GWAS for porcine blood lipid traits in Duroc x Erhualian F 2 and Sutai pigs [9]. As in humans, GWAS approaches should be extended to a large number of pig populations in order to achieve a comprehensive and reliable picture of genomic variation affecting serum lipid concentrations.…”