Journal Article

Detection of QTL for traits related to adaptation to sub-optimal climatic conditions in chickens

Tixier-Boichard, Michèle, Chen, Chih-Feng, Wu, Shih-Wen, Wang, Woei-Fuh, Lien, Ching-Yi, Ng, Chen Siang

2017

Overview

Background Growth traits can be used as indicators of adaptation to sub-optimal conditions. The current study aimed at identifying quantitative trait loci (QTL) that control performance under variable temperature conditions in chickens. Methods An F2 population was produced by crossing the Taiwan Country chicken L2 line (selected for body weight, comb area, and egg production) with an experimental line of Rhode Island Red layer R- (selected for low residual feed consumption). A total of 844 animals were genotyped with the 60 K Illumina single nucleotide polymorphism (SNP) chip. Whole-genome interval linkage mapping and a genome-wide association study (GWAS) were performed for body weight at 0, 4, 8, 12, and 16 weeks of age, shank length at 8 weeks of age, size of comb area at 16 weeks of age, and antibody response to sheep red blood cells at 11 weeks of age (7 and 14 days after primary immunization). Relevant genes were identified based on functional annotation of candidate genes and potentially relevant SNPs were detected by comparing whole-genome sequences of several birds between the parental lines. Results Whole-genome QTL analysis revealed 47 QTL and 714 effects associated with 178 SNPs were identified by GWAS with 5% Bonferroni genome-wide significance. Little overlap was observed between the QTL and GWAS results, with only two chromosomal regions detected by both approaches, i.e. one on GGA24 (GGA for Gallus gallu s chromosome) for BW04 and one on GGAZ for six growth-related traits. Based on whole-genome sequence, differences between the parental lines based on several birds were screened in the genome-wide QTL regions and in a region detected by both methods, resulting in the identification of 106 putative candidate genes with a total of 15,443 SNPs, of which 41 were missense and 1698 were not described in the dbSNP archive. Conclusions The QTL detected in this study for growth and morphological traits likely influence adaptation of chickens to sub-tropical climate. Using whole-genome sequence data, we identified candidate SNPs for further confirmation of QTL in the F2 design. A strong QTL effect found on GGAZ underlines the importance of sex-linked inheritance for growth traits in chickens.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Acclimatization - genetics / Actin / Adaptation / Adipose tissue / Age / Agriculture / AMP / AMP-activated protein kinase / Animal Genetics and Genomics / Animals / Annotations / Antibodies / Antibody response / Association analysis / Bile / Biomedical and Life Sciences / Birds / Blood / Blood cells / Body weight / Bone histomorphometry / Bone marrow / Cardiovascular system / Chickens / Chickens - genetics / chromosome mapping / Chromosomes / Chronic obstructive pulmonary disease / Climate / Climatic conditions / climatic factors / Egg production / Embryos / Erythrocytes / Evolutionary Biology / F 2 region / feed intake / Female / Food consumption / Food intake / Gallus gallus / Gene mapping / Gene sequencing / Genes / Genome-wide association studies / genome-wide association study / Genomes / genotyping / growth traits / Heredity / Immune response / Immunization / Kinases / Life Sciences / Lung diseases / Male / Nucleotide sequence / Nucleotides / Nutrition research / Polymorphism / Polymorphism, Single Nucleotide / Population / Poultry / Proteins / Quality control / Quantitative Trait Loci / Quantitative Trait Locus / Quantitative Trait Locus Detection / Quantitative Trait Locus Effect / Quantitative Trait Locus Mapping / Quantitative Trait Locus Region / Research Article / Rhode Island Red / Rodents / Sex linkage / sheep / Sheep red blood cells / Single-nucleotide polymorphism / Social behavior / Studies / subtropics / Taiwan / temperature / Temperature effects / Tropical climates