Identification of candidate genes for blood metabolites in Iranian chickens using a genome-wide association study

Abstract

1. In order to identify loci associated with metabolic traits, a genome-wide association study was carried out in a chicken F2 population derived from a reciprocal cross between Iranian Urmia indigenous chickens and Arian broiler line using Illumina 60K Chicken single nucleotide polymorphism (SNP) BeadChip. 2. Six traits including plasma level of triglycerides (TGs), cholesterol (Chol), glucose (Glu), total protein, albumin (Alb) and globulin (Glo) were recorded. The association between the identified SNPs and metabolic traits was estimated by general linear model (GLM) and compressed mixed linear model (CMLM). 3. A total of 38 SNPs were identified at the genome-wide significant and suggestive levels, of which 5 SNPs reached a 5% Bonferroni genome-wide significance (P < 2.58E-6) for TG, Alb and Glo through CMLM, and 21 SNPs were significantly associated with TG, Chol, Glu, Alb and Glo through GLM. 4. Gene ontology showed that these SNPs were located within or near the candidate genes responsible for metabolic traits. 5. In conclusion, the identified candidate genes provided novel information for molecular mechanisms underlying metabolic traits. These findings are important in marker-assisted selection in the chicken breeding scheme.

Genome-wide association study of 17 serum biochemical indicators in a chicken F2 resource population

“…In addition, TP can also be used as a potential biomarker to select the fat traits of ducks [21]. Previous research has identified six QTLs related to the TP trait that are located on GGA1, GGA2, GGA12, GGA18 and GGAZ [25]; however, our study has identified a new QTL on GGA1 that is located within the COPG2 gene. The coatomer is a cytosolic protein complex that further mediates biosynthetic protein transport from the endoplasmic reticulum (ER) via the Golgi to the trans-Golgi network.…”

“…The GLU trait was mapped to GGA17 in our study. A previous study has mapped GLU traits elsewhere on GGA17 [25]. In addition, a total of 23 QTLs on different chromosomes have been associated with GLU levels in studies based on different experimental designs [13,[25][26][27][28][29][30].…”

“…A previous study has mapped GLU traits elsewhere on GGA17 [25]. In addition, a total of 23 QTLs on different chromosomes have been associated with GLU levels in studies based on different experimental designs [13,[25][26][27][28][29][30]. For example, Hee-Bok Park et al performed QTL analysis on an F2 population with 874 individuals composing 75 full-sib families and found that one QTL on GGA20 at the 41 Mb site and one QTL on GGA27 at the 21 Mb site were related to the GLU trait [28].…”

Identification of new genes and quantitative trait locis associated with growth curve parameters in F2 chicken population using genome‐wide association study

“…Several studies have reported the results of genome-wide association analysis of body weight measurements at different ages in chickens (Gu et al 2011;Van Goor et al 2015). Recently, an F2 chicken population created from reciprocal crosses between Iranian native slow-growing and Arian fast-growing line chickens was studied in order to investigate the meat production and quality, immunity, residual feed intake, metabolic traits and body weight traits (Begli et al 2017;Emrani et al 2017;Maghsoudi et al 2017;Raeesi et al 2017;Javanrouh-Aliabad et al 2018). In spite of availability of age-related traits on chickens, no studies have been found to study the SNPs association with growth curve characteristics.…”

“…2017; Javanrouh‐Aliabad et al . 2018). In spite of availability of age‐related traits on chickens, no studies have been found to study the SNPs association with growth curve characteristics.…”