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. 2012;7(2):e30910.
doi: 10.1371/journal.pone.0030910. Epub 2012 Feb 16.

Genome-wide association study identified a narrow chromosome 1 region associated with chicken growth traits

Liang Xie  1 , Chenglong Luo, Chengguang Zhang, Rong Zhang, Jun Tang, Qinghua Nie, Li Ma, Xiaoxiang Hu, Ning Li, Yang Da, Xiquan Zhang
Affiliations

Genome-wide association study identified a narrow chromosome 1 region associated with chicken growth traits

Liang Xie et al. PLoS One. 2012.

Abstract

Chicken growth traits are important economic traits in broilers. A large number of studies are available on finding genetic factors affecting chicken growth. However, most of these studies identified chromosome regions containing putative quantitative trait loci and finding causal mutations is still a challenge. In this genome-wide association study (GWAS), we identified a narrow 1.5 Mb region (173.5-175 Mb) of chicken (Gallus gallus) chromosome (GGA) 1 to be strongly associated with chicken growth using 47,678 SNPs and 489 F2 chickens. The growth traits included aggregate body weight (BW) at 0-90 d of age measured weekly, biweekly average daily gains (ADG) derived from weekly body weight, and breast muscle weight (BMW), leg muscle weight (LMW) and wing weight (WW) at 90 d of age. Five SNPs in the 1.5 Mb KPNA3-FOXO1A region at GGA1 had the highest significant effects for all growth traits in this study, including a SNP at 8.9 Kb upstream of FOXO1A for BW at 22-48 d and 70 d, a SNP at 1.9 Kb downstream of FOXO1A for WW, a SNP at 20.9 Kb downstream of ENSGALG00000022732 for ADG at 29-42 d, a SNP in INTS6 for BW at 90 d, and a SNP in KPNA3 for BMW and LMW. The 1.5 Mb KPNA3-FOXO1A region contained two microRNA genes that could bind to messenger ribonucleic acid (mRNA) of IGF1, FOXO1A and KPNA3. It was further indicated that the 1.5 Mb GGA1 region had the strongest effects on chicken growth during 22-42 d.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. SNP effects on chicken growth traits in the 167–179 Mb region of GGA1.
The green line was the 5% Bonferroni genome-wide significance threshold. The rectangular box with blue border framed the 3 Mb region of GGA1 (172–175 Mb) with the most significant effects for all 23 traits. Red arrows highlight genes and the green arrows are the two non-coding RNA genes.
Figure 2
Figure 2. Linkage disequilibrium of GGA1.
A. Linkage disequilibrium pattern of the F2 population from White Recessive Rock and Xinghua chickens crossing on GGA1. B. Linkage disequilibrium between SNPs in the 1.5 Mb GGA1 region of 173.5–175 Mb. Strongest LD signals were in red and weakest LD in blue.
Figure 3
Figure 3. Molecular interactions between microRNAs and three prime untranslated regions (3′UTR) of FOXO1A, KPNA3 and IGF1.
Red letters indicate the 3′ UTR sequences of the target genes. Green letters indicate the matured sequences of gga-miR-15a or gga-miR-16-1.
See this image and copyright information in PMC

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