Genome-wide association study revealed a promising region and candidate genes for eggshell quality in an F2 resource population

Congjiao Sun; Liang Qu; Guoqiang Yi; Jingwei Yuan; Zhongyi Duan; Manman Shen; Lujiang Qu; Guiyun Xu; Kehua Wang; Ning Yang

doi:10.1186/s12864-015-1795-7

Genome-wide association study revealed a promising region and candidate genes for eggshell quality in an F2 resource population

BMC Genomics. 2015 Jul 31;16(1):565. doi: 10.1186/s12864-015-1795-7.

Authors

Congjiao Sun¹, Liang Qu², Guoqiang Yi³, Jingwei Yuan⁴, Zhongyi Duan⁵, Manman Shen⁶, Lujiang Qu⁷, Guiyun Xu⁸, Kehua Wang⁹, Ning Yang¹⁰

Affiliations

¹ National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. cjsun@cau.edu.cn.
² Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China. quliang19820603@163.com.
³ National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. yiguoqiang20@hotmail.com.
⁴ National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. amstrongyuan@163.com.
⁵ National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. dzy806@163.com.
⁶ Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China. shenman2005@163.com.
⁷ National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. quluj@cau.edu.cn.
⁸ National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. ncppt@cau.edu.cn.
⁹ Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China. sqbreeding@126.com.
¹⁰ National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. nyang@cau.edu.cn.

Abstract

Background: Eggshell is subject to quality loss with aging process of laying hens, and damaged eggshells result in economic losses of eggs. However, the genetic architecture underlying the dynamic eggshell quality remains elusive. Here, we measured eggshell quality traits, including eggshell weight (ESW), eggshell thickness (EST) and eggshell strength (ESS) at 11 time points from onset of laying to 72 weeks of age and conducted comprehensive genome-wide association studies (GWAS) in 1534 F2 hens derived from reciprocal crosses between White Leghorn (WL) and Dongxiang chickens (DX).

Results: ESWs at all ages exhibited moderate SNP-based heritability estimates (0.30 ~ 0.46), while the estimates for EST (0.21 ~ 0.31) and ESS (0.20 ~ 0.27) were relatively low. Eleven independent univariate genome-wide screens for each trait totally identified 1059, 1026 and 1356 significant associations with ESW, EST and ESS, respectively. Most significant loci were in a region spanning from 57.3 to 71.4 Mb of chromosome 1 (GGA1), which together account for 8.4 ~ 16.5% of the phenotypic variance for ESW from 32 to 72 weeks of age, 4.1 ~ 6.9% and 2.95 ~ 16.1% for EST and ESS from 40 to 72 weeks of age. According to linkage disequilibrium (LD) and conditional analysis, the significant SNPs in this region were in extremely strong linkage disequilibrium status. Ultimately, two missense SNPs in GGA1 and one in GGA4 were considered as promising loci on three independent genes including ITPR2, PIK3C2G, and NCAPG. The homozygotes of advantageously effective alleles on PIK3C2G and ITPR2 possessed the best eggshell quality and could partly counteract the negative effect of aging process. NCAPG had certain effect on eggshell quality for young hens.

Conclusions: Identification of the promising region as well as potential candidate genes will greatly advance our understanding of the genetic basis underlying dynamic eggshell quality and has the practical significance in breeding program for the improvement of eggshell quality, especially at the later part of laying cycle.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Animals
Body Weight / genetics
Chickens / genetics*
Egg Shell / growth & development*
Eggs*
Female
Genome-Wide Association Study*
Humans
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci / genetics*