title: Genome-wide association study revealed a promising region and candidate genes for eggshell quality in an F2 resource population.
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.
authors.affiliation: 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.
authors.forename: Congjiao
authors.initials: C
authors.lastname: Sun
authors.affiliation: Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China. quliang19820603@163.com.
authors.forename: Liang
authors.initials: L
authors.lastname: Qu
authors.affiliation: 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.
authors.forename: Guoqiang
authors.initials: G
authors.lastname: Yi
authors.affiliation: 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.
authors.forename: Jingwei
authors.initials: J
authors.lastname: Yuan
authors.affiliation: 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.
authors.forename: Zhongyi
authors.initials: Z
authors.lastname: Duan
authors.affiliation: Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China. shenman2005@163.com.
authors.forename: Manman
authors.initials: M
authors.lastname: Shen
authors.affiliation: 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.
authors.forename: Lujiang
authors.initials: L
authors.lastname: Qu
authors.affiliation: 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.
authors.forename: Guiyun
authors.initials: G
authors.lastname: Xu
authors.affiliation: Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu, 225125, China. sqbreeding@126.com.
authors.forename: Kehua
authors.initials: K
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Ning
authors.initials: N
authors.lastname: Yang
mesh_terms: D000483:Alleles; D000818:Animals; D001835:Body Weight / Q000235:genetics; D002645:Chickens / Q000235:genetics*; D004528:Egg Shell / Q000254:growth & development*; D004531:Eggs; D005260:Female; D055106:Genome-Wide Association Study; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*