title: The GTPase activating Rap/RanGAP domain-like 1 gene is associated with chicken reproductive traits.
abstract: BACKGROUND
  Abundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG) axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits.
  
  
  RESULTS
  Suppressive subtractive hybridization (SSH), genome-wide association study (GWAS), and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH) chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300). Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE). Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner.
  
  
  CONCLUSIONS
  Our findings demonstrate that the GARNL1 gene contributes to chicken reproductive traits.
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Shen
authors.forename: Hua
authors.initials: H
authors.lastname: Zeng
authors.forename: Liang
authors.initials: L
authors.lastname: Xie
authors.forename: Jun
authors.initials: J
authors.lastname: He
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.forename: Xiujuan
authors.initials: X
authors.lastname: Xie
authors.forename: Chenglong
authors.initials: C
authors.lastname: Luo
authors.forename: Haiping
authors.initials: H
authors.lastname: Xu
authors.forename: Min
authors.initials: M
authors.lastname: Zhou
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Nie
authors.forename: Xiquan
authors.initials: X
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002645:Chickens / Q000235:genetics*; D005260:Female; D020690:GTPase-Activating Proteins / Q000235:genetics*; D005787:Gene Frequency; D055106:Genome-Wide Association Study; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000235:genetics*; D009425:Nesting Behavior; D009693:Nucleic Acid Hybridization; D010058:Oviposition / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D019655:Quantitative Trait, Heritable; D012098:Reproduction / Q000235:genetics*; D013382:Subtraction Technique
chemical_list: D020690:GTPase-Activating Proteins; D009419:Nerve Tissue Proteins; C495326:RALGAPA1 protein, human