Novel Polymorphisms in RAPGEF6 Gene Associated with Egg-Laying Rate in Chinese Jing Hong Chicken using Genome-Wide SNP Scan

Abstract

The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked great concern in the poultry industry. In this study, we calculated the egg-laying rate at weeks 61–69 (60 days) of Jing Hong chickens parent generation as the phenotype, and the genotype were detected by the chicken 600K Affymetrix Axiom High Density (HD) Single Nucleotide Polymorphisms (SNP)-array. The Genome-Wide Association Study (GWAS) result showed that the egg production trait is significantly associated with five SNPs (AX-75745366, AX-75745380, AX-75745340, AX-75745388, and AX-75745341), which are in the rap guanine nucleotide exchange factor 6 (RAPGEF6) gene on chicken chromosome 13. A total of 1676 Chinese commercial Jing Hong laying hens—including two populations, P1 population (858 hens) and P2 population (818 hens)—were genotyped using the Polymerase Chain Reaction-Restriction Fragments Length Polymorphisms (PCR-RFLP) method for the association analysis of egg-laying rates for the verification of the GWAS results. Genotypic and allelic frequencies of five SNPs were inconsistent with Hardy–Weinberg equilibrium, and the average population genetics parameters considering all the SNP values; i.e., gene homozygosity (Ho), gene heterozygosity (He), the effective number of alleles (Ne), and the polymorphism information content (PIC) were 0.75, 0.25, 1.40, and 0.20 in P1; 0.71, 0.29, 1.46, and 0.24 in P2; and 0.73, 0.27, 1.43, and 0.22 in P1 + P2 populations, respectively. The association analysis results revealed that out of the five polymorphisms, three of them (AX-75745366, AX-75745340, and AX-75745341; Patent applying No: 201810428916.5) had highly significant effects on egg-laying rates according to the GWAS results. Population-specific association analyses also showed similar significant association effects with this trait. Four haplotypes (AAGG, AAAG, AGGG, and AGAG) were inferred based on significant loci (AX-75745340 and AX-75745341) and also showed significant associations with the egg-laying rate, where haplotype AAGG had the highest egg-laying rate, with the exception of the egg-laying rate in P1 population, followed by other haplotypes. Furthermore, genotypes TT, AA, and GG showed the highest egg-laying rate compared to the corresponding genotypes at AX-75745366, AX-75745340, and AX-75745341 SNP loci in P1+P2, respectively. A similar result was found in the population-specific analysis except for the P1 population, in which TC genotype showed the highest egg-laying rate. No significant association was found in the egg-laying rate during the 60 days laying period for the SNPs (AX-75745380 and AX-75745388) in any group of population (p ≥ 0.05). Collectively, we report for the first time that 3 SNPs in the RAPGEF6 gene were significantly associated with the egg-laying rate during the later stage of egg production, which could be used as the potential candidate molecular genetic markers that would be able to facilitate in the selection and improvement of egg production traits through chicken breeding.

Research Progress on Oviposition-Related Genes in Insects

“…At present, the field of ovulation-related gene research is still in the stage of studying the functions of single genes ( Azmal et al 2019 , Zhou et al 2019 ). For example, a study found that the recombinant Homeobox protein akr ( Akr ) gene reduced the oviposition amount of Dermanyssus gallinae (Acarina: Dermatophagoideae), and the application of recombinant Deg-akr protein produced by the Akr gene to the adult body surface of D. gallinae affected egg-laying behavior, resulting in a 42% reduction in oviposition ( Lima-Barbero et al 2019 ).…”

T329S Mutation in the FMO3 Gene Alleviates Lipid Metabolic Diseases in Chickens in the Late Laying Period

“…Under the action of multiple lipid transfer proteins, these lipids are assembled into very low density lipoprotein (VLDL) particles that are transported to the follicle [ 18 , 24 ]. For this reason, and coupled with the extension of the laying cycle from the first 72–80 weeks, some breeding companies have even prolonged the laying age to 100 weeks [ 25 , 26 ]. Continuous egg production with a high dietary consumption of carbohydrate can markedly induce adiposity, increasing the risk of FLD, as well AS [ 25 , 27 ].…”

Pathway-based analysis enables deeper mining of GWAS data on H/L in chickens

“…Genome-wide association study(GWAS) can provide preliminary results in genetic research on complex traits in animals. Many single nucleotide polymorphism (SNP) loci and qualitative trait loci(QTL) with strong statistical signi cance have been discovered [6][7][8][9]. GWAS has become a powerful tool for studying important economic traits of livestock and poultry and has promoted research on marker-assisted breeding.…”