Polymorphisms of vasoactive intestinal peptide receptor-1 gene and their genetic effects on broodiness in chickens.

Broodiness is a polygenic trait controlled by a small number of autosomal genes. Vasoactive intestinal peptide receptor-1 (VIPR-1) gene could be a candidate of chicken broodiness, and its genomic variations and genetic effects on chicken broodiness traits were analyzed in this study. The partial cloning and sequencing of the VIPR-1 gene showed that the average nucleotide diversity was 0.00669 +/- 0.00093 in Red Jungle Fowls (RJF), and 0.00582 +/- 0.00026 in domestic chickens. One hundred twenty-eight variation sites were identified in the 11,136-bp region of the chicken VIPR-1 gene. Twenty variation sites were genotyped using PCR-RFLP or PCR method to analyze average diversity, linkage-disequilibrium pattern, and haplotype structure in RJF, Xinghua chickens, Ningdu Sanhuang chickens, Baier Huang chickens, and Leghorn Layers. The RJF, Xinghua, Ningdu Sanhuang, and Baier Huang exhibited distinct characteristic of decreasing r(2) value over physical distance. Haplotype analyses showed that some variation sites of the 27-kb region from exon 6 to exon 11 could be associated with broodiness. The distribution of genotypic and allelic frequencies, and heterozygosities in the above 5 populations showed that A-284G, A+457G, C+598T, D+19820I, C+37454T, C+42913T, and C+53327T might be associated with broodiness. The 7 sites and the other 4 sites were genotyped in 644 NDH individuals under cage condition and were used for association analyses between each site and chicken broodiness traits. A significant association (P < 0.05) was found between C+598T in intron 2 and broody frequency (%). Another significant association (P < 0.05) was found between C+53327T and duration of broodiness, in which allele C was positive for DB.