Mapping and genotypic analysis of the NK-lysin gene in chicken

Abstract

Background: Antimicrobial peptides (AMP) are important elements of the first line of defence against pathogens in animals. NK-lysin is a cationic AMP that plays a critical role in innate immunity. The chicken NK-lysin gene has been cloned and its antimicrobial and anticancer activity has been described but its location in the chicken genome remains unknown. Here, we mapped the NK-lysin gene and examined the distribution of a functionally significant single nucleotide polymorphism (SNP) among different chicken inbred lines and heritage breeds.

Results: A 6000 rad radiation hybrid panel (ChickRH6) was used to map the NK-lysin gene to the distal end of chromosome 22. Two additional genes, the adipocyte enhancer-binding protein 1-like gene (AEBP1) and the DNA polymerase delta subunit 2-like (POLD2) gene, are located in the same NW_003779909 contig as NK-lysin, and were thus indirectly mapped to chromosome 22 as well. Previously, we reported a functionally significant SNP at position 271 of the NK-lysin coding sequence in two different chicken breeds. Here, we examined this SNP and found that the A allele appears to be more common than the G allele in these heritage breeds and inbred lines.

Conclusions: The chicken NK-lysin gene mapped to the distal end of chromosome 22. Two additional genes, AEBP1 and POLD2, were indirectly mapped to chromosome 22 also. SNP analyses revealed that the A allele, which encodes a peptide with a higher antimicrobial activity, is more common than the G allele in our tested inbred lines and heritage breeds.

Figure 1

Sequencing chromatogram of pooled DNA. DNA from homozygous chicken (A and G allele) was mixed in 1:0, 3:1, 2:1, 1:1, 1:2 and 0:1 A to G ratios and used as PCR template and sequenced; each chromatogram peak was compared to peaks from pooled DNA samples of heritage breeds and shows the estimated A to G ratio.

Figure 2

Radiation hybrid mapping of the NK-lysin gene and other markers on chromosome GGA22. The GGA22 RH map (left) is 352 cR long and is aligned to the chicken genome assembly (right); the location of the NK-lysin gene is indicated at the distal end of chromosome GGA22.