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

Lee MO, Yang E, Morisson M, Vignal A, Huang YZ, Cheng HH, Muir WM, Lamont SJ, Lillehoj HS, Lee SH, Womack JE - Genet. Sel. Evol. (2014)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Veterinary Pathobiology, Texas A & M University, College Station, TX 77843, USA. jwomack@cvm.tamu.edu.

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.

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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.
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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.

Mentions: Previously, we identified a SNP at nucleotide 271 of the NK-lysin coding sequence and discovered that the encoded protein variants have different cytotoxicities for bacteria and anticancer activity [26]. Here, we genotyped this SNP among 32 heritage breeds and 10 inbred lines. The DNA from the heritage breeds was obtained from pooled blood samples from eight to 26 animals. We compared the A and G peak heights based on the sequencing chromatogram to estimate allele frequency (Figure 1). A single A peak was detected in eight breeds and a single G peak was detected only in two of the 32 breeds (Table 2). Twenty-two of the 32 breeds analysed by pooled DNA revealed peaks for both A and G alleles. Eleven breeds showed A and G chromatogram peaks of similar height, indicating that the frequencies of the A and G alleles in the pooled DNA were approximately equal. Seven samples had a peak at least twice as high for allele A than for allele G. Only four of the 22 breeds carried G as the major allele. Thus, the A allele is more common than the G allele across all tested heritage breeds (Table 2).


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

Lee MO, Yang E, Morisson M, Vignal A, Huang YZ, Cheng HH, Muir WM, Lamont SJ, Lillehoj HS, Lee SH, Womack JE - Genet. Sel. Evol. (2014)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4120735&req=5

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.
Mentions: Previously, we identified a SNP at nucleotide 271 of the NK-lysin coding sequence and discovered that the encoded protein variants have different cytotoxicities for bacteria and anticancer activity [26]. Here, we genotyped this SNP among 32 heritage breeds and 10 inbred lines. The DNA from the heritage breeds was obtained from pooled blood samples from eight to 26 animals. We compared the A and G peak heights based on the sequencing chromatogram to estimate allele frequency (Figure 1). A single A peak was detected in eight breeds and a single G peak was detected only in two of the 32 breeds (Table 2). Twenty-two of the 32 breeds analysed by pooled DNA revealed peaks for both A and G alleles. Eleven breeds showed A and G chromatogram peaks of similar height, indicating that the frequencies of the A and G alleles in the pooled DNA were approximately equal. Seven samples had a peak at least twice as high for allele A than for allele G. Only four of the 22 breeds carried G as the major allele. Thus, the A allele is more common than the G allele across all tested heritage breeds (Table 2).

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Veterinary Pathobiology, Texas A & M University, College Station, TX 77843, USA. jwomack@cvm.tamu.edu.

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.

Show MeSH