Development of a 60K SNP Chip for Chickens
Author Information
Author(s): Groenen Martien AM, Megens Hendrik-Jan, Zare Yalda, Warren Wesley C, Hillier LaDeana W, Crooijmans Richard PMA, Vereijken Addie, Okimoto Ron, Muir William M, Cheng Hans H
Primary Institution: Animal Breeding and Genomics Centre, Wageningen University, The Netherlands
Hypothesis
To design a moderate density SNP chip in chicken consisting of SNPs known to be segregating at high to medium allele frequencies.
Conclusion
The high success rate of the SNPs on the Illumina chicken 60K Beadchip emphasizes the power of Next generation sequence technology for SNP identification and selection.
Supporting Evidence
- The SNP chip contains 57,636 SNPs that were shown to be segregating in chicken populations.
- The overall validation rate of the SNPs on the chip was 94%.
- Two new linkage groups were constructed representing two micro-chromosomes not covered by the current genome assembly.
Takeaway
Scientists created a special tool to help study chicken genetics better by identifying many tiny differences in their DNA.
Methodology
The study involved designing a SNP chip using Illumina sequencing on reduced representation libraries from different chicken populations.
Limitations
The study faced challenges in obtaining a uniform coverage of the chicken genome, particularly for the smallest micro-chromosomes.
Participant Demographics
The study included DNA samples from four commercial breeding lines of chickens: two broiler lines and two layer lines.
Digital Object Identifier (DOI)
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