The novel IMAGE001 genotyping array as a valuable alternative for genetic diversity screening in chicken: a demonstration in a local chicken breed in Belgium

Screening for genetic diversity in live-stock species breeds is of utmost importance, especially for local, small populations that are at the risk of extinc-tion. Luckily, recent developments in technology increase access to genotyping, also for numerically small breeds. One of these new technologies is the IMAGE001 single nucleotide polymorphism genotyping array that includes markers for 6 different species (cow, pig, sheep, chicken, horse and goat). For our current study, we studied the Turkey-headed Malines chicken, a local chicken breed in Belgium, for the first time. A total of 110 animals were genotyped, together with 29 samples from 4 supposedly related breeds. The genotypes were used to assess the genetic diversity of this local breed. Our analysis revealed an average inbreeding coefficient of 0.20 through runs of homozygosity analysis, and effec-tive population size estimation based on linkage disequi-librium indicated a low genetic diversity (Ne = 34). Moreover, a principal component analysis and a genetic differentiation study (FST) were performed using these marker data to position the Turkey-headed Malines rela-tive to the 4 other indigenous Belgian chicken breeds. Finally, we discussed the practical implications of the overlap between the IMAGE001 array and other exist-ing chicken genotyping arrays. This study is the first use of the novel IMAGE001 array to evaluate a local chicken breed, and demonstrates it as a viable option for geno-mic characterization a breed. Moreover, with this research, we are able to provide a good basis for further evaluation of the Belgian chicken heritage.

Automated summary

Screening for genetic diversity in livestock species breeds is crucial, especially for small populations at risk of extinction. This study used the IMAGE001 genotyping array to evaluate the genetic diversity of the Turkey-headed Malines chicken breed in Belgium. The results showed low genetic diversity in this local breed. This research is the first to use the IMAGE001 array for genotyping a local chicken breed and provides a solid foundation for further evaluation of Belgian chicken heritage.