Application of next-generation sequencing for the high-resolution typing of MHC- B in Korean native chicken

Thisarani Kalhari Ediriweera; Prabuddha Manjula; Eunjin Cho; Minjun Kim; Jun Heon Lee

doi:10.3389/fgene.2022.886376

Application of next-generation sequencing for the high-resolution typing of MHC- B in Korean native chicken

Front Genet. 2022 Oct 28:13:886376. doi: 10.3389/fgene.2022.886376. eCollection 2022.

Authors

Thisarani Kalhari Ediriweera¹, Prabuddha Manjula², Eunjin Cho¹, Minjun Kim³, Jun Heon Lee^{1

3}

Affiliations

¹ Department of Bio-AI Convergence, College of Engineering, Chungnam National University, Daejeon, Korea.
² Department of Animal Science, Uva Wellassa University, Badulla, Sri Lanka.
³ Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Korea.

Abstract

The major histocompatibility complex-B (MHC-B) region of chicken is crucially important in their immunogenesis and highly diverse among different breeds, lines, and even populations. Because it determines the resistance/susceptibility to numerous infectious diseases, it is important to analyze this genomic region, particularly classical class I and II genes, to determine the variation and diversity that ultimately affect antigen presentation. This study investigated five lines of indigenous Korean native chicken (KNC) and the Ogye breed using next-generation sequencing (NGS) data with Geneious Prime-based assembly and variant calling with the Genome Analysis Toolkit (GATK) best practices pipeline. The consensus sequences of MHC-B (BG1-BF2) were obtained for each chicken line/breed and their variants were analyzed. All of the Korean native chicken lines possessed an excessive number of variants, including an ample amount of high-impact variants that provided useful information regarding modified major histocompatibility complex molecules. The study confirmed that next-generation sequencing techniques can effectively be used to detect MHC variabilities and the KNC lines are highly diverse for the MHC-B region, suggesting a substantial divergence from red junglefowl.

Keywords: Korean native chicken; MHC-B; NGS; assembly; variants.