Table 1.

The development of major histocompatibility complex (MHC) genotyping methods in birds over four decades, with the advantages (Pros) and disadvantages (Cons) associated with different methods and future perspectives.

	Past		Present	Near Future
	(1990s)	(2000s)	(2010+)	(2019+)	(2019+)
Method	Fragment analysis of genomic DNA (RFLP & Southern blot) [15,23]	Fragment analyses of PCR products (e.g., DGGE) [83,84,85]	High-throughput sequencing of PCR products (e.g., Illumina amplicon sequencing) [40,86,87]	Long-read sequencing (PacBio & Oxford nanopore)	Amplification of specific gene copies (High-throughput sequencing & qPCR)
Pros	No PCR artifacts Robust gene copy numbers	Moderate resolution	High resolution High coverage	No PCR artifacts Very long reads (100,000 bp possible) Gene synteny	Expression data Gene-specific amplification
Cons	Low resolution No sequence data	Artifactual alleles possible No sequence data	Artifactual alleles possible Short reads (up to 300 bp)	Low coverage Sequencing errors	Limited data on MHC diversity