Diversity and evolution of the highly polymorphic tandem repeat LEI0258 in the chicken MHC-B region

Abstract

The chicken major histocompatibility complex (MHC) is located on the microchromosome 16 and is described as the most variable region in the genome. The genes of the MHC play a central role in the immune system. Particularly, genes encoding proteins involved in the antigen presentation to T cells. Therefore, describing the genetic polymorphism of this region is crucial in understanding host-pathogen interactions. The tandem repeat LEI0258 is located within the core area of the B region of the chicken MHC (MHC-B region) and its genotypes correlate with serology. This marker was used to provide a picture of the worldwide diversity of the chicken MHC-B region and to categorize chicken MHC haplotypes. More than 1,600 animals from 80 different populations or lines of chickens from Africa, Asia, and Europe, including wild fowl species, were genotyped at the LEI0258 locus. Fifty novel alleles were described after sequencing. The resulting 79 alleles were classified into 12 clusters, based on the SNPs and indels found within the sequences flanking the repeats. Furthermore, hypotheses were formulated on the evolutionary dynamics of the region. This study constitutes the largest variability report for the chicken MHC and establishes a framework for future diversity or association studies.

Genetic diversity of different indigenous chicken ecotypes using highly polymorphic MHC-linked and non-MHC microsatellite markers

“…Heterozygosity values for MHC-linked markers were higher than for non-MHC markers and in agreement with findings by Chazara et al (2013) using wild species and unselected chicken populations. Ho were slightly lower than He in TT and LM ecotypes, suggesting selection against heterozygotes (Mogesse, 2007) and limited artificial selection (Dana, 2011) Kericho and Nandi counties).…”

Establishment of six homozygous MHC-B haplotype populations associated with susceptibility to Marek’s disease in Chinese specific pathogen-free BWEL chickens

“…Encouragingly, the association between the LEI0258 marker and serologically defined MHC-B haplotypes was highly consistent for the same haplotype from multiple sources (Chazara et al, 2013(Chazara et al, , 2011Fulton et al, 2006;Nikbakht et al, 2013). It can be used as a preliminary screening tool in any population or breed of chickens, but also in well characterized populations.…”

“…Four microsatellite markers have been located within the chicken MHC-B region, LEI0258, MCW0371, MCW0312 and MHC-D (Buitenhuis et al, 2003;Crooijmans et al, 1997;Fulton et al, 2006;McConnell et al, 1999;Sironi et al, 2011), which can be effectively used to determine MHC-B haplotypes. Especially, LEI0258 marker genotypes could provide good indications of MHC-B haplotypes and can be used for preliminary screening in chicken populations (Chazara et al, 2013(Chazara et al, , 2011Fulton et al, 2006;Nikbakht et al, 2013). It has been increasingly used in research and breeding for planning crosses and has become an important genetic factor to take into account in chicken breeding.…”

DNA Markers for the Genetic Diversity in Korean Native Chicken Breeds: A Review

“…두 번째는 유전체 전체에 고루 분포하고 있고, 단순 한 염기가 반복하는 구조를 가지고 있어 다형성이 매우 높 은 microsatellite(MS) 마커를 이용한 분류방법이 있는데, 이 방법은 현재 미국의 FBI에서 Combined DNA Index System (CODIS)에 성별 분석이 가능한 마커를 포함한 13개 MS(STR) 마커를 이용하여 법의학적 개인식별에도 활용되고 있는 방 법이다 (Kaya and Yildiz, 2008;Hares, 2012). 세 번째 분류 방 법은 동물의 면역반응에 관여하여 다형성이 매우 높은 구조 를 가지고 있는 Major Histocompatibility Complex(MHC) 영 역의 변이를 이용한 방법이다 (Chazara et al, 2013). 근래에는 chicken genome sequencing 결과를 토대로 개발된 HD-SNP chip 데이터를 이용하여 다형성이 높고, 품종 특이성을 가진 마커를 선발하여 품종 구분에 이용하는 방법이 개발되기도 하였으며, 이 방법의 경우 전 자동화된 분석 기술과 낮아지고 있는 분석비용으로 MS 마커를 대체할 수 있는 수단이 될 수 있다 (Muir et al, 2008).…”