Abstract
The major histocompatibility complex (MHC) is a highly polymorphic gene region that regulates cellular communication in all specific immune responses. In this study, we investigated 11 microsatellite (MS) markers in the MHC-B region of chicken populations from four countries: Sri Lanka, Bangladesh, South Korea, and Nigeria. The MS markers were divided into two sets. Set 1 included five novel MS markers, which we assessed using 192 samples from 21 populations. Set 2 included six previously reported markers, which we assessed using 881 samples from 29 populations. The Set 1 MS markers had lower polymorphism (polymorphic information content (PIC) < 0.5) than the Set 2 markers (PIC = 0.4–0.9). In all populations, the LEI0258 marker was the most polymorphic, with a total of 38 alleles (PIC = 0.912, expected heterozygosity (He) = 0.918). Local populations from Sri Lanka, Bangladesh, and Nigeria had higher allele diversity and more haplotypes for Set 2 MS markers than Korean and commercial populations. The Sri Lankan Karuwalagaswewa village population had the highest MHC diversity (mean allele number = 8.17, He = 0.657), whereas the white leghorn population had the lowest (mean allele number = 2.33, He = 0.342). A total of 409 haplotypes (89 shared and 320 unique), with a range of 4 (Rhode Island red) to 46 (Karuwalagaswewa village (TA)), were identified. Among the shared haplotypes, the B21-like haplotype was identified in 15 populations. The genetic relationship observed in a neighbour-joining tree based on the DA distance agreed with the breeding histories and geographic separations. The results indicated high MHC diversity in the local chicken populations. The difference in the allelic pattern among populations presumably reflects the effects of different genotypes, environments, geographic variation, and breeding policies in each country. The selection of MHC allele in domestic poultry can vary due to intensification of poultry production. Preserved MHC diversity in local chicken provides a great opportunity for future studies that address the relationships between MHC polymorphisms and differential immune responses.
Highlights
Characterising the non-neutral genomic region that is likely to be under natural selection can reflect evolutionarily relevant and adaptive processes within and between populations [1]
All alleles observed for major histocompatibility complex (MHC)-S2 were homozygous in all populations, and zero heterozygosity is reported
A high number of polymorphic MS markers have been reported in the MHC class I, II, and III genes of humans, swine, and mice, whereas only six MS markers have been reported in the chicken MHC-B region
Summary
Characterising the non-neutral genomic region that is likely to be under natural selection can reflect evolutionarily relevant and adaptive processes within and between populations [1]. Many studies have managed to quantify adaptively important gene families. They have found that diversity is maintained by forces of natural selection, such as balancing selection or positive selection. The major histocompatibility complex (MHC) genes in vertebrates are among the gene families that play a critical role in host immunity [2,3,4,5,6,7,8]. The MHC is located on the q-arm of micro-chromosome 16 (GGA16). Compared to the MHC of higher vertebrates, such as humans, swine, and mice, the chicken
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