High Levels of Genetic Variation in MHC-Linked Microsatellite Markers from Native Chicken Breeds

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.

Genetic Diversity Analysis of Class Ii MHC in Indigenous Poultry- A Comparison With Commercial Breed

“…Compared to the present result very low genetic identity was reported between White Leghorn and KNC white of Korea as well as Ghagus and Nicobari Haunshi et al, 2020;Manjula et al, 2021). The Nei's original measure of genetic distance between Tellicherry and broiler was estimated to be 0.1958 and Nei's unbiased measure of genetic distance to be 0.1718.…”

“…The Nei's original measure of genetic distance between Tellicherry and broiler was estimated to be 0.1958 and Nei's unbiased measure of genetic distance to be 0.1718. Compared to this result very high genetic distance was reported between White Leghorn and KNC white of Korea as well as Ghagus and Nicobari (Thakur et al, 2017;Haunshi et al, 2020;Manjula et al, 2021). At the same time based on polymorphism analysis with SNP chip data close relationship with Korean KNC with Rhode Island Red and Cornish was revealed (Manjula et al, 2021).…”

“…The broiler has been under intensive selection and breeding for economic traits for several generations showed lower heterozygosity at MHC loci. Sri Lankan Karuwalagsewa, Nigerian, Bangladeshi, Tanzanian Chunya as well as Msimbazi and Indian Kadaknath as well as Ghagus had higher or similar MHC heterozygosity (Thakur et al, 2017;Manjula et al, 2021;Mwambene et al, 2019;Haunshi et al, 2020). At the same time Dahlem red, Nicobari and White Leghorn populations had low heterozygosity compared to Tellicherry (Thakur et al, 2017;Haunshi et al, 2020).…”

Microsatellite Marker LEI0258 Variability in Six Indonesian Local Chicken Populations

“…The range of the LEI0258 allele in this study was 193-509 bp. This is different from the study of Manjula et al [15] identified 38 LEI0258 allele range of 193-539 bp. In Chinese indigenous chicken strains, 69 alleles were identified, ranging from 193-489 bp [16], 26 alleles in North American and European layer-type chickens [9], and 22 alleles in 2 commercial layer and five non-commercial layer chickens, range 182 to 552 bp [8].…”

Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations

“…In addition to LEI0258, there are also many microsatellite loci such as MCW0370 and MCW0371. The use of these high polymorphism markers is of great significance for the study of chicken MHC diversity (Esmailnejad et al, 2017;Manjula et al, 2021).…”