LEI0258 microsatellite variability and its association with humoral and cell mediated immune responses in broiler chickens

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

The chicken major histocompatibility complex (MHC) on chromosome 16 is the most polymorphic region across the whole genome, and also an ideal model for genetic diversity investigation. The MHC B-F/B-L region is 92 kb in length with high GC content consisting of 18 genes and one pseudogene (Blec4), which plays important roles in immune response. To evaluate polymorphism of the Chinese indigenous chickens as well as to analyze the effect of selection to genetic diversity, we used WaferGen platform to identify sequence variants of the B-F/B-L region in 21 chicken populations, including the Red Jungle Fowl (RJF), Cornish (CS), White Leghorns (WLs), 16 Chinese domestic breeds, and two well-known inbred lines 63 and 72. A total of 3,319 single nucleotide polymorphism (SNPs) and 181 INDELs in the B-F/B-L region were identified among 21 populations, of which 2,057 SNPs (62%) and 159 INDELs (88%) were novel. Most of the variants were within the intron and the flanking regions. The average variation density was 36 SNPs and 2 INDELs per kb, indicating dramatical high diversity of this region. Furthermore, BF2 was identified as the hypervariable genes with 67 SNPs per kb. Chinese domestic populations showed higher diversity than the WLs and CS. The indigenous breeds, Nandan Yao (NY), Xishuangbanna Game (XG), Gushi (GS), and Xiayan (XY) chickens, were the top four with the highest density of SNPs and INDELs. The highly inbred lines 63 and 72 have the lowest diversity, which might be resulted from a long-term intense selection for decades. Collectively, we refined the genetic map of chicken MHC B-F/B-L region, and illustrated genetic diversity of 21 chicken populations. Abundant genetic variants were identified, which not only strikingly expanded the current Ensembl SNP database, but also provided comprehensive data for researchers to further investigate association between variants in MHC and immune traits.

Genetic diversity at major histocompatibility complex and its effect on production and immune traits in indigenous chicken breeds of India

The genetic diversity at major histocompatibility complex (MHC) in indigenous chicken breeds of India (Ghagus and Nicobari) in comparison with the White Leghorn (WLH) breed was investigated by genotyping the MHC-linked LEI0258 marker. Altogether 38 alleles and 96 genotypes were observed among three breeds. The observed and effective alleles were highest in Ghagus (23, 8.3) followed by Nicobari (14, 3.2) and WLH (10 and 2.2) breeds. The size of alleles ranged from 193 to 489 bp in Ghagus, 193 to 552 bp in Nicobari and 241 to 565 bp in the WLH breed. The number of private alleles was also highest in Ghagus (18) followed by Nicobari (8) and WLH (5) breeds. The most frequent allele was 261 bp in WLH (66 %), 343 bp in Nicobari (50.4 %) and 309 bp in the Ghagus (28.15 %) breed. Observed and expected heterozygosities were highest in Ghagus (0.83, 0.88) followed by Nicobari (0.58, 0.68) and WLH (0.53, 0.54). The genetic distance (Nei) between Ghagus and Nicobari breeds (2.24) was higher as compared to that of Ghagus and WLH (1.23) and that between Nicobari and WLH breeds (0.89). Association analysis revealed significant influence of MHC alleles on body weight, egg production in Ghagus and WLH breeds and antibody titres to Newcastle disease vaccine in the Nicobari breed.