Development of a high‐resolution typing method for SLA‐3, swine MHC class I antigen 3

Youk, Seungyeon; Le, Minh-Tri; Kang, Mingue; Ahn, Byeongyong; Choi, Mi Hyun; Kim, K.; Kim, T.H.; Kim, J.H.; Ho, Chak Sum; Park, C.

doi:10.1111/age.13161

Cited by 3 publications

(2 citation statements)

References 19 publications

(43 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, the genetic characteristics of the two protein families are similar. For swine leukocyte antigen (SLA) genes, which is the MHC genes of pig, it has been well documented that the presence of an extremely large number of alleles, a large difference in allelic constitution among different breeds, and breed-speci c alleles [42][43][44][45][46][47] are most likely to result from independent breeding histories for different breeds. In addition, the characteristics of pig OR genes analyzed in this current study showed similarities to those of the SLA genes described above.…”

Section: Discussionmentioning

confidence: 99%

Individual and population diversity of 20 representative olfactory receptor genes in pigs

Kang

Ahn

Youk

et al. 2023

Preprint

View full text Add to dashboard Cite

Understanding the influence of genetic variations in olfactory receptor (OR) genes on the olfaction-influenced phenotypes such as behaviors, reproduction, and feeding is important in animal biology. However, our understanding of the complexity of the OR subgenome is limited. In this study, we analyzed 1,120 typing results of 20 representative OR genes belonging to 13 OR families on 14 pig chromosomes from 56 individuals belonging to seven different breeds using a sequence-based OR typing method. We showed that the presence of copy number variations, conservation of locus-specific diversity, abundance of breed-specific alleles, presence of a loss-of-function allele, and low-level purifying selection in pig OR genes could be common characteristics of OR genes in mammals. The observed nucleotide sequence diversity of pig ORs was higher than that of dogs. To the best of our knowledge, this is the first report on the individual- or population-level characterization of a large number of OR family genes in livestock species.

show abstract

Section: Discussionmentioning

confidence: 99%

Individual and population diversity of 20 representative olfactory receptor genes in pigs

Kang

Ahn

Youk

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…However, MHC class I genes consisting of Patr-A, Patr-B, and Patr-C exhibit only 86% sequence identity to class I genes in humans [31][32][33]. Progress in understanding the genetic diversity of MHC systems of cattle and pigs, known as the bovine leukocyte antigen (BoLA) and swine leukocyte antigen (SLA), respectively, have also been made using comprehensive typing methods [18,30,[34][35][36][37][38][39].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human

Youk,

Kang,

Ahn

et al. 2023

Genes

Self Cite

View full text Add to dashboard Cite

Comparative analyses of MHC gene diversity and evolution across different species could offer valuable insights into the evolution of MHC genes. Intra- and inter-species sequence diversity and conservation of 12 classical major histocompatibility complex (MHC) class I genes from cattle, chimpanzees, pigs, and humans was analyzed using 20 representative allelic groups for each gene. The combined analysis of paralogous loci for each species revealed that intra-locus amino-acid sequence variations in the peptide-binding region (PBR) of MHC I genes did not differ significantly between species, ranging from 8.44% for SLA to 10.75% for BoLA class I genes. In contrast, intraspecies differences in the non-PBRs of these paralogous genes were more pronounced, varying from 4.59% for SLA to 16.89% for HLA. Interestingly, the Shannon diversity index and rate of nonsynonymous substitutions for PBR were significantly higher in SLA and BoLA than those in Patr and HLA. Analysis of peptide-binding pockets across all analyzed MHC class I genes of the four species indicated that pockets A and E showed the lowest and highest diversity, respectively. The estimated divergence times suggest that primate and artiodactyl MHC class I genes diverged 60.41 Mya, and BoLA and SLA genes diverged 35.34 Mya. These results offer new insights into the conservation and diversity of MHC class I genes in various mammalian species.

show abstract

Individual and population diversity of 20 representative olfactory receptor genes in pigs

Kang,

Ahn,

Youk

et al. 2023

Sci Rep

Self Cite

View full text Add to dashboard Cite

Understanding the influence of genetic variations in olfactory receptor (OR) genes on the olfaction-influenced phenotypes such as behaviors, reproduction, and feeding is important in animal biology. However, our understanding of the complexity of the OR subgenome is limited. In this study, we analyzed 1120 typing results of 20 representative OR genes belonging to 13 OR families on 14 pig chromosomes from 56 individuals belonging to seven different breeds using a sequence-based OR typing method. We showed that the presence of copy number variations, conservation of locus-specific diversity, abundance of breed-specific alleles, presence of a loss-of-function allele, and low-level purifying selection in pig OR genes could be common characteristics of OR genes in mammals. The observed nucleotide sequence diversity of pig ORs was higher than that of dogs. To the best of our knowledge, this is the first report on the individual- or population-level characterization of a large number of OR family genes in livestock species.

show abstract

Development of a high‐resolution typing method for SLA‐3, swine MHC class I antigen 3

Cited by 3 publications

References 19 publications

Individual and population diversity of 20 representative olfactory receptor genes in pigs

Individual and population diversity of 20 representative olfactory receptor genes in pigs

Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human

Individual and population diversity of 20 representative olfactory receptor genes in pigs

Contact Info

Product

Resources

About