Discovery of novel MHC-class I alleles and haplotypes in Filipino cynomolgus macaques (Macaca fascicularis) by pyrosequencing and Sanger sequencing: Mafa-class I polymorphism.
Although the low polymorphism of the major histocompatibility complex (MHC) transplantation genes in the Filipino cynomolgus macaque (Macaca fascicularis) is expected to have important implications in the selection and breeding of animals for medical research, detailed polymorphism information is still lacking for many of the duplicated class I genes. To better elucidate the degree and types of MHC polymorphisms and haplotypes in the Filipino macaque population, we genotyped 127 unrelated animals by the Sanger sequencing method and high-resolution pyrosequencing and identified 112 different alleles, 28 at cynomolgus macaque MHC (Mafa)-A, 54 at Mafa-B, 12 at Mafa-I, 11 at Mafa-E, and seven at Mafa-F alleles, of which 56 were newly described. Of them, the newly discovered Mafa-A8*01:01 lineage allele had low nucleotide similarities (<86%) with primate MHC class I genes, and it was also conserved in the Vietnamese and Indonesian populations. In addition, haplotype estimations revealed 17 Mafa-A, 23 Mafa-B, and 12 Mafa-E haplotypes integrated with 84 Mafa-class I haplotypes and Mafa-F alleles. Of these, the two Mafa-class I haplotypes, F/A/E/B-Hp1 and F/A/E/B-Hp2, had the highest haplotype frequencies at 10.6 and 10.2%, respectively. This suggests that large scale genetic screening of the Filipino macaque population would identify these and other high-frequency Mafa-class I haplotypes that could be used as MHC control animals for the benefit of biomedical research.
Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan. tshiina@is.icc.u-tokai.ac.jp.
Takashi
T
Shiina
Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan.|Ina Research Inc., 2148-188 Nishiminowa, Ina, Nagano, 399-4501, Japan.
Yukiho
Y
Yamada
Laboratoire d'Immunogénétique moléculaire, Université Toulouse III, Faculte de Medecine Purpan, Laboratoire d'immunologie, 1 Avenue Jean Poulhes, Hôpital Rangueil, TSA50032, 31059, Toulouse, Cedex 9, France.
Alice
A
Aarnink
Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan.
Shingo
S
Suzuki
Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan.
Anri
A
Masuya
Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan.
Sayaka
S
Ito
Ina Research Inc., 2148-188 Nishiminowa, Ina, Nagano, 399-4501, Japan.
Daisuke
D
Ido
Ina Research Inc., 2148-188 Nishiminowa, Ina, Nagano, 399-4501, Japan.
Hisashi
H
Yamanaka
Research Center for Animal Life Science, Shiga University of Medical Science, School of Medicine, Setatsukinowa, Ohtsu, Shiga, 520-2192, Japan.
Chizuru
C
Iwatani
Research Center for Animal Life Science, Shiga University of Medical Science, School of Medicine, Setatsukinowa, Ohtsu, Shiga, 520-2192, Japan.
Hideaki
H
Tsuchiya
Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Ohtsu, Shiga, 520-2192, Japan.
Hirohito
H
Ishigaki
Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Ohtsu, Shiga, 520-2192, Japan.
Yasushi
Y
Itoh
Department of Pathology, Shiga University of Medical Science, Setatsukinowa, Ohtsu, Shiga, 520-2192, Japan.
Kazumasa
K
Ogasawara
Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1143, Japan.|Centre for Forensic Science, The University of Western Australia, Nedlands,, WA, 6008, Australia.
Jerzy K
JK
Kulski
Laboratoire d'Immunogénétique moléculaire, Université Toulouse III, Faculte de Medecine Purpan, Laboratoire d'immunologie, 1 Avenue Jean Poulhes, Hôpital Rangueil, TSA50032, 31059, Toulouse, Cedex 9, France.
Antoine
A
Blancher
D000483:Alleles; D000818:Animals; D005787:Gene Frequency; D005838:Genotype; D006239:Haplotypes; D015395:Histocompatibility Antigens Class I / Q000145:classification / Q000235:genetics*; D008252:Macaca fascicularis / Q000235:genetics*; D010679:Philippines; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*
D015395:Histocompatibility Antigens Class I
Cynomolgus macaque; Haplotype; MHC; Major histocompatibility complex; NGS; Next generation sequencing; Polymorphism; Sanger sequencing