Shiqian Xu

Chinese Academy of Medical Sciences & Peking Union Medical College

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Katsushi Tokunaga

National Center for Global Health and Medicine

Tadashi Imanishi

Tokai University

Ruirui Xiang

Peking University

Hao Sun

Chinese Academy of Medical Sciences & Peking Union Medical College

Xianwei Wang

Shandong Province Animal Husbandry and Veterinary Bureau

Takashi Gojobori

King Abdullah University of Science and Technology

Jun Ohashi

The University of Tokyo

Ruimin Qiao

Henan Agricultural University

Jiayou Chu

Peking Union Medical College Hospital

Jiankun Yu

Shandong Provincial Hospital

Cooperative Institutions

Henan Agricultural University

Chinese Academy of Sciences

South China University of Technology

Bioscience (China)

Chinese Academy of Medical Sciences & Peking Union Medical College

Hebei Medical University

Sun Yat-sen University

Tokai University

Shandong Province Animal Husbandry and Veterinary Bureau

Chinese Academy of Agricultural Sciences

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HLA‐A, HLA‐B, and HLA‐DRB1 alleles and haplotypes in Naxi and Han populations in southwestern China (Yunnan province)

Tissue Antigens (2005)

Li Shi Shiqian Xu Jun Ohashi Hao Sun Jiankun Yu

Abstract The frequencies of the human leukocyte antigen alleles HLA‐A, HLA‐B, and HLA‐DRB1 and the A‐B‐DRB1, A‐B, and B‐DRB1 haplotypes were studied in Naxi and Yunnan Han populations using polymerase chain reaction (PCR)‐sequence‐specific amplification for alleles A and B and a PCR‐microtiter plate hybridization method for the DRB1 allele. A total of 8 A, 19 B, and 30 DRB1 alleles were found in the Naxi population, and 15 A, 21 B, and 36 DRB1 alleles were found in Yunnan Han population. The common A‐B‐DRB1 haplotypes in the Naxi population were A*24‐B*15‐DRB1*1202, A*11‐B*15‐DRB1*0405, A*11‐B*15‐DRB1*1202, A*11‐B*38‐DRB1*08032, and A*11‐B*55‐DRB1*0405; the common A‐B haplotypes were A*11‐B*15, A*11‐B*38, and A*24‐B*15; and the common B‐DRB1 haplotypes were B*15‐DRB1*1202, B*38‐DRB1*08032, and B*48‐DRB1*1201. In the Yunnan Han population, the common A‐B‐DRB1 haplotypes were A*24‐B*15‐DRB1*1501, A*24‐B*46‐DRB1*08032, and A*24‐B*15‐DRB1*1201; the common A‐B haplotypes were A*24‐B*15, A*24‐B*46, and A*34‐B*46; and the common B‐DRB1 haplotypes were B*15‐DRB1*1501, B*46‐DRB1*09012, and B*46‐DRB1*1401. Phylogenetic tree and principal component analyzes based on HLA‐A, HLA‐B, and DRB1 allele frequencies suggested that the Naxi ethnic group belongs to the southern Chinese groups, while the Yunnan Han population is a characteristic population located intermediate between northern and southern Chinese groups, although they live in the southwest of China.

HLA-B

HLA-A

HLA-DRB1

HLA-B Antigens

10.1111/j.1399-0039.2005.00526.x

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Citations (43)

Genomic prediction accounting for dominance and epistatic genetic effects on litter size traits in Large White pigs

Journal of Animal Science (2025)

Jianmei Chen Tengfei Dou Ziyi Wu Liyao Bai Man Xu

Abstract Litter size traits of sows are crucial for the economic benefits of the pig industry. Three phenotypic traits of 1,206 Large White (LW) pigs, that is, the total number born (TNB), number born alive (NBA), and number of healthy piglets (NHP), were recorded. We evaluated a series of genomic best linear unbiased prediction (GBLUP) models that sequentially added additive effects (model A), dominance effects (model A+D), and epistatic effects (model A+D+AA, model A+D+AA+AD, and model A+D+AA+AD+DD) using chip data and imputed whole-genome sequencing (WGS) data to estimate genetic parameters and predictive accuracy. The reproductive traits of sows showed low heritability in this study, with narrow heritability of the three traits ranging from 0.030 to 0.064, and broad heritability ranging from 0.125 to 0.145. The inclusion of non-additive effects in the model improved the accuracy of genomic selection. In the chip data, compared with that of the A model, the A+D+AA+AD+DD model showed the greatest increase in accuracy for TNB, NBA, and NHP, with improvements of 1.78, 1.67, and 1.74%, respectively. Additionally, the accuracy of the imputed WGS data was greater compared to the chip data. For the TNB, NBA, and NHP traits, the predictive accuracy of the imputed WGS data improved by 3.26, 7.72, and 3.00%, respectively, compared with that of the chip data. In summary, these results suggest that non-additive effects in genomic selection could improve prediction accuracy and should be considered in pig genomic evaluation procedures.

Epistasis

Dominance (genetics)

Mixed model

Additive genetic effects

genetic model

Litter

Genomic Selection

10.1093/jas/skaf004

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Determination of HLA class II alleles by genotyping in a Manchu population in the northern part of China and its relationship with Han and Japanese populations

Tissue Antigens (1995)

Lili Geng Tadashi Imanishi Katsushi Tokunaga D. Zhu Nobuhisa Mizuki

Abstract: The genetic polymorphism of the HLA class II loci was investigated in a Manchu population resident in the northern part of China and compared with those of other Asian populations including Japanese and Han. In 8 DQA1 alleles, the most frequent allele was DQA1*03 with the gene frequency of 25.5%. Of 15 DQB1 alleles tested, 11 were observed and the most common allele was DQB1*0301 with the gene frequency of 24.5%. Among 19 DPB1 alleles, 11 were detected and DPB1*0501 (43.8%) was the most frequent allele as observed in other Asian populations such as Japanese, Chinese and Korean. Of 43 DRB1 alleles tested, 21 were detected and DRB1*0901 (14.0%), *1501 (11.0%), *1201 (11.0%), *07 (9.0%) and *1401 (9.0%) were highly predominant and account for the high frequencies of DR9, DR2, DR5, DR7 and DR6. In the DRB3 gene (DR52), DRB3*0202 (18.0%) was the most frequent. With respect to the DRB4 gene (DR53), the gene frequency of DRB4*0101 was 35.0%. Of 3 DRB5 alleles detected, DRB5*0101 (11.0%) was highly predominant. Comparison of HLA class II allele frequencies in Manchu with those in Japanese and Han Chinese populations (South & North) detected some significant differences and genetic divergence between these Oriental populations. The dendrogram constructed by the neighbor‐joining (NJ) method based on the allele frequencies of DQA1, DQB1, DPB1 and DRB1 of 10 representative populations over the world suggested that Manchu is the closest, but at the same genetic distance to both Northern and Southern Han Chinese.

10.1111/j.1399-0039.1995.tb02486.x

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Citations (52)

Comprehensive identification of high-frequency and co-occurring Mafa-DPA1, Mafa-DQA1, Mafa-DRA, and Mafa-DOA alleles in Vietnamese cynomolgus macaques

Immunogenetics (2013)

Ruirui Xiang Huiling Zhang Qing Deng Rui Yue Haite Tang

Vietnamese

Histocompatibility

10.1007/s00251-013-0713-x

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Citations (5)