Search

Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq). SLAF-seq technology has several distinguishing characteristics: i) deep sequencing to ensure genotyping accuracy; ii) reduced representation strategy to reduce sequencing costs; iii) pre-designed reduced representation scheme to optimize marker efficiency; and iv) double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations. [ABSTRACT FROM AUTHOR]

Abstract: HLA-A, -B, and -C alleles were genotyped by sequencing-based typing (SBT) in 102 unrelated ethnic Mongolian individuals living in Inner Mongolia and 110 Hui individuals inhabiting the Qihai plateau in Northern China. In all, 28 HLA-A, 49 HLA-B, and 27 HLA-C alleles in Mongolians and 29 HLA-A, 41 HLA-B, and 27 HLA-C alleles in Hui were detected in this study. A*24G1, A*110101/1121N and A*02G1 are the three most frequent HLA-A alleles both in Mongolians and Hui. At the HLA-B locus, only B*51G1 was found with a frequency of more than 10% in Hui. Cw*070201G1 is the most common HLA-C allele both in Mongolian and Hui. The most frequent HLA-A:C:B, HLA-A:C, and HLA-C:B haplotypes are A*330301-Cw*030201/030202-B*5801, A*330301-Cw*030201/030202, and Cw*030201/030202-B*5801 in Mongolian and A*0207/0215N-Cw*010201/010202-B*4601, A*02G1-Cw*070201G1, and Cw*010201/010202-B*4601 in Hui, respectively. The genetic distance (GD) estimated according to HLA-A, -B, and -C allele frequency indicates that Mongolian and Hui have the closest relationship, and both are closer to Northern Han rather than Southern Han, suggesting that the two ethnicities might have been subjected to intensive gene exchange with Northern Han in history. The dendrogram based on the GD measurements further demonstrates that Mongolian and Hui cluster as a branch with Northern Han Chinese and Northeast Asians. Our results may lead to better understanding of the origins and relationships of Chinese ethnic groups and provide the genetic background for disease association studies. [Copyright &y& Elsevier]

Summary: The majority of Miaos, Bouyeis, and Shuis are distributed in the Guizhou province of southwest China. They live within vast areas, while each ethnicity lives in individual concentrated communities in small areas. Their origin, migration, and relationship have long been interesting to anthropologists. In the present study, polymorphism of HLA-A, -B, and -C genes was investigated using the sequencing-based typing method in the Miao, Bouyei, and Shui from Guizhou, southwest China. Generally, Miao, Bouyei, and Shui share the most high-frequency alleles, suggesting that these three ethnic groups might be subject to intensive gene exchange because of their close location. However, it appears that some alleles distribute ethnic-specifically for each ethnicity. The dendrogram constructed according to the neighbor-joining method demonstrates that Miao, Bouyei, and Shui cluster together and form a branch with other southern Chinese ethnic groups, indicating that Miao, Bouyei, and Shui are three genetically close ethnic groups and inherit more characteristics of southern Chinese populations. The study will increase our understanding of the HLA polymorphism in Chinese populations. [Copyright &y& Elsevier]