A 30-InDel Assay for Genetic Variation and Population Structure Analysis of Chinese Tujia Group

Abstract

In the present study, thirty autosomal insertion and deletion polymorphic loci were simultaneously amplified and genotyped in a multiplex system, and their allelic frequencies as well as several forensic parameters were obtained in a sample of 236 unrelated healthy Tujia individuals. All the loci were in Hardy-Weinberg equilibrium after applying a Bonferroni correction and all pair-wise loci showed no significant linkage disequilibrium. These loci were observed to be relatively informative and discriminating, quite efficient for forensic applications. Allelic frequencies of 30 loci were compared between the Tujia group and other reference populations, and the results of analysis of molecular variance indicated the Tujia group showed the least significant differences with the Shanghai Han at one locus, and the most with Central Spanish population at 22 loci. We analyzed the population genetic structure by the principal component analysis, the clustering of STRUCTURE program and a Neighbor-Joining tree, and then evaluated the genetic relationships among Tujia and other 15 populations.

The three-hybrid genetic composition of an Ecuadorian population using AIMs-InDels compared with autosomes, mitochondrial DNA and Y chromosome data

“…InDels showed low allele frequency differentials between Ecuadorian regions: δ < 0.178 among Amazonia- Highlands, δ < 0.194 among Amazonia-Coast and δ < 0.14 among Highlands-Coast. Moreover, Hardy-Weinberg analysis did not show any significance, which suggests that there is no process that affects the conditions of Hardy-Weinberg equilibrium 46,47 .…”

Autosomal DIPs for population genetic structure and differentiation analyses of Chinese Xinjiang Kyrgyz ethnic group

“…2 . Statistically significant differences were detected between the studied Kyrgyz group and Kazakh group 11 at two loci; Uygur group 11 at seven loci; Bai group 15 at ten loci; Tibet Tibetan and Qinghai Tibetan group 16 at 12 loci; Beijing Han 11 and Uruguayan group 17 at 15 loci; Central Spanish group 18 at 16 loci; Tujia 19 and Xibe group 20 at 17 loci; Basque 18 and Dane group 21 at 18 loci; Hungarian group 22 at 19 loci; Guangdong Han 23 and South Korean group 24 at 20 loci; Shanghai Han 25 and She group 25 at 21 loci; Yi group 26 at 22 loci; and six Mexican groups 27 at 21–26 loci, respectively. According to the diagram, the Kyrgyz group had the lowest genetic divergence with Kazakh group (significant differences found at two loci) in contrast with Mexican Amerindian group (significant differences found at 26 loci).…”

Autosomal InDel polymorphisms for population genetic structure and differentiation analysis of Chinese Kazak ethnic group

“…Interpopulation differentiations were compared using the analyses of molecular variance (AMOVA) method. As shown in Supplementary Table 2 , we calculated pairwise p values between the studied Kazak group and 23 previously published populations including Kazak1 [ 7 ], Uigur [ 7 ], Yi [ 10 ], Xibe [ 11 ], Tujia [ 12 ], South Korean [ 13 ], She [ 14 ], two Tibetan groups [ 15 ], three Han populations [ 7 , 14 , 16 ] in different regions, six Mexican groups [ 17 ], four European groups and Uruguayan group [ 18 – 21 ] (The geographical locations of the studied Kazak and other reference populations were shown in Supplementary Figure 2 ) based on allele frequencies of 30 InDel loci. The least differences were observed between the studied Kazak group and Kazak1, Uigur groups with significant differences at 1, 6 loci, respectively.…”