Excessive addition split peak formed by the non-templated nucleotide addition property of Taq DNA polymerase after PCR amplification

Because of its non-template addition feature, Taq DNA polymerase can catalyze one or more extra nucleotides onto the 3′ terminus of PCR products. An extra peak is observed at DYS391 locus after the PCR products stored for 4 days at 4°C. To explore the formation mechanism of this artifact, PCR primers and amplicon sequences of Y-STR loci are analyzed, furthermore, PCR products storage conditions and termination of PCR are discussed. The extra peak is a + 2 addition product, which we call excessive addition split peak (EASP). The most significant difference between EASP and the incomplete addition of adenine product is that the size of EASP is about one base larger than the true allele, and the EASP locates on the right side of the real allelic peak. The EASP cannot be eliminated by increasing loading mixture volume and conducting heat denaturation prior to electrophoresis injection. However, the EASP is not observed when the PCR is terminated with ethylenediaminetetraacetic acid or formamide. These findings suggest that formation of EASP is a result of 3′ end non-template extension by Taq DNA polymerase, rather than being the result of DNA fragment secondary structure produced under a suboptimal electrophoresis condition. In addition, the EASP formation is affected by the primer sequences and the storage conditions of PCR products

Multiple genetic analyses to investigate the polymorphisms of Chinese Mongolian population with an efficient short tandem repeat panel

Aim To determine allele frequencies and forensic statistics of 22 autosomal short tandem repeat loci in Chinese Mongolian population. Methods Blood specimens were collected from 134 unrelated healthy Mongolian individuals, and 22 short tandem repeat loci were co-amplified and genotyped. Allele frequencies and forensic parameters were calculated, and population genetic differences were analyzed among Mongolian population and other eight Chinese populations: Northern Han, Guangdong Han, Chengdu Han, Xinjiang Hui, Xinjiang Uygur, Hainan Li, Qinghai Tibetan, and Hainan Han. Results All the loci were in the Hardy-Weinberg equilibrium, and after Bonferroni correction there was no linkage disequilibrium between them. The allele frequencies of these 22 loci were between 0.0037 and 0.3657. This panel had high discriminating power and genetic polymorphism in the Mongolian population, with combined power of discrimination of 0.999999999999999999999999998399 and combined probability of exclusion of 0.9999999999566925. Structure analysis showed no evidence that these nine Chinese populations had different component distribution. However, genetic distance analysis showed significant differences among them (P < 0.05). Conclusion The combined application of these 22 loci could be useful for forensic purposes in the Mongolian population. Mongolian population had smaller genetic distances from the populations in northern China (Northern Han, Xinjiang Uygur, and Xinjiang Hui) than from the populations in Hainan province (Hainan Han and Hainan Li populations)

Opportunity for marine fisheries reform in China

China's 13th Five-Year Plan, launched in March 2016, provides a sound policy platform for the protection of marine ecosystems and the restoration of capture fisheries within China's exclusive economic zone. What distinguishes China among many other countries striving for marine fisheries reform is its size- accounting for almost one-fifth of global catch volume-and the unique cultural context of its economic and resource management. In this paper, we trace the history of Chinese government priorities, policies, and outcomes related to marine fisheries since the 1978 Economic Reform, and examine how the current leadership's agenda for "ecological civilization" could successfully transform marine resource management in the coming years. We show how China, like many other countries, has experienced a decline in the average trophic level of its capture fisheries during the past few decades, and how its policy design, implementation, and enforcement have influenced the status of its wild fish stocks. To reverse the trend in declining fish stocks, the government is introducing a series of new programs for sustainable fisheries and aquaculture, with greater traceability and accountability in marine resource management and area controls on coastal development. As impressive as these new plans are on paper, we conclude that serious institutional reforms will be needed to achieve a true paradigm shift in marine fisheries management in China. In particular, we recommend new institutions for science-based fisheries management, secure fishing access, policy consistency across provinces, educational programs for fisheries managers, and increasing public access to scientific data.Additional co-authors: Yingqi Zhou, Ping Zhuang, and Rosamond L. Naylo

Population Genetic Diversity and Clustering Analysis for Chinese Dongxiang Group With 30 Autosomal InDel Loci Simultaneously Analyzed

In comparison with the most preferred genetic marker utilized in forensic science (STR), insertion/deletion analysis possesses further benefits, like absence of stutter peak, low mutation rate, and enabling mixed stain analysis. At present, a total of 169 unrelated healthy Dongxiang individuals dwelling in Dongxiang Autonomous county of Gansu province were recruited in our study to appraise the forensic usefulness of the panel including 30 autosomal diallelic genetic markers. The insertion allele frequencies were in the range of 0.1598 at HLD 111 to 0.8550 at HLD 118. The cumulative match of probability and the combined probability of exclusion were estimated based on independence of pairwise loci, with the values of 3.96 × 10-11 and 0.9886, respectively, which showed tremendous potential of this panel to be qualified for forensic personal identification in Chinese Dongxiang group. And it could also be used as a complementary tool for forensic parentage testing when combined with standard STR genetic markers. Furthermore, calculation of the DA distance and Fst values of pairwise populations, phylogenetic reconstruction, multidimensional scaling analysis, structure clustering analysis were also conducted to probe the genetic relationships between Dongxiang group and the other 30 reference populations. Results demonstrated that Dongxiang ethnic group might be genetically closer related with most Chinese populations involved in our study, especially Tibet groups, Xibe group, and several Han populations

RETRACTED: Forensic characteristics and genetic affinity analyses of Xinjiang Mongolian group using a novel six fluorescent dye‐labeled typing system including 41 Y‐STRs and 3 Y‐InDels

Abstract Background Y‐chromosomal genetic marker haplotypes of individuals can define the paternal kinship or genealogies to which they belong and further provide clues for forensic individual identifications. Studying the genetic structure of the Mongolian group will help to bring to light the Mongolian ethnic origin, and explicate the genetic affinities among the studied and compared populations. Some forensic scientists have studied the genetic background of the Mongolian group based on different molecular genetic markers. These studies were of very great reference significance for the Mongolian group genetic research, whereas the investigation of Y‐STR haplotype data in the Xinjiang Mongolian group is still insufficient. Methods Genetic characteristics of 182 unrelated healthy male Mongolian individuals were revealed by 41 Y‐chromosomal short tandem repeat and 3 insertion/deletion molecular genetic markers. Furthermore, analyses of molecular variance programs, multi‐dimensional scaling plots, and phylogenetic tree reconstructions were operated to explore the genetic relationships of the Xinjiang Mongolian group with comparative 23 populations from China and 33 populations from worldwide nations. Results The genetic diversity values ranged from 0.0641 (rs771783753) to 0.9502 (DYF387S1). A total of 165 distinct haplotypes were identified, of which 150 (90.91%) were unique. The discrimination capacity, match probability, and haplotype diversity of 44 loci were 0.9066, 0.0067, and 0.9988, respectively. Additionally, the Mongolian group had the most intimate relationship with Gansu Dongxiang (RST = 0.0165), followed by HulunBuir Mongolian (RST = 0.0187), Inner Mongolia Daur (RST = 0.0202) as well as other three minority ethnic groups from the Xinjiang region (RST < 0.05) in all compared Chinese populations, and clustered together with the majority of Asian populations in a worldwide scale. Conclusions Consequently, the 44 loci could be well applied in forensic applications of the Mongolian group. The haplotypes available in here made new contributions to the existing population genetic information and would be of great value in population studies