The Evaluation of Insertion and Deletion Polymorphism in Population and Personal Identification Amidst Chinese Populations

For comprehensive understanding of practical application and evaluation on the power of30 commonly used InDeis(Qiagen Investigator DIPplex®kit),we captured population data from 25 Chinese populations and employed F-statistics for population genetics analysis.The results indicated that the distributions of allelic frequencies among populations were in different levels.Furthermore,the phylogeny confoiming pairwise FST distances showed that the difierentiation of majority populations were consistent with their geographic locations and historic dispersals.We conduct the comprehensive correlation analysis between FST and heterozygosity of30 InDel loci and provided strong evidence for ongoing InDei loci selection.The Fst values of 30 InDels were calculated within 25 Chinese populations,and then,these loci were characterized definitely based on their roles in population genetics or individual identification.Data indicated that 17 InDels with FST<0.01 could be utilized regarding Chinese individual identification(total discrimination power=0.999985 and cumulative matching probability=0.00000009).We comprehensively reconstructed the population structure and filled the gap of evaluating the ability of InDels in personal as well as population identification.The application of InDel loci in the forensic area would convincingly promote the development matter of forensic population identification and personal discrimination.

Identification and Fine Mapping of Heading Date Related Mutant Gene in Rice

A rice heading-date-related mutant was isolated from a ^60Co-y-ray-induced mutation pool of Zhejing 22, a conventional japonica cultivar in Zhejiang Province, China. The mutant was characterized by a delayed heading date of almost 20 d longer than the wild type plant. Genetic analysis revealed that the mutation was controlled by a single nuclear-encoded recessive gene that was designed as HD（t） （heading date tentatively）. To isolate the HD（t） gene, a map-based cloning approach was employed using 479 F2 mutant individual plants derived from the cross between the hd（t） mutant （japonica） x Zhenshan 97 （indica）. Finally, the HD（t） gene was mapped to an approximate 53 kb region between the insertion and deletion （InDel） markers of 10-61W and 10-66W on chromosome 10. According to the genome sequence of Nipponbare, the target region contains 11 annotated genes. It is helpful for future cloning of HD（t） gene based on this fine mapping results.

Genetic Characterization of Indigenous Rice Varieties in Eastern Himalayan Region of Northeast India

The eastern Himalayan region of Northeast （NE） India is home to a large number of indigenous rice varieties, which are traditionally classified as Oryza sativa subspecies indica, japonica or intermediate types. The classification based on traditional Cheng’s index is often inconclusive due to phenotypic plasticity of morphological characters, which are influenced by environmental conditions. We used molecular markers specific for indica and japonica subspecies to assess the degree of genetic relatedness of indigenous rice varieties in NE India. The results revealed that majority of upland （jum） and glutinous rice varieties, traditionally considered as japonica, were genetically close to the subspecies indica. All varieties of boro ecotype were found to be indica type, and only a few varieties cultivated in lowland and upland areas were japonica type. Some of the lowland varieties of the sali ecotype were intermediate between indica and japonica, and they showed a closer genetic affinity to O. rufipogon.

Developmental validation of the novel six-dye Goldeneye^(TM)DNA ID System 35InDel kit for forensic application

Insertion/deletion polymorphisms(InDels)have been treated as a prospective and helpful genetic marker in the fields of forensic human identification,anthropology and population genetics for the past few years.In this study,we developed a six-dye multiplex typing system consisting of 34 autosomal InDels and Amelogenin for forensic application.The contained InDels were specifically selected for Chinese population with the MAF≥0.25 in East Asia,which do not overlap with the markers of Investigator^(■)DIPplex kit.The typing system was named as GoldeneyeTM DNA ID System 35InDel Kit,and a series of developmental validation studies including repeatability/reproducibility,concordance,accuracy,sensitivity,stability,species specificity and population genetics were conducted on this kit.We confirmed that the 35InDel kit is precise,sensitive,species specific and robust for forensic practice.Moreover,the 35InDel kit is capable of typing DNA extracted from forensic routine case-type samples as well as degraded samples and mixture samples.All markers are proved to be highly polymorphic with an average observed heterozygosity(He)of 0.4582.The combined power of discrimination(CPD)is 0.999999999999978 and the combined power of exclusion in duos(CPE_(D))and trios(CPE_(T))are 0.978837 and 0.999573,respectively,which are higher than those of the Investigator^(■)DIPplex kit.Thus,the GoldeneyeTM DNA ID System 35InDel kit is suitable for forensic human identification and could serve as a supplementary typing system for paternity testing.