scholarly journals Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6861 ◽  
Author(s):  
Weian Du ◽  
Chunlei Feng ◽  
Ting Yao ◽  
Cheng Xiao ◽  
Hongyan Huang ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Regional Distribution ◽  
Principal Component ◽  
Personal Identification ◽  
Bonferroni Correction ◽  
Forensic Application ◽  
Discrimination Power ◽  
Forensic Efficiency ◽  
Hardy Weinberg Equilibrium ◽  
And Cluster Analysis

Aim In this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application. Result No deviations for all 30 loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520–0.9480, 0.0950–0.8780, and 0.0850–0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802–0.5802, 0.1908–0.6053, and 0.1400–0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region. Conclusion This study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations.

scholarly journals A set informative multiple autosomal markers for human identification: forensic research and population genetics analysis in a Chinese Xinjiang Hui group

2017 ◽  
Author(s):  
Tong Xie ◽  
Yuxin Guo ◽  
Ling Chen ◽  
Yating Fang ◽  
Yunchun Tai ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Genetic Relationships ◽  
Statistical Parameter ◽  
Strong Support ◽  
Personal Identification ◽  
Forensic Identification ◽  
Parameter Analysis ◽  
Individual Identification ◽  
Cumulative Probability ◽  
Discrimination Power

AbstractIn recent years, insertion/deletion (InDel) markers became a promising and useful supporting tool in forensic identification cases and biogeographic research field. In this study, 30 InDel loci were explored to reveal the genetic diversities and genetic relationships between Chinese Xinjiang Hui group and the 24 previously studied populations using varies methods such as forensic statistical parameter analysis, phylogenetic reconstruction, STRUCTURE analysis, multi-dimensional scaling, and principal component analysis. The observed heterozygosity and expected heterozygosity ranged from 0.1971 (HLD118) to 0.5092 (HLD 92), 0.2222 (HLD 114) to 0.5000 (HLD 6), respectively. Besides, after Bonferroni correction, no deviations from Hardy-Weinberg equilibrium tests were found at all 30 loci in Xinjiang Hui group. The cumulative probability of exclusion and combined discrimination power were 0.988849 and 0.99999999999378, respectively, which indicated that the 30 loci could be used as complementary genetic markers for paternity test and be qualified for personal identification in forensic cases. In this study, we found that Xinjiang Hui group had close relationships with most Chinese groups, especially Han populations, and all the results based on different genetic methods we used had a strong support for this finding. The 30 InDel loci has important significance in forensic identification research, in spite of this, for a better understanding of genetic background of the Chinese Xinjiang Hui group, molecular genetic genotyping at various genetic markers is necessary in future studies.Summary StatementWe report here, a promising Individual identification and population differentiation maker which could be used in forensic cases.

GENETIC DIVERSITY OF EXTRA-EARLY YELLOW MAIZE HYBRIDS UNDER STRIGA ENVIRONMENTS

2021 ◽  
Vol 5 (1) ◽  
pp. 302-308
Author(s):  
Abdulwahab Saliu Shaibu
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Block Design ◽  
Crop Improvement ◽  
Principal Component ◽  
Environment Interaction ◽  
Maize Hybrids ◽  
Group I ◽  
Significant Difference ◽  
And Cluster Analysis

The success of any breeding program depends on the ability to determine germplasm diversity and genetic relationships among breeding materials. Genetic diversity is an invaluable aid in crop improvement. This study was carried out to determine the genetic diversity among 70 extra-early yellow maize hybrids under Striga environments. Cluster and principal component (PC) analyses were used to determine the genetic diversity of the hybrids. Data on morphological and agronomical data were collected. The experiment was set up in two locations (Abuja and Mokwa) in a randomized incomplete block design experiment with two replications. A significant difference was observed among the hybrids in all the traits studied and a significant genotype × environment interaction was observed for all traits except for plant height, anthesis silking interval and Striga count at 8 and 10 WAP. The principal component reveals that the first three components account for 86% variability. PC1 gave maximum variability (43%) and was loaded with PC1 and the first four PCs can be utilized in hybridization programs. The principal component biplot reveals the relationship among traits and the distance of each variable in determining variability among hybrids. The cluster diagram reveals five distinct groups. Group IV consisted of Striga tolerant hybrids and group I consisted of susceptible hybrids. Both principal component and cluster analysis revealed the genetic diversity among the hybrids and identified genotypes that were Striga tolerant and could be selected as choice of parental materials to develop Striga resistant materials

scholarly journals Forensic Application Evaluation of a Novel Canine STR System in Pembroke Welsh Corgi and Shiba Inu Groups

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Yating Fang ◽  
Jinlong Yang ◽  
Yajun Deng ◽  
Bofeng Zhu
Keyword(s):  
Capillary Electrophoresis ◽  
Linkage Disequilibrium ◽  
Tandem Repeat ◽  
Genetic Relationships ◽  
Forensic Application ◽  
Str Loci ◽  
Hardy Weinberg Equilibrium ◽  
Str System ◽  
Short Tandem ◽  
Forensic Parameters

Aim. To evaluate the forensic application values of 19 autosomal short tandem repeat (STR) loci in canines. Methods. The 19 STR loci in two canine groups (Pembroke Welsh Corgis, n = 200 ; Shiba Inus, n = 175 ) were analysed by the capillary electrophoresis platform. The allele frequencies and forensic parameters were calculated, and the genetic relationships between these two canine groups and a previously reported Labrador group were analysed. Results. These two canine groups conformed to the Hardy-Weinberg equilibrium at all STRs except for locus VGL3438 in the Pembroke Welsh Corgi group, and there was no linkage disequilibrium among pairwise loci at the 19 STRs. All STRs were polymorphic in the Pembroke Welsh Corgi and Shiba Inu groups, of which the locus C38 had the highest polymorphism. And it was found that the genetic relationship between the Pembroke Welsh Corgi and Labrador groups were closer in the three canine groups (Pembroke Welsh Corgi, Shiba Inu and Labrador). Conclusion. The 19 STR loci had high genetic polymorphisms and forensic application values in Pembroke Welsh Corgi and Shiba Inu groups.

scholarly journals Morphologic and Agronomic Diversity of Brassica napus Crops

2008 ◽  
Vol 133 (1) ◽  
pp. 48-54 ◽  
Author(s):  
Pilar Soengas ◽  
Maria Elena Cartea ◽  
Pablo Velasco ◽  
Guillermo Padilla ◽  
Amando Ordás
Keyword(s):  
Cluster Analysis ◽  
Brassica Napus ◽  
Agronomic Traits ◽  
Genetic Relationships ◽  
Winter Season ◽  
Principal Component ◽  
Group Method ◽  
Pair Group ◽  
Total Variability ◽  
And Cluster Analysis

A Brassica napus L. crop called nabicol traditionally has been grown by farmers in northwestern Spain for many years and is an important horticultural product during the winter season. The relationship of nabicol to other B. napus crops has been studied based on simple sequence repeat (SSR) data. However, molecular and morphologic classifications often disagree. The objectives of this research were to study the morphologic and agronomic relationships of nabicol landraces to other B. napus crops and to compare those relationships with the ones already known, based on SSR data. Thirty-five B. napus populations from different geographic origins and uses were evaluated. Data were recorded on 17 morphologic and agronomic traits. Principal component analysis and cluster analysis were performed to classify the populations. Eight principal components (94% of the total variability) were standardized to produce the Mahalanobis' generalized distances, and a cluster analysis was conducted using the unweighted pair group method with arithmetic averages. There are no major differences between B. napus var. pabularia (DC.) Rchb. (nabicol, couve-nabiça, forage rape) and B. napus var. oleifera DC. (oilseed rape), and they probably share a common origin. Rape kale (B. napus var. pabularia) and rutabaga [B. napus var. napobrassica (L.) Rchb.] cultivars are separated from the rest and probably they have an independent origin or domestication. Molecular and morphologic classifications are complementary, and both are necessary to classify germplasm correctly and to clarify genetic relationships among B. napus crops.

scholarly journals Genetic polymorphisms and forensic efficiency of 19 X-chromosomal STR loci for Xinjiang Mongolian population

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5117 ◽  
Author(s):  
Ling Chen ◽  
Yuxin Guo ◽  
Cheng Xiao ◽  
Weibin Wu ◽  
Qiong Lan ◽  
...  
Keyword(s):  
Minority Group ◽  
Genetic Research ◽  
Bonferroni Correction ◽  
Significance Level ◽  
Autonomous Region ◽  
Str Loci ◽  
Asian Populations ◽  
Forensic Efficiency ◽  
Hardy Weinberg Equilibrium ◽  
High Utility

Aim X-chromosomal short tandem repeat (X-STR) loci are playing an increasingly important role in some complex kinship cases in recent years. To investigate the forensic efficiency of X-STRs of Mongolian minority group from Xinjiang Uygur Autonomous Region, China, and further depict the genetic relationship among Xinjiang Mongolians and other populations, 267 blood samples from unrelated healthy Xinjiang Mongolians were amplified by an AGCU X-19 STR kit. Results No deviations for all 19 X-STR loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.0026) in female samples. The most frequent allele was allele 10 at locus DXS10164 with the frequency 0.5663. The polymorphism information content values of the 19 X-STR loci were more than 0.5 with the highest polymorphism at the locus DXS10135. The cumulative power of discrimination were 0.99999999999999999999988761005481 in females and 0.999999999999903 in males, respectively; and the cumulative mean exclusion chances were 0.9999999969738068321121 in duos and 0.999999999998952 in trios, respectively. The seven linkage groups were extremely informative, with all the haplotype diversities greater than 0.9487. No linkage disequilibrium was observed for a significance level of 0.00029 (p = 0.05/171) after Bonferroni correction. The DA distances, multidimensional scaling plot and phylogenetic tree based on the 11 overlapping X-STR loci all presented that the Xinjiang Mongolian population was genetically different from other Asian populations, including the Mongolian population from Inner Mongolia Autonomous Region, China. Conclusion This study indicated that the 19 X-STR multiplex PCR system was of high utility value for both forensic practices and population genetic research in Xinjiang Mongolian group.

scholarly journals Principal Component and Cluster Analysis as a Tool in the Assessment of Tomato Hybrids and Cultivars

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
G. Evgenidis ◽  
E. Traka-Mavrona ◽  
M. Koutsika-Sotiriou
Keyword(s):  
Yield Components ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Principal Component ◽  
Breeding Value ◽  
Phenotypic Traits ◽  
Quality Stability ◽  
Germplasm Diversity ◽  
Data Yield ◽  
And Cluster Analysis

Determination of germplasm diversity and genetic relationships among breeding materials is an invaluable aid in crop improvement strategies. This study assessed the breeding value of tomato source material. Two commercial hybrids along with an experimental hybrid and four cultivars were assessed with cluster and principal component analyses based on morphophysiological data, yield and quality, stability of performance, heterosis, and combining abilities. The assessment of commercial hybrids revealed a related origin and subsequently does not support the identification of promising offspring in their crossing. The assessment of the cultivars discriminated them according to origin and evolutionary and selection effects. On the Principal Component 1, the largest group with positive loading included, yield components, heterosis, general and specific combining ability, whereas the largest negative loading was obtained by qualitative and descriptive traits. The Principal Component 2 revealed two smaller groups, a positive one with phenotypic traits and a negative one with tolerance to inbreeding. Stability of performance was loaded positively and/or negatively. In conclusion, combing ability, yield components, and heterosis provided a mechanism for ensuring continued improvement in plant selection programs.

scholarly journals Karyotypic Characteristics and Genetic Relationships of Apricot Accessions from Different Ecological Groups

2021 ◽  
Vol 146 (1) ◽  
pp. 68-76
Author(s):  
Wenwen Li ◽  
Liqiang Liu ◽  
Weiquan Zhou ◽  
Yanan Wang ◽  
Xiang Ding ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Principal Component ◽  
Small Chromosome ◽  
Prunus Armeniaca ◽  
Ecological Group ◽  
Ecological Groups ◽  
Central Asian ◽  
Satellite Chromosomes ◽  
And Cluster Analysis ◽  
Karyotype Symmetry

The present study aims to reveal the karyotypic characteristics and genetic relationships of apricot (Prunus armeniaca L.) accessions from different ecological groups. Fourteen, 9, and 30 accessions from the Central Asian ecological group, North China ecological group, and Dzhungar-Ili ecological group, respectively, were analyzed according to the conventional pressing plate method. The results showed that all the apricot accessions from the different ecological groups were diploid (2n = 2x = 16). The total haploid length of the chromosome set of the selected accessions ranged from 8.11 to 12.75 μm, which was a small chromosome, and no satellite chromosomes were detected. All accessions had different numbers of median-centromere chromosomes or sub-median-centromere chromosomes. The karyotypes of the selected accessions were classified as 1A or 2A. Principal component analysis revealed that the long-arm/short-arm ratio (0.968) and the karyotype symmetry index (−0.979) were the most valuable parameters, and cluster analysis revealed that the accessions from the Central Asian ecological group and Dzhungar-Ili ecological group clustered together. In terms of karyotypic characteristics, the accessions from the Dzhungar-Ili ecological group and Central Asian ecological group were closely related.

The Utilization of Ftir (Fourier Transform Infra-Red) Method Combined with Chemometrics For Authentication of Indonesian Coffee Powder

2017 ◽  
Vol 9 (3) ◽  
Author(s):  
Firmansyah A. ◽  
Winingsih W. ◽  
Soebara Y S
Keyword(s):  
Fourier Transform ◽  
Natural Product ◽  
High Performance ◽  
Principal Component ◽  
Raw Material ◽  
Attenuated Total Reflectance ◽  
Coffee Bean ◽  
Product Analysis ◽  
Total Reflectance ◽  
And Cluster Analysis

Analysis of natural product remain challenging issues for analytical chemist, since natural products are complicated system of mixture. The most popular methods of choice used for quality control of raw material and finished product are high performance liquid chromatography (HPLC), gas chromatography (GC) and mass spectrometry (MS). The utilization of FTIR-ATR (Fourier Transform Infrared-Attenuated Total Reflectance) method in natural product analysis is still limited. This study attempts to expand the use of FTIR spectroscopy in authenticating Indonesian coffee powder.The coffee samples studied were taken from nine regions in Indonesia, namely Aceh Gayo, Flores, Kintamani, Mandheling, Papua, Sidikalang, Toraja, Kerinci and Lampung.The samples in the form of coffee bean from various regions were powdered . The next step conducted was to determine the spectrum using the FTIR-ATR (Attenuated Total Reflectance) using ZnSe crystal of 8000 resolution. Spectrum samples, then, were analyzed using chemometrics. The utilized chemometric model was the principal component analysis (PCA) and cluster analysis (CA). Based on the chemometric analysis, there are similarities between Aceh Gayo coffee with Toraja coffee, Mandailing coffee, Kintamani coffee and Flores coffee. Sidikalang coffee has a similarity to Flores coffee; Papua coffee has a similarity to Sidikalang coffee; Lampung coffee has a similarity to Sidikalang coffee, while Kerinci coffee has a similarity to Papua coffee.

Fingerprint of PGI Mantova Cucumis melo by ICP-MS and Chemometric Analysis

2020 ◽  
Vol 17 (1) ◽  
pp. 94-104
Author(s):  
Antonio F. Mottese ◽  
Maria R. Fede ◽  
Francesco Caridi ◽  
Giuseppe Sabatino ◽  
Giuseppe Marcianò ◽  
...  
Keyword(s):  
Cucumis Melo ◽  
Principal Component ◽  
Inorganic Elements ◽  
Discrimination Power ◽  
Icp Ms ◽  
High Discrimination ◽  
Strong Relation ◽  
Trace Element Contents ◽  
Safe Food

Background and Objectives: In this work, yellow and green varieties of Cucumis melo fruits belonging to different cultivars were studied. In detail, three Sicilian cultivars of winter melons tutelated by TAP (Traditional agro-alimentary products) labels were considered, whereas asun protected the Calabrian winter melon was studied too. With the aim to compare the selective uptakes of inorganic elements among winter and summer fruits, the “PGI Melone Mantovano” was investigated. The purpose of this work was to apply the obtained results i) to guarantee the quality and healthiness of fruits, ii) to producers defend, iii) to help the customers in safe food purchase. Method: All samples were analyzed by ICP-MS and the obtained results, subsequently, were subjected to Cluster analysis (CA), Principal component analysis (PCA) and Canonical discriminant analysis (CDA). Results: CA results were generally in agreement with samples origin, whereas the PCA elaboration has confirmed the presence of a strong relation between fruit origins and trace element contents. In particular, two principal components justified the 57.32% of the total variance (PC1= 40.95%, PC2= 16.37%). Finally, the CDA approach has provided several functions with high discrimination power, confirmed by the correct classification of all samples (100%). Conclusions: CA, PCA and CDA could represent an integrated to label to discriminate the origin of agri-food products and, thus, protect and guarantee their healthiness.

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