scholarly journals Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rizwana Begum Syed Nabi ◽  
Kwang-Soo Cho ◽  
Rupesh Tayade ◽  
Ki Won Oh ◽  
Myoung Hee Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Association Studies ◽  
Diversity Analysis ◽  
Genome Wide Association Studies ◽  
Genotype Distribution ◽  
Genetic Diversity Analysis ◽  
Genetic Base ◽  
Cultivated Peanut ◽  
Improvement Programs

AbstractCultivated peanut (Arachis hypogaea) is one of the important legume oilseed crops. Cultivated peanut has a narrow genetic base. Therefore, it is necessary to widen its genetic base and diversity for additional use. The objective of the present study was to assess the genetic diversity and population structure of 96 peanut genotypes with 9478 high-resolution SNPs identified from a 48 K ‘Axiom_Arachis’ SNP array. Korean set genotypes were also compared with a mini-core of US genotypes. These sets of genotypes were used for genetic diversity analysis. Model-based structure analysis at K = 2 indicated the presence of two subpopulations in both sets of genotypes. Phylogenetic and PCA analysis clustered these genotypes into two major groups. However, clear genotype distribution was not observed for categories of subspecies, botanical variety, or origin. The analysis also revealed that current Korean genetic resources lacked variability compared to US mini-core genotypes. These results suggest that Korean genetic resources need to be expanded by creating new allele combinations and widening the genetic pool to offer new genetic variations for Korean peanut improvement programs. High-quality SNP data generated in this study could be used for identifying varietal contaminant, QTL, and genes associated with desirable traits by performing mapping, genome-wide association studies.

Genetic Diversity Analysis of Korean Peanut Germplasm Using 48 K SNPs ‘Axiom_Arachis’ Array and Its Application for Cultivar Differentiation

2021 ◽  
Author(s):  
Rizwana Begum Syed Nabi ◽  
Kwang-Soo Cho ◽  
Rupesh Tayade ◽  
Ki Won Oh ◽  
Myoung Hee Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Association Studies ◽  
Diversity Analysis ◽  
Genome Wide Association Studies ◽  
Genotype Distribution ◽  
Genetic Diversity Analysis ◽  
Genetic Base ◽  
Cultivated Peanut ◽  
Improvement Programs

Abstract Cultivated peanut (Arachis hypogaea) is one of the important legume oilseed crops. Cultivated peanut has a narrow genetic base. Therefore, it is necessary to widen its genetic base and diversity for additional use. The objective of the present study was to assess the genetic diversity and population structure of 96 peanut genotypes with 9478 high-resolution SNPs identified from a 48K ‘Axiom_Arachis’ SNP array. Korean set genotypes were also compared with a mini-core of US genotypes. These sets of genotypes were used for genetic diversity analysis. Model-based structure analysis at K = 2 indicated the presence of two subpopulations in both sets of genotypes. Phylogenetic and PCA analysis clustered these genotypes into two major groups. However, clear genotype distribution was not observed for categories of subspecies, botanical variety, or origin. The analysis also revealed that current Korean genetic resources lacked variability. These results suggest that Korean genetic resources need to be expanded by creating new allele combinations and widening the genetic pool to offer new genetic variations for Korean peanut improvement programs. High-quality SNP data generated in this study could be used for identifying varietal contaminant, QTL, and genes associated with desirable traits by performing mapping, genome-wide association studies.

Molecular markers and antioxidant activity in berry crops: Genetic diversity analysis

2012 ◽  
Vol 92 (6) ◽  
pp. 1121-1133 ◽  
Author(s):  
S. C. Debnath ◽  
Y. L. Siow ◽  
J. Petkau ◽  
D. An ◽  
N. V. Bykova
Keyword(s):  
Genetic Diversity ◽  
Antioxidant Activity ◽  
Molecular Markers ◽  
Molecular Techniques ◽  
Diversity Analysis ◽  
Full Potential ◽  
Genetic Diversity Analysis ◽  
Wide Range ◽  
Berry Crops ◽  
Improvement Programs

Debnath, S. C., Siow, Y. L., Petkau, J., An, D. and Bykova, N. V. 2012. Molecular markers and antioxidant activity in berry crops: Genetic diversity analysis. Can. J. Plant Sci. 92: 1121–1133. An improved understanding of important roles of dietary fruits in maintaining human health has led to a dramatic increase of global berry crop production. Berry fruits contain relatively high levels of vitamin C, cellulose and pectin, and produce anthocyanins, which have important therapeutic values, including antitumor, antiulcer, antioxidant and anti-inflammatory activities. There is a need to develop reliable methods to identify berry germplasm and assess genetic diversity/relatedness for dietary properties in berry genotypes for practical breeding purposes through genotype selection in a breeding program for cultivar development, and proprietary-rights protection. The introduction of molecular biology techniques, such as DNA-based markers, allows direct comparison of different genetic materials independent of environmental influences. Significant progress has been made in diversity analysis of wild cranberry, lowbush blueberry, lingonberry and cloudberry germplasm, and in strawberry and raspberry cultivars and advanced breeding lines developed in Canada. Inter simple sequence repeat (ISSR) markers detected an adequate degree of polymorphism to differentiate among berry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in the current berry improvement programs. Although multiple factors affect antioxidant activity, a wide range of genetic diversity has been reported in wild and cultivated berry crops. Diversity analysis based on molecular markers did not agree with those from antioxidant activity. The paper also discusses the issues that still need to be addressed to utilize the full potential of molecular techniques including expressed sequence tag-polymerase chain reaction (EST-PCR) analysis to develop improved environment-friendly berry cultivars suited to the changing needs of growers and consumers.

Genetic Diversity Analysis among 27 Indian Goat Populations using Microsatellite Markers

2020 ◽  
Author(s):  
Rajkumar Sah ◽  
Santpal Dixit
Keyword(s):  
Genetic Diversity ◽  
Association Studies ◽  
Research Work ◽  
Diversity Analysis ◽  
National Bureau ◽  
Genetic Diversity Analysis ◽  
Well Differentiated ◽  
Inbreeding Level ◽  
High Level ◽  
Indian Goat

Background: Livestock genetic diversity studies focus on their within and diversity, breed history, adaptive variations, ancestral information, site of domestication and parentage testing and assess the genetic uniformity, admixture or subdivision, inbreeding, or introgression in the population which is helpful in breed formation and their sustainable utilization.Methods: The present research work was conducted during the year 2016-17 at National Bureau of Animal Genetics Resources, Karnal-132001. STR data of 25 markers on 1237 random samples of 27 goat populations was used for analysis. The genetic diversity analysis of new population viz: Narayanpatna, Raighar, Kalahandi, Malkangiri of Odisha state and Rohilkhandi (UK) and their association studies with other Indian goat breeds was performed.Result: It was found that used markers are highly polymorphic- and the studied breeds/population showed great diversity and distributed mostly on the basis of physio-geographical condition and type of production but among new populations diversity was least which might be due to exchange of animal for breeding purposes. The studied new goat populations were well differentiated from other goat breeds which might be due to physio-geographical condition and breeding practices, so these may be considered as separate breeds/populations. In conclusion, the results showed high level of conserved genetic diversity in the Indian goat breeds. The smaller and isolated new population showed less diversity and a higher inbreeding level as compared to registered breeds.

scholarly journals Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e110856 ◽  
Author(s):  
Spurthi N. Nayak ◽  
Jian Song ◽  
Andrea Villa ◽  
Bhuvan Pathak ◽  
Tomas Ayala-Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Core Collection ◽  
Diversity Analysis ◽  
Saccharum Spp ◽  
Genetic Diversity Analysis

Strong Association between Serotonin Transporter 5-HTTVNTR Variant and Psychoactive Substance (Nicotine) Use in the Turkish Cypriot Population

2020 ◽  
Vol 21 (6) ◽  
pp. 466-470
Author(s):  
Emine Kandemis ◽  
Gulten Tuncel ◽  
Ozen Asut ◽  
Sehime G. Temel ◽  
Mahmut C. Ergoren
Keyword(s):  
Serotonin Transporter ◽  
Association Studies ◽  
Strong Association ◽  
Smoking Behavior ◽  
Population Based ◽  
Genome Wide Association Studies ◽  
Genotype Distribution ◽  
Psychological Traits ◽  
Wide Range ◽  
Turkish Cypriot

Background: The use of psychoactive substances is one of the most dangerous social problems worldwide. Nicotine dependence results from the interaction between neurobiological, environmental and genetic factors. Serotonin is a neurotransmitter that has a wide range of central nervous system activities. The serotonin transporter gene has been previously linked to psychological traits. Objective: A variable number of tandem repeats within the serotonin transporter-linked polymorphic gene region are believed to alter the transcriptional efficiency of the 5-HTT gene. Therefore, we aimed to investigate the association between this polymorphic site and smoking behavior in the Turkish Cypriot population. Methods: A total of 259 (100 smokers, 100 non-smokers and 59 ex-smokers) Turkish Cypriots were included in this population-based cross-sectional study. Genomic DNA was extracted from peripheral blood samples and the 5-HTTVNTR2 polymorphisms were determined by the PCR-RFLP. Results: The allelic frequency and genotype distribution results of this study showed a strong association (P<0.0001) between smokers and non-smokers. No statistical significance was found between non-smokers and ex-smokers. Conclusion: This is the first genetic epidemiology study to investigate the allelic frequencies of 5-HTTVNTR2 polymorphisms associated with smoking behavior in the Turkish Cypriot population. Based on the results of this study, genome-wide association studies should be designed for preventive medicine in this population.

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