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

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 p...

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Autores principales:	Rizwana Begum Syed Nabi, Kwang-Soo Cho, Rupesh Tayade, Ki Won Oh, Myoung Hee Lee, Jung In Kim, Sungup Kim, Suk-Bok Pae, Eunyoung Oh
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/38e6f4a3d4b44693a705d9404fb3b286
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spelling	oai:doaj.org-article:38e6f4a3d4b44693a705d9404fb3b2862021-12-02T16:46:34ZGenetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation10.1038/s41598-021-96074-42045-2322https://doaj.org/article/38e6f4a3d4b44693a705d9404fb3b2862021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-96074-4https://doaj.org/toc/2045-2322Abstract 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 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.Rizwana Begum Syed NabiKwang-Soo ChoRupesh TayadeKi Won OhMyoung Hee LeeJung In KimSungup KimSuk-Bok PaeEunyoung OhNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rizwana Begum Syed Nabi Kwang-Soo Cho Rupesh Tayade Ki Won Oh Myoung Hee Lee Jung In Kim Sungup Kim Suk-Bok Pae Eunyoung Oh Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation
description	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 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.
format	article
author	Rizwana Begum Syed Nabi Kwang-Soo Cho Rupesh Tayade Ki Won Oh Myoung Hee Lee Jung In Kim Sungup Kim Suk-Bok Pae Eunyoung Oh
author_facet	Rizwana Begum Syed Nabi Kwang-Soo Cho Rupesh Tayade Ki Won Oh Myoung Hee Lee Jung In Kim Sungup Kim Suk-Bok Pae Eunyoung Oh
author_sort	Rizwana Begum Syed Nabi
title	Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation
title_short	Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation
title_full	Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation
title_fullStr	Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation
title_full_unstemmed	Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation
title_sort	genetic diversity analysis of korean peanut germplasm using 48 k snps ‘axiom_arachis’ array and its application for cultivar differentiation
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/38e6f4a3d4b44693a705d9404fb3b286
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Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation

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