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Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

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dc.contributor.authorLee, Hea-Young-
dc.contributor.authorRo, Na-Young-
dc.contributor.authorJeong, Hee-Jin-
dc.contributor.authorKwon, Jin-Kyung-
dc.contributor.authorJo, Jinkwan-
dc.contributor.authorHa, Yeaseong-
dc.contributor.authorJung, Ayoung-
dc.contributor.authorHan, Ji-Woong-
dc.contributor.authorVenkatesh, Jelli-
dc.contributor.authorKang, Byoung-Cheorl-
dc.date.accessioned2017-02-09T00:27:08Z-
dc.date.available2017-02-09T00:27:08Z-
dc.date.issued2016-11-14-
dc.identifier.citationBMC Genetics, 17(1):142ko_KR
dc.identifier.urihttps://hdl.handle.net/10371/100563-
dc.descriptionThis article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made.
ko_KR
dc.description.abstractAbstract

Background
Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum.


Results
To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (HE = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (HE = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection CC240 with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher genetic diversity (I = 0.95) and genetic evenness (J = 0.80), and represented a wider range of phenotypic variation (MD = 9.45 %, CR = 98.40 %).


Conclusions
A total of 240 accessions were selected from 3,821 Capsicum accessions based on transcriptome-based 48 SNP markers with genome-wide distribution and 32 traits using a systematic approach. This core collection will be a primary resource for pepper breeders and researchers for further genetic association and functional analyses.
ko_KR
dc.language.isoenko_KR
dc.publisherBioMed Centralko_KR
dc.subjectCapsicum spp.ko_KR
dc.subjectCore collectionko_KR
dc.subjectGenetic diversityko_KR
dc.subjectGermplasmko_KR
dc.subjectPopulation structureko_KR
dc.titleGenetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasmko_KR
dc.typeArticleko_KR
dc.contributor.AlternativeAuthor이혜영-
dc.contributor.AlternativeAuthor노나영-
dc.contributor.AlternativeAuthor정희진-
dc.contributor.AlternativeAuthor권진경-
dc.contributor.AlternativeAuthor조진관-
dc.contributor.AlternativeAuthor하예성-
dc.contributor.AlternativeAuthor정아영-
dc.contributor.AlternativeAuthor한지웅-
dc.contributor.AlternativeAuthor강병철-
dc.identifier.doi10.1186/s12863-016-0452-8-
dc.language.rfc3066en-
dc.rights.holderThe Author(s).-
dc.date.updated2017-01-06T10:17:52Z-
Appears in Collections:
College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Plant Science (식물생산과학부)Journal Papers (저널논문_식물생산과학부)
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