Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.

Tartary buckwheat (Fagopyrum tataricum Gartn.) is a highly functional crop that is poised to be the target of many future breeding efforts. The reliable ex situ conservation of various genetic resources is essential for the modern breeding of tartary buckwheat varieties. We developed PCR-based co-do...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Hwang-Bae Sohn, Su-Jeong Kim, Su-Young Hong, Sin-Gi Park, Dong-Ha Oh, Sunghoon Lee, Hwa Yeun Nam, Jung Hwan Nam, Yul-Ho Kim
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6082b95d40dd4da5a10dfe49d113c175
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:6082b95d40dd4da5a10dfe49d113c175
record_format	dspace
spelling	oai:doaj.org-article:6082b95d40dd4da5a10dfe49d113c1752021-12-02T20:03:59ZDevelopment of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.1932-620310.1371/journal.pone.0250786https://doaj.org/article/6082b95d40dd4da5a10dfe49d113c1752021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0250786https://doaj.org/toc/1932-6203Tartary buckwheat (Fagopyrum tataricum Gartn.) is a highly functional crop that is poised to be the target of many future breeding efforts. The reliable ex situ conservation of various genetic resources is essential for the modern breeding of tartary buckwheat varieties. We developed PCR-based co-dominant insertion/deletion (InDel) markers to discriminate tartary buckwheat genetic resources. First, we obtained the whole genome from 26 accessions across a superscaffold-scale reference genome of 569.37 Mb for tartary buckwheat cv. "Daegwan 3-7." Next, 171,926 homogeneous and 53,755 heterogeneous InDels were detected by comparing 26 accessions with the "Daegwan 3-7" reference sequence. Of these, 100 candidate InDels ranging from 5-20 bp in length were chosen for validation, and 50 of them revealed polymorphisms between the 26 accessions and "Daegwan 3-7." The validated InDels were further tested through the assessment of their likelihood to give rise to a single or a few PCR products in 50 other accessions, covering most tartary buckwheat genome types. The major allele frequencies ranged from 0.5616 at the TB42 locus to 0.9863 at the TB48 locus, with the average PIC value of 0.1532 with a range of 0.0267-0.3712. To create a user-friendly system, the homology of the genotypes between and among the accessions were visualized in both one- (1D) and two-dimensional (2D) barcode types by comparing amplicon polymorphisms with the reference variety, "Daegwan 3-7." A phylogenetic tree and population structure of the 76 accessions according to amplicon polymorphisms for the 50 InDel markers corresponded to those using non-synonymous single nucleotide polymorphism variants, indicating that the barcode system based on the 50 InDels was a useful tool to improve the reliability of identification of tartary buckwheat accessions in the germplasm stocks.Hwang-Bae SohnSu-Jeong KimSu-Young HongSin-Gi ParkDong-Ha OhSunghoon LeeHwa Yeun NamJung Hwan NamYul-Ho KimPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 6, p e0250786 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hwang-Bae Sohn Su-Jeong Kim Su-Young Hong Sin-Gi Park Dong-Ha Oh Sunghoon Lee Hwa Yeun Nam Jung Hwan Nam Yul-Ho Kim Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.
description	Tartary buckwheat (Fagopyrum tataricum Gartn.) is a highly functional crop that is poised to be the target of many future breeding efforts. The reliable ex situ conservation of various genetic resources is essential for the modern breeding of tartary buckwheat varieties. We developed PCR-based co-dominant insertion/deletion (InDel) markers to discriminate tartary buckwheat genetic resources. First, we obtained the whole genome from 26 accessions across a superscaffold-scale reference genome of 569.37 Mb for tartary buckwheat cv. "Daegwan 3-7." Next, 171,926 homogeneous and 53,755 heterogeneous InDels were detected by comparing 26 accessions with the "Daegwan 3-7" reference sequence. Of these, 100 candidate InDels ranging from 5-20 bp in length were chosen for validation, and 50 of them revealed polymorphisms between the 26 accessions and "Daegwan 3-7." The validated InDels were further tested through the assessment of their likelihood to give rise to a single or a few PCR products in 50 other accessions, covering most tartary buckwheat genome types. The major allele frequencies ranged from 0.5616 at the TB42 locus to 0.9863 at the TB48 locus, with the average PIC value of 0.1532 with a range of 0.0267-0.3712. To create a user-friendly system, the homology of the genotypes between and among the accessions were visualized in both one- (1D) and two-dimensional (2D) barcode types by comparing amplicon polymorphisms with the reference variety, "Daegwan 3-7." A phylogenetic tree and population structure of the 76 accessions according to amplicon polymorphisms for the 50 InDel markers corresponded to those using non-synonymous single nucleotide polymorphism variants, indicating that the barcode system based on the 50 InDels was a useful tool to improve the reliability of identification of tartary buckwheat accessions in the germplasm stocks.
format	article
author	Hwang-Bae Sohn Su-Jeong Kim Su-Young Hong Sin-Gi Park Dong-Ha Oh Sunghoon Lee Hwa Yeun Nam Jung Hwan Nam Yul-Ho Kim
author_facet	Hwang-Bae Sohn Su-Jeong Kim Su-Young Hong Sin-Gi Park Dong-Ha Oh Sunghoon Lee Hwa Yeun Nam Jung Hwan Nam Yul-Ho Kim
author_sort	Hwang-Bae Sohn
title	Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.
title_short	Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.
title_full	Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.
title_fullStr	Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.
title_full_unstemmed	Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.
title_sort	development of 50 indel-based barcode system for genetic identification of tartary buckwheat resources.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/6082b95d40dd4da5a10dfe49d113c175
work_keys_str_mv	AT hwangbaesohn developmentof50indelbasedbarcodesystemforgeneticidentificationoftartarybuckwheatresources AT sujeongkim developmentof50indelbasedbarcodesystemforgeneticidentificationoftartarybuckwheatresources AT suyounghong developmentof50indelbasedbarcodesystemforgeneticidentificationoftartarybuckwheatresources AT singipark developmentof50indelbasedbarcodesystemforgeneticidentificationoftartarybuckwheatresources AT donghaoh developmentof50indelbasedbarcodesystemforgeneticidentificationoftartarybuckwheatresources AT sunghoonlee developmentof50indelbasedbarcodesystemforgeneticidentificationoftartarybuckwheatresources AT hwayeunnam developmentof50indelbasedbarcodesystemforgeneticidentificationoftartarybuckwheatresources AT junghwannam developmentof50indelbasedbarcodesystemforgeneticidentificationoftartarybuckwheatresources AT yulhokim developmentof50indelbasedbarcodesystemforgeneticidentificationoftartarybuckwheatresources
_version_	1718375604649197568

Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.

Ejemplares similares