Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species

Abstract Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservo...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Sherry Lou Hechanova, Kamal Bhattarai, Eliza Vie Simon, Graciana Clave, Pathmasiri Karunarathne, Eok-Keun Ahn, Charng-Pei Li, Jeom-Sig Lee, Ajay Kohli, N. Ruaraidh Sackville Hamilton, Jose E. Hernandez, Glenn B. Gregorio, Kshirod K. Jena, Gynheung An, Sung-Ryul Kim
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d48831a00667446098ff3792b50824c4
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:d48831a00667446098ff3792b50824c4
record_format	dspace
spelling	oai:doaj.org-article:d48831a00667446098ff3792b50824c42021-12-02T16:55:53ZDevelopment of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species10.1038/s41598-021-88533-92045-2322https://doaj.org/article/d48831a00667446098ff3792b50824c42021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88533-9https://doaj.org/toc/2045-2322Abstract Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservoir” for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.Sherry Lou HechanovaKamal BhattaraiEliza Vie SimonGraciana ClavePathmasiri KarunarathneEok-Keun AhnCharng-Pei LiJeom-Sig LeeAjay KohliN. Ruaraidh Sackville HamiltonJose E. HernandezGlenn B. GregorioKshirod K. JenaGynheung AnSung-Ryul KimNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sherry Lou Hechanova Kamal Bhattarai Eliza Vie Simon Graciana Clave Pathmasiri Karunarathne Eok-Keun Ahn Charng-Pei Li Jeom-Sig Lee Ajay Kohli N. Ruaraidh Sackville Hamilton Jose E. Hernandez Glenn B. Gregorio Kshirod K. Jena Gynheung An Sung-Ryul Kim Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species
description	Abstract Wild relatives of rice in the genus Oryza (composed of 24 species with 11 different genome types) have been significantly contributing to the varietal improvement of rice (Oryza sativa). More than 4000 accessions of wild rice species are available and they are regarded as a “genetic reservoir” for further rice improvement. DNA markers are essential tools in genetic analysis and breeding. To date, genome-wide marker sets for wild rice species have not been well established and this is one of the major difficulties for the efficient use of wild germplasm. Here, we developed 541 genome-wide InDel markers for the discrimination of alleles between the cultivated species O. sativa and the other seven AA-genome species by positional multiple sequence alignments among five AA-genome species with four rice varieties. The newly developed markers were tested by PCR-agarose gel analysis of 24 accessions from eight AA genome species (three accessions per species) along with two representative cultivars (O. sativa subsp. indica cv. IR24 and subsp. japonica cv. Nipponbare). Marker polymorphism was validated for 475 markers. The number of polymorphic markers between IR24 and each species (three accessions) ranged from 338 (versus O. rufipogon) to 416 (versus O. longistaminata) and the values in comparison with Nipponbare ranged from 179 (versus O. glaberrima) to 323 (versus O. glumaepatula). These marker sets will be useful for genetic studies and use of the AA-genome wild rice species.
format	article
author	Sherry Lou Hechanova Kamal Bhattarai Eliza Vie Simon Graciana Clave Pathmasiri Karunarathne Eok-Keun Ahn Charng-Pei Li Jeom-Sig Lee Ajay Kohli N. Ruaraidh Sackville Hamilton Jose E. Hernandez Glenn B. Gregorio Kshirod K. Jena Gynheung An Sung-Ryul Kim
author_facet	Sherry Lou Hechanova Kamal Bhattarai Eliza Vie Simon Graciana Clave Pathmasiri Karunarathne Eok-Keun Ahn Charng-Pei Li Jeom-Sig Lee Ajay Kohli N. Ruaraidh Sackville Hamilton Jose E. Hernandez Glenn B. Gregorio Kshirod K. Jena Gynheung An Sung-Ryul Kim
author_sort	Sherry Lou Hechanova
title	Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species
title_short	Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species
title_full	Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species
title_fullStr	Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species
title_full_unstemmed	Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species
title_sort	development of a genome-wide indel marker set for allele discrimination between rice (oryza sativa) and the other seven aa-genome oryza species
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/d48831a00667446098ff3792b50824c4
work_keys_str_mv	AT sherrylouhechanova developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT kamalbhattarai developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT elizaviesimon developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT gracianaclave developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT pathmasirikarunarathne developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT eokkeunahn developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT charngpeili developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT jeomsiglee developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT ajaykohli developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT nruaraidhsackvillehamilton developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT joseehernandez developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT glennbgregorio developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT kshirodkjena developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT gynheungan developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies AT sungryulkim developmentofagenomewideindelmarkersetforallelediscriminationbetweenriceoryzasativaandtheothersevenaagenomeoryzaspecies
_version_	1718382829161676800

Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa) and the other seven AA-genome Oryza species

Ejemplares similares