SNPs, InDels, and Microsatellites within and Near to Rice NBS-LRR Resistance Gene Candidates

Plant resistance genes (R-genes) drive the immune responses of crops against specific pathotypes of disease-causing organisms. Over time, genetic diversity in R-genes and R-pseudogenes has arisen among different rice varieties. This bioinformatics study was carried out to (i) predict the full sets o...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Mark J. Quinton-Tulloch, Katherine A. Steele
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	pathogen resistance NBS-LRR NLR <i>Oryza sativa</i> rice blast Agriculture S
Acceso en línea:	https://doaj.org/article/3ca78f0cd5e443fa9a1b40d231164068
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:3ca78f0cd5e443fa9a1b40d231164068
record_format	dspace
spelling	oai:doaj.org-article:3ca78f0cd5e443fa9a1b40d2311640682021-11-25T16:10:47ZSNPs, InDels, and Microsatellites within and Near to Rice NBS-LRR Resistance Gene Candidates10.3390/agronomy111122972073-4395https://doaj.org/article/3ca78f0cd5e443fa9a1b40d2311640682021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4395/11/11/2297https://doaj.org/toc/2073-4395Plant resistance genes (R-genes) drive the immune responses of crops against specific pathotypes of disease-causing organisms. Over time, genetic diversity in R-genes and R-pseudogenes has arisen among different rice varieties. This bioinformatics study was carried out to (i) predict the full sets of candidate nucleotide-binding site leucine-rich repeat (NLR) R-genes present in six rice genomes; (ii) detect variation within candidate R-genes; (iii) identify potential selectable markers within and near to LRR genes among 75 diverse <i>indica</i> rice genomes. Four high quality <i>indica</i> genomes, plus the standard <i>japonica</i> and <i>indica</i> reference genomes, were analysed with widely available bioinformatic tools to identify candidate R-genes and R-pseudogenes. They were detected in clusters, consistent with previous studies. BLAST analysis of cloned protein sequences of 31 R-gene loci gave confidence in this approach for detection of cloned NLR R-genes. Approximately 10% of candidate R-genes were located within 1 kb of a microsatellite (SSR) marker. Sequence comparisons among <i>indica</i> rice genomes detected SNPs or InDels in 334 candidate rice R-genes. There were significantly more SNPs and InDels within the identified NLR R-gene candidates than in other types of gene. The genome-wide locations of candidate R-genes and their associated markers are presented here for the potential future development of improved disease-resistant varieties. Limitations of in silico approaches used for R-gene discovery are discussed.Mark J. Quinton-TullochKatherine A. SteeleMDPI AGarticlepathogenresistanceNBS-LRRNLR<i>Oryza sativa</i>rice blastAgricultureSENAgronomy, Vol 11, Iss 2297, p 2297 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	pathogen resistance NBS-LRR NLR <i>Oryza sativa</i> rice blast Agriculture S
spellingShingle	pathogen resistance NBS-LRR NLR <i>Oryza sativa</i> rice blast Agriculture S Mark J. Quinton-Tulloch Katherine A. Steele SNPs, InDels, and Microsatellites within and Near to Rice NBS-LRR Resistance Gene Candidates
description	Plant resistance genes (R-genes) drive the immune responses of crops against specific pathotypes of disease-causing organisms. Over time, genetic diversity in R-genes and R-pseudogenes has arisen among different rice varieties. This bioinformatics study was carried out to (i) predict the full sets of candidate nucleotide-binding site leucine-rich repeat (NLR) R-genes present in six rice genomes; (ii) detect variation within candidate R-genes; (iii) identify potential selectable markers within and near to LRR genes among 75 diverse <i>indica</i> rice genomes. Four high quality <i>indica</i> genomes, plus the standard <i>japonica</i> and <i>indica</i> reference genomes, were analysed with widely available bioinformatic tools to identify candidate R-genes and R-pseudogenes. They were detected in clusters, consistent with previous studies. BLAST analysis of cloned protein sequences of 31 R-gene loci gave confidence in this approach for detection of cloned NLR R-genes. Approximately 10% of candidate R-genes were located within 1 kb of a microsatellite (SSR) marker. Sequence comparisons among <i>indica</i> rice genomes detected SNPs or InDels in 334 candidate rice R-genes. There were significantly more SNPs and InDels within the identified NLR R-gene candidates than in other types of gene. The genome-wide locations of candidate R-genes and their associated markers are presented here for the potential future development of improved disease-resistant varieties. Limitations of in silico approaches used for R-gene discovery are discussed.
format	article
author	Mark J. Quinton-Tulloch Katherine A. Steele
author_facet	Mark J. Quinton-Tulloch Katherine A. Steele
author_sort	Mark J. Quinton-Tulloch
title	SNPs, InDels, and Microsatellites within and Near to Rice NBS-LRR Resistance Gene Candidates
title_short	SNPs, InDels, and Microsatellites within and Near to Rice NBS-LRR Resistance Gene Candidates
title_full	SNPs, InDels, and Microsatellites within and Near to Rice NBS-LRR Resistance Gene Candidates
title_fullStr	SNPs, InDels, and Microsatellites within and Near to Rice NBS-LRR Resistance Gene Candidates
title_full_unstemmed	SNPs, InDels, and Microsatellites within and Near to Rice NBS-LRR Resistance Gene Candidates
title_sort	snps, indels, and microsatellites within and near to rice nbs-lrr resistance gene candidates
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/3ca78f0cd5e443fa9a1b40d231164068
work_keys_str_mv	AT markjquintontulloch snpsindelsandmicrosatelliteswithinandneartoricenbslrrresistancegenecandidates AT katherineasteele snpsindelsandmicrosatelliteswithinandneartoricenbslrrresistancegenecandidates
_version_	1718413310924161024

SNPs, InDels, and Microsatellites within and Near to Rice NBS-LRR Resistance Gene Candidates

Ejemplares similares