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Inferring defense-related gene families in Arabidopsis and wheat

BACKGROUND: A large number of disease resistance genes or QTLs in crop plants are identified through conventional genetics and genomic tools, but their functional or molecular characterization remains costly, labor-intensive and inaccurate largely due to the lack of deep sequencing of large and comp...

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Autores principales: Yang, Rong-Cai, Peng, Fred Y., Hu, Zhiqiu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738178/
https://www.ncbi.nlm.nih.gov/pubmed/29258426
http://dx.doi.org/10.1186/s12864-017-4381-3
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author Yang, Rong-Cai
Peng, Fred Y.
Hu, Zhiqiu
author_facet Yang, Rong-Cai
Peng, Fred Y.
Hu, Zhiqiu
author_sort Yang, Rong-Cai
collection PubMed
description BACKGROUND: A large number of disease resistance genes or QTLs in crop plants are identified through conventional genetics and genomic tools, but their functional or molecular characterization remains costly, labor-intensive and inaccurate largely due to the lack of deep sequencing of large and complex genomes of many important crops such as allohexaploid wheat (Triticum aestivum L.). On the other hand, gene annotation and relevant genomic resources for disease resistance and other defense-related traits are more abundant in model plant Arabidopsis (Arabidopsis thaliana). The objectives of this study are (i) to infer homology of defense-related genes in Arabidopsis and wheat and (ii) to classify these homologous genes into different gene families. RESULTS: We employed three bioinformatics and genomics approaches to identifying candidate genes known to affect plant defense and to classifying these protein-coding genes into different gene families in Arabidopsis. These approaches predicted up to 1790 candidate genes in 11 gene families for Arabidopsis defense to biotic stresses. The 11 gene families included ABC, NLR and START, the three families that are already known to confer rust resistance in wheat, and eight new families. The distributions of predicted SNPs for individual rust resistance genes were highly skewed towards specific gene families, including eight one-to-one uniquely matched pairs: Lr21-NLR, Lr34-ABC, Lr37-START, Sr2-Cupin, Yr24-Transcription factor, Yr26-Transporter, Yr36-Kinase and Yr53-Kinase. Two of these pairs, Lr21-NLR and Lr34-ABC, are expected because Lr21 and Lr34 are well known to confer race-specific and race-nonspecific resistance to leaf rust (Puccinia triticina) and they encode NLR and ABC proteins. CONCLUSIONS: Our inference of 11 known and new gene families enhances current understanding of functional diversity with defense-related genes in genomes of model plant Arabidopsis and cereal crop wheat. Our comparative genomic analysis of Arabidopsis and wheat genomes is complementary to the conventional map-based or marker-based approaches for identification of genes or QTLs for rust resistance genes in wheat and other cereals. Race-specific and race-nonspecific candidate genes predicted by our study may be further tested and combined in breeding for durable resistance to wheat rusts and other pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi: 10.1186/s12864-017-4381-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-57381782017-12-21 Inferring defense-related gene families in Arabidopsis and wheat Yang, Rong-Cai Peng, Fred Y. Hu, Zhiqiu BMC Genomics Research Article BACKGROUND: A large number of disease resistance genes or QTLs in crop plants are identified through conventional genetics and genomic tools, but their functional or molecular characterization remains costly, labor-intensive and inaccurate largely due to the lack of deep sequencing of large and complex genomes of many important crops such as allohexaploid wheat (Triticum aestivum L.). On the other hand, gene annotation and relevant genomic resources for disease resistance and other defense-related traits are more abundant in model plant Arabidopsis (Arabidopsis thaliana). The objectives of this study are (i) to infer homology of defense-related genes in Arabidopsis and wheat and (ii) to classify these homologous genes into different gene families. RESULTS: We employed three bioinformatics and genomics approaches to identifying candidate genes known to affect plant defense and to classifying these protein-coding genes into different gene families in Arabidopsis. These approaches predicted up to 1790 candidate genes in 11 gene families for Arabidopsis defense to biotic stresses. The 11 gene families included ABC, NLR and START, the three families that are already known to confer rust resistance in wheat, and eight new families. The distributions of predicted SNPs for individual rust resistance genes were highly skewed towards specific gene families, including eight one-to-one uniquely matched pairs: Lr21-NLR, Lr34-ABC, Lr37-START, Sr2-Cupin, Yr24-Transcription factor, Yr26-Transporter, Yr36-Kinase and Yr53-Kinase. Two of these pairs, Lr21-NLR and Lr34-ABC, are expected because Lr21 and Lr34 are well known to confer race-specific and race-nonspecific resistance to leaf rust (Puccinia triticina) and they encode NLR and ABC proteins. CONCLUSIONS: Our inference of 11 known and new gene families enhances current understanding of functional diversity with defense-related genes in genomes of model plant Arabidopsis and cereal crop wheat. Our comparative genomic analysis of Arabidopsis and wheat genomes is complementary to the conventional map-based or marker-based approaches for identification of genes or QTLs for rust resistance genes in wheat and other cereals. Race-specific and race-nonspecific candidate genes predicted by our study may be further tested and combined in breeding for durable resistance to wheat rusts and other pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi: 10.1186/s12864-017-4381-3) contains supplementary material, which is available to authorized users. BioMed Central 2017-12-19 /pmc/articles/PMC5738178/ /pubmed/29258426 http://dx.doi.org/10.1186/s12864-017-4381-3 Text en © The Author(s). 2017 Open AccessThis 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. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Yang, Rong-Cai
Peng, Fred Y.
Hu, Zhiqiu
Inferring defense-related gene families in Arabidopsis and wheat
title Inferring defense-related gene families in Arabidopsis and wheat
title_full Inferring defense-related gene families in Arabidopsis and wheat
title_fullStr Inferring defense-related gene families in Arabidopsis and wheat
title_full_unstemmed Inferring defense-related gene families in Arabidopsis and wheat
title_short Inferring defense-related gene families in Arabidopsis and wheat
title_sort inferring defense-related gene families in arabidopsis and wheat
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738178/
https://www.ncbi.nlm.nih.gov/pubmed/29258426
http://dx.doi.org/10.1186/s12864-017-4381-3
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