Inferring defense-related gene families in Arabidopsis and wheat

Abstract 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...

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Main Authors: Rong-Cai Yang, Fred Y. Peng, Zhiqiu Hu
Format: Article
Language:English
Published: BMC 2017-12-01
Series:BMC Genomics
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12864-017-4381-3
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author Rong-Cai Yang
Fred Y. Peng
Zhiqiu Hu
author_facet Rong-Cai Yang
Fred Y. Peng
Zhiqiu Hu
author_sort Rong-Cai Yang
collection DOAJ
description Abstract 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.
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spelling doaj.art-0a15aeae22ba4515aebf5b9705e874ce2022-12-22T01:27:13ZengBMCBMC Genomics1471-21642017-12-0118111310.1186/s12864-017-4381-3Inferring defense-related gene families in Arabidopsis and wheatRong-Cai Yang0Fred Y. Peng1Zhiqiu Hu2Feed Crops Section, Alberta Agriculture and ForestryDepartment of Agricultural, Food and Nutritional Science, University of Alberta, 410 Agriculture/Forestry CentreFeed Crops Section, Alberta Agriculture and ForestryAbstract 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.http://link.springer.com/article/10.1186/s12864-017-4381-3Comparative genomicsArabidopsisArabidopsis thalianaGene familiesRust resistance genesDNA markers
spellingShingle Rong-Cai Yang
Fred Y. Peng
Zhiqiu Hu
Inferring defense-related gene families in Arabidopsis and wheat
BMC Genomics
Comparative genomics
Arabidopsis
Arabidopsis thaliana
Gene families
Rust resistance genes
DNA markers
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 Comparative genomics
Arabidopsis
Arabidopsis thaliana
Gene families
Rust resistance genes
DNA markers
url http://link.springer.com/article/10.1186/s12864-017-4381-3
work_keys_str_mv AT rongcaiyang inferringdefenserelatedgenefamiliesinarabidopsisandwheat
AT fredypeng inferringdefenserelatedgenefamiliesinarabidopsisandwheat
AT zhiqiuhu inferringdefenserelatedgenefamiliesinarabidopsisandwheat