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EST-Based Approach for Dissecting Root Architecture in Barley Using Mutant Traits of Other Species

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Root Genomics

Abstract

During the past decades, a considerable number of genes and gene networks have been well described in the model species Arabidopsis thaliana. This knowledge can be adapted for more complex plant systems as barley, rice, or maize. Despite their agronomic importance, only a little is known about molecular basis of root formation in crop species, and only few mutants together with corresponding genes have been well characterized. In order to approach the large crop genomes, several projects have generated enormous number of expressed sequence tags (ESTs), which presumably represent most of the particular genome transcripts. In this chapter, we describe the approach undertaken to search for potential orthologous genes involved in root morphogenesis between Arabidopsis, rice, and barley. In silico analyses, which combine similarity, phylogeny, and syntheny-based approaches, have been performed. Based on a literature search for genes responsible for root growth and development, a total number of 259 genes in Arabidopsis and 35 genes in monocotyledons have been selected. Taking into account the appropriate barley ESTs coverage, the collection of 49 Arabidopsis and 10 monocot genes have been chosen and proposed to be good candidates for molecular cloning in barley. From that, 22 Arabidopsis genes were involved in lateral root (LR) formation, 19 genes in primary root development, and eight genes in root hair formation. Out of 21 monocotyledonous genes, for which the sequence was publicly available, we selected six rice, two corn, and two wheat genes. The arrangement of exon/intron positions of the selected Arabidopsis and rice genes revealed a high level of conservation. These comprehensive gene lists provide strong platform for molecular studies and will accelerate gene identification in barley and related species.

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Authors and Affiliations

  1. Department of Genetics, Silesian University, Katowice, Poland

    Beata Orman, Aleksander Ligeza, Iwona Szarejko & Miroslaw Maluszynski

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  1. Beata Orman
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  2. Aleksander Ligeza
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  3. Iwona Szarejko
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  4. Miroslaw Maluszynski
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Correspondence to Iwona Szarejko .

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  1. Centro de Genômica e, Fitomelhoramento (CGF), Universidade Federal de Pelotas (UFPel), Pelotas, 96001-970, Rio Grande do Sul, Brazil

    Antonio Costa de Oliveira

  2. ICRISAT, Centre of Excellence in Genomics (CEG), Patancheru, 502 324, Andra Pradesh, India

    Rajeev K. Varshney

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Orman, B., Ligeza, A., Szarejko, I., Maluszynski, M. (2011). EST-Based Approach for Dissecting Root Architecture in Barley Using Mutant Traits of Other Species. In: Costa de Oliveira, A., Varshney, R. (eds) Root Genomics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85546-0_2

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