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Logo of bmcpsBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Plant Biology
 
BMC Plant Biol. 2012; 12: 42.
Published online Mar 23, 2012. doi:  10.1186/1471-2229-12-42
PMCID: PMC3353201
Identification of expressed resistance gene-like sequences by data mining in 454-derived transcriptomic sequences of common bean (Phaseolus vulgaris L.)
Zhanji Liu,corresponding author1,2,5 Mollee Crampton,3,6 Antonette Todd,1 and Venu Kalavacharlacorresponding author1,4
1College of Agriculture & Related Sciences, Delaware State University, Dover, DE 19901, USA
2Hi-Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China
3Department of Biological Sciences, Delaware State University, Dover, DE 19901, USA
4Center of Integrated Biological and Environmental Research (CIBER), Delaware State University, Dover, DE 19901, USA
5Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
6Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA
corresponding authorCorresponding author.
Zhanji Liu: zliu/at/uga.edu; Mollee Crampton: mcrampto/at/udel.edu; Antonette Todd: atodd/at/desu.edu; Venu Kalavacharla: vkalavacharla/at/desu.edu
Received August 24, 2011; Accepted March 23, 2012.
Abstract
Background
Common bean (Phaseolus vulgaris L.) is one of the most important legumes in the world. Several diseases severely reduce bean production and quality; therefore, it is very important to better understand disease resistance in common bean in order to prevent these losses. More than 70 resistance (R) genes which confer resistance against various pathogens have been cloned from diverse plant species. Most R genes share highly conserved domains which facilitates the identification of new candidate R genes from the same species or other species. The goals of this study were to isolate expressed R gene-like sequences (RGLs) from 454-derived transcriptomic sequences and expressed sequence tags (ESTs) of common bean, and to develop RGL-tagged molecular markers.
Results
A data-mining approach was used to identify tentative P. vulgaris R gene-like sequences from approximately 1.69 million 454-derived sequences and 116,716 ESTs deposited in GenBank. A total of 365 non-redundant sequences were identified and named as common bean (P. vulgaris = Pv) resistance gene-like sequences (PvRGLs). Among the identified PvRGLs, about 60% (218 PvRGLs) were from 454-derived sequences. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis confirmed that PvRGLs were actually expressed in the leaves of common bean. Upon comparison to P. vulgaris genomic sequences, 105 (28.77%) of the 365 tentative PvRGLs could be integrated into the existing common bean physical map. Based on the syntenic blocks between common bean and soybean, 237 (64.93%) PvRGLs were anchored on the P. vulgaris genetic map and will need to be mapped to determine order. In addition, 11 sequence-tagged-site (STS) and 19 cleaved amplified polymorphic sequence (CAPS) molecular markers were developed for 25 unique PvRGLs.
Conclusions
In total, 365 PvRGLs were successfully identified from 454-derived transcriptomic sequences and ESTs available in GenBank and about 65% of PvRGLs were integrated into the common bean genetic map. A total of 30 RGL-tagged markers were developed for 25 unique PvRGLs, including 11 STS and 19 CAPS markers. The expressed PvRGLs identified in this study provide a large sequence resource for development of RGL-tagged markers that could be used further for genetic mapping of disease resistant candidate genes and quantitative trait locus/loci (QTLs). This work also represents an additional method for identifying expressed RGLs from next generation sequencing data.
Keywords: Common bean (Phaseolus vulgaris L.), 454 pyrosequencing, ESTs, Resistance gene-like sequences, Molecular markers
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