Abstract
BackgroundCommon 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.ResultsA 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.ConclusionsIn 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.
Highlights
Common bean (Phaseolus vulgaris L.) is one of the most important legumes in the world
A total of 259 contigs and nine singletons from 454-derived sequences and 629 common bean expressed sequence tags (ESTs) were identified with scores more than or equal to 100 and E values less than or equal to 1e-10
The average size of PvRGLs was about 1,110 base pairs, some fragments were 2,500 base pairs or longer. Among these 365 tentative PvRGLs, 166 (45.48%) PvRGLs were from 454-derived sequences, 147 (40.27%) were from common bean ESTs, and 52 (14.25%) PvRGLs were present in both of the groups (See Additional file 2: Characterization of 365 tentative PvRGLs)
Summary
Common bean (Phaseolus vulgaris L.) is one of the most important legumes in the world. Based on the amino acid sequence comparison among cloned R genes, several highly conserved domains, such as NBS, LRR, protein kinase (PK), transmembrane domain (TM), and TIR were identified as the majority of known R genes [6,7,8,9]. These distinct conserved domains provide scientists a convenient way to identify and clone additional R genes and RGLs or resistance gene analogs (RGAs). The fifth class includes all other R genes that confer resistance through different mechanisms, for example, Hm1 in maize and mlo in barley [3,17]
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