Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla: Isolation, RFLP marker development, and physical mapping

<p>Abstract</p> <p>Background</p> <p>Many commercial banana varieties lack sources of resistance to pests and diseases, as a consequence of sterility and narrow genetic background. Fertile wild relatives, by contrast, possess greater variability and represent potential sources of disease resistance genes (R-genes). The largest known family of plant R-genes encode proteins with nucleotide-binding site (NBS) and C-terminal leucine-rich repeat (LRR) domains. Conserved motifs in such genes in diverse plant species offer a means for isolation of candidate genes in banana which may be involved in plant defence.</p> <p>Results</p> <p>A computational strategy was developed for unbiased conserved motif discovery in NBS and LRR domains in R-genes and homologues in monocotyledonous plant species. Degenerate PCR primers targeting conserved motifs were tested on the wild cultivar <it>Musa acuminata </it>subsp. <it>burmannicoides</it>, var. Calcutta 4, which is resistant to a number of fungal pathogens and nematodes. One hundred and seventy four resistance gene analogs (RGAs) were amplified and assembled into 52 contiguous sequences. Motifs present were typical of the non-TIR NBS-LRR RGA subfamily. A phylogenetic analysis of deduced amino-acid sequences for 33 RGAs with contiguous open reading frames (ORFs), together with RGAs from <it>Arabidopsis thaliana </it>and <it>Oryza sativa</it>, grouped most <it>Musa </it>RGAs within monocotyledon-specific clades. RFLP-RGA markers were developed, with 12 displaying distinct polymorphisms in parentals and F1 progeny of a diploid <it>M. acuminata </it>mapping population. Eighty eight BAC clones were identified in <it>M. acuminata </it>Calcutta 4, <it>M. acuminata </it>Grande Naine, and <it>M. balbisiana </it>Pisang Klutuk Wulung BAC libraries when hybridized to two RGA probes. Multiple copy RGAs were common within BAC clones, potentially representing variation reservoirs for evolution of new R-gene specificities.</p> <p>Conclusion</p> <p>This is the first large scale analysis of NBS-LRR RGAs in <it>M. acuminata </it>Calcutta 4. Contig sequences were deposited in GenBank and assigned numbers <ext-link ext-link-type="gen" ext-link-id="ER935972">ER935972</ext-link> – <ext-link ext-link-type="gen" ext-link-id="ER936023">ER936023</ext-link>. RGA sequences and isolated BACs are a valuable resource for R-gene discovery, and in future applications will provide insight into the organization and evolution of NBS-LRR R-genes in the <it>Musa </it>A and B genome. The developed RFLP-RGA markers are applicable for genetic map development and marker assisted selection for defined traits such as pest and disease resistance.</p

Insights into the Musa genome: Syntenic relationships to rice and between Musa species

<p>Abstract</p> <p>Background</p> <p><it>Musa </it>species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning <it>Musa </it>genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of <it>Musa </it>genomic sequence have been conducted. This study compares genomic sequence in two <it>Musa </it>species with orthologous regions in the rice genome.</p> <p>Results</p> <p>We produced 1.4 Mb of <it>Musa </it>sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for <it>Musa</it>-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the <it>Musa </it>lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from <it>M. acuminata </it>and <it>M. balbisiana </it>revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya.</p> <p>Conclusion</p> <p>These results point to the utility of comparative analyses between distantly-related monocot species such as rice and <it>Musa </it>for improving our understanding of monocot genome evolution. Sequencing the genome of <it>M. acuminata </it>would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated <it>Musa </it>polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.</p

Insights into the Musa genome: Syntenic relationships to rice and between Musa species-2

hypothetical genes are represented in white. The probe used to identify the BAC clones is indicated in brackets. Conserved genes between the two regions are connected by shaded areas. (A) Dot plot analysis of the two pairs of homeologous BACs from and .(B) Diagram of the syntenic regions between the two BAC clones.<p><b>Copyright information:</b></p><p>Taken from "Insights into the Musa genome: Syntenic relationships to rice and between Musa species"</p><p>http://www.biomedcentral.com/1471-2164/9/58</p><p>BMC Genomics 2008;9():58-58.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270835.</p><p></p

Insights into the Musa genome: Syntenic relationships to rice and between Musa species-0

hypothetical genes are represented in white. The probes used to identify the BAC clones are indicated in brackets. Conserved genes between and rice regions are connected by shaded areas. (A) Syntenic relationship between MBP_91N22 BAC clone and rice chromosome 1. (B) Syntenic relationship between MA4_25J11 BAC clone and rice chromosome 1 and 5. The numbers above the genes correspond to the locus numbers used for phylogenetic analyses. (C) Syntenic relationship between MA4_8L21 BAC clone and rice chromosome 3.<p><b>Copyright information:</b></p><p>Taken from "Insights into the Musa genome: Syntenic relationships to rice and between Musa species"</p><p>http://www.biomedcentral.com/1471-2164/9/58</p><p>BMC Genomics 2008;9():58-58.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270835.</p><p></p

Insights into the Musa genome: Syntenic relationships to rice and between Musa species-3

Extensive event pre-dating the ginger-or rice-divergences.<p><b>Copyright information:</b></p><p>Taken from "Insights into the Musa genome: Syntenic relationships to rice and between Musa species"</p><p>http://www.biomedcentral.com/1471-2164/9/58</p><p>BMC Genomics 2008;9():58-58.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270835.</p><p></p

Insights into the Musa genome: Syntenic relationships to rice and between Musa species-1

Rs are taken from Figure 5B. Stars indicate duplication events in the most recent common ancestor of major grain lineages (i.e. rice, wheat and maize). MA4_25J11 BAC clone was isolated by the SbRPG132 probe.<p><b>Copyright information:</b></p><p>Taken from "Insights into the Musa genome: Syntenic relationships to rice and between Musa species"</p><p>http://www.biomedcentral.com/1471-2164/9/58</p><p>BMC Genomics 2008;9():58-58.</p><p>Published online 30 Jan 2008</p><p>PMCID:PMC2270835.</p><p></p