Genome-wide mapping of NBS-LRR genes and their association with disease resistance in soybean

BackgroundR genes are a key component of genetic interactions between plants and biotrophic bacteria and are known to regulate resistance against bacterial invasion. The most common R proteins contain a nucleotide-binding site and a leucine-rich repeat (NBS-LRR) domain. Some NBS-LRR genes in the soybean genome have also been reported to function in disease resistance. In this study, the number of NBS-LRR genes was found to correlate with the number of disease resistance quantitative trait loci (QTL) that flank these genes in each chromosome. NBS-LRR genes co-localized with disease resistance QTL. The study also addressed the functional redundancy of disease resistance on recently duplicated regions that harbor NBS-LRR genes and NBS-LRR gene expression in the bacterial leaf pustule (BLP)-induced soybean transcriptome.ResultsA total of 319 genes were determined to be putative NBS-LRR genes in the soybean genome. The number of NBS-LRR genes on each chromosome was highly correlated with the number of disease resistance QTL in the 2-Mb flanking regions of NBS-LRR genes. In addition, the recently duplicated regions contained duplicated NBS-LRR genes and duplicated disease resistance QTL, and possessed either an uneven or even number of NBS-LRR genes on each side. The significant difference in NBS-LRR gene expression between a resistant near-isogenic line (NIL) and a susceptible NIL after inoculation of Xanthomonas axonopodis pv. glycines supports the conjecture that NBS-LRR genes have disease resistance functions in the soybean genome.ConclusionsThe number of NBS-LRR genes and disease resistance QTL in the 2-Mb flanking regions of each chromosome was significantly correlated, and several recently duplicated regions that contain NBS-LRR genes harbored disease resistance QTL for both sides. In addition, NBS-LRR gene expression was significantly different between the BLP-resistant NIL and the BLP-susceptible NIL in response to bacterial infection. From these observations, NBS-LRR genes are suggested to contribute to disease resistance in soybean. Moreover, we propose models for how NBS-LRR genes were duplicated, and apply Ks values for each NBS-LRR gene cluster.

[1]  T. Galitski,et al.  Rearrangements of the Bacterial Chromosome : Formation and Applications , 1999 .

[2]  P. Langridge,et al.  Barley disease resistance gene analogs of the NBS-LRR class: identification and mapping , 2003, Molecular Genetics and Genomics.

[3]  Jonathan D. G. Jones,et al.  The plant immune system , 2006, Nature.

[4]  K. Kim,et al.  Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean1[C][W] , 2009, Plant Physiology.

[5]  T. Joshi,et al.  Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. , 2008, Molecular plant-microbe interactions : MPMI.

[6]  R. Michelmore,et al.  The Major Resistance Gene Cluster in Lettuce Is Highly Duplicated and Spans Several Megabases , 1998, Plant Cell.

[7]  J. R. Lobry,et al.  SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis , 2007 .

[8]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[9]  D. V. Phillips,et al.  Molecular mapping of Rxp conditioning reaction to bacterial pustule in soybean. , 2001, The Journal of heredity.

[10]  Jonathan D. G. Jones,et al.  Plant pathogens and integrated defence responses to infection , 2001, Nature.

[11]  R. Shoemaker,et al.  Genetic and physical localization of the soybean Rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of NBS-LRR genes. , 2003, Molecular plant-microbe interactions : MPMI.

[12]  Blake C. Meyers,et al.  Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009308. , 2003, The Plant Cell Online.

[13]  R. Visser,et al.  A genome-wide genetic map of NB-LRR disease resistance loci in potato , 2011, Theoretical and Applied Genetics.

[14]  Steven B. Cannon,et al.  SoyBase, the USDA-ARS soybean genetics and genomics database , 2009, Nucleic Acids Res..

[15]  M. Yoon,et al.  RNA-Seq Analysis of a Soybean Near-Isogenic Line Carrying Bacterial Leaf Pustule-Resistant and -Susceptible Alleles , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

[16]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[17]  R. Michelmore,et al.  Erratum: Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis (Plant Cell (2003) 15 (809-834)) , 2003 .

[18]  S. Kamoun,et al.  From Guard to Decoy: A New Model for Perception of Plant Pathogen Effectors , 2008, The Plant Cell Online.

[19]  T. Sakurai,et al.  Genome sequence of the palaeopolyploid soybean , 2010, Nature.

[20]  H. Krishnan,et al.  R gene-controlled host specificity in the legume–rhizobia symbiosis , 2010, Proceedings of the National Academy of Sciences.

[21]  Haibao Tang,et al.  Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny. , 2011, The New phytologist.

[22]  U. Bastolla,et al.  Structural approaches to sequence evolution : molecules, networks, populations , 2007 .

[23]  C. Durel,et al.  Resistance gene analogues identified through the NBS-profiling method map close to major genes and QTL for disease resistance in apple , 2005, Theoretical and Applied Genetics.

[24]  R. Shoemaker,et al.  Genome duplication in soybean (Glycine subgenus soja). , 1996, Genetics.

[25]  T. Shindo,et al.  Fungal Effector Protein AVR2 Targets Diversifying Defense-Related Cys Proteases of Tomato[W] , 2008, The Plant Cell Online.

[26]  Hh Flor,et al.  Host-parasite interaction in flax rust–its genetics and other implications , 1955 .

[27]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[28]  P. Cregan,et al.  Bulked Segregant Analysis Using the GoldenGate Assay to Locate the Rpp3 Locus that Confers Resistance to Soybean Rust in Soybean , 2009 .

[29]  J. Hacker,et al.  Ecological fitness, genomic islands and bacterial pathogenicity , 2001, EMBO reports.

[30]  G. Hartman,et al.  Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and In Silico Mapping in Relation to Resistance Markers , 2009 .

[31]  E. Neidle,et al.  Selection for gene clustering by tandem duplication. , 2003, Annual review of microbiology.