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.

Alleles or tightly linked genes at the soybean (Glycine max L. Merr.) Rpg1 locus confer resistance to strains of Pseudomonas syringae pv. glycinea that express the avirulence genes avrB or avrRpm1. We have previously mapped Rpg1-b (the gene specific for avrB) to a cluster of resistance genes (R genes) with diverse specificities in molecular linkage group F. Here, we describe the high-resolution physical and genetic mapping of Rpg1-b to a 0.16-cM interval encompassed by two overlapping BAC clones spanning approximately 270 kilobases. Rpg1-b is part of a complex locus containing numerous genes related to previously characterized coiled coil-nucleotide binding site-leucine rich repeat (CC-NBS-LRR)-type R genes that are spread throughout this region. Phylogenetic and Southern blot analyses group these genes into four distinct subgroups, some of which are conserved in the common bean, Phaseolus vulgaris, indicating that this R gene cluster may predate the divergence of Phaseolus and Glycine. Members from different subgroups are physically intermixed and display a high level of polymorphism between soybean cultivars, suggesting that this region is rearranging at a high frequency. At least five CC-NBS-LRR-type genes cosegregate with Rpg1-b in our large mapping populations.

Ashfield T ，Bocian A ，Held D ，Henk AD ，Marek LF ，Danesh D ，Peñuela S ，Meksem K ，Lightfoot DA ，Young ND ，Shoemaker RC ，Innes RW ... -  《MOLECULAR PLANT-MICROBE INTERACTIONS》

Targeted isolation, sequence analysis, and physical mapping of nonTIR NBS-LRR genes in soybean.

Most cloned plant disease resistance genes (R-genes) code for proteins belonging to the nucleotide binding site (NBS) leucine-rich repeat (LRR) superfamily. NBS-LRRs can be divided into two classes based on the presence of a TIR domain ( Toll and interleukin receptor-like sequence) or a coiled coil motif (nonTIR) in their N-terminus. We used conserved motifs specific to nonTIR-NBS-LRR sequences in a targeted PCR approach to generate nearly 50 genomic soybean sequences with strong homology to known resistance gene analogs (RGAs) of the nonTIR class. Phylogenetic analysis classified these sequences into four main subclasses. A representative clone from each subclass was used for genetic mapping, bacterial artificial chromosome (BAC) library screening, and construction of RGA-containing BAC contigs. Of the 14 RGAs that could be mapped genetically, 12 localized to a 25-cM region of soybean linkage group F already known to contain several classical disease resistance loci. A majority of the genomic region encompassing the RGAs was physically isolated in eight BAC contigs, together spanning more than 1 Mb of genomic sequence with at least 12 RGA copies. Phylogenetic and sequence analysis, together with genetic and physical mapping, provided insights into the genome organization and evolution of this large cluster of soybean RGAs.

Peñuela S ，Danesh D ，Young ND 《-》

Two classes of highly similar coiled coil-nucleotide binding-leucine rich repeat genes isolated from the Rps1-k locus encode Phytophthora resistance in soybean.

A series of single genes protect soybean from the root and stem disease caused by the oomycete pathogen Phytophthora sojae. In the last two decades, Rps1-k has been the most stable and widely used Phytophthora resistance gene for the major soybean-producing regions of the United States. Four highly similar genes encoding coiled coil-nucleotide binding-leucine rich repeat (CC-NB-LRR)-type proteins were isolated from the Rps1-k locus. These genes were grouped into two classes based on their sequence identity. Class I contains three genes with identical open reading frames (ORF) and 5' end regions. Two of these genes were also identical at the 3' untranslated regions; the third gene showed a recombination breakpoint in the 3' untranslated region resulting in the combination of 3' end sequences of members from both classes. Reverse transcription-polymerase chain reaction analyses suggested that members of both classes of genes are transcribed at low levels. Representative members from each gene class were expressed in transgenic soybean plants. Analyses of independent R0, R1, R2, and R3 progeny populations suggested that both gene classes confer Phytophthora resistance in soybean. A possible evolutionary mechanism for the Class I gene family is proposed.

Gao H ，Narayanan NN ，Ellison L ，Bhattacharyya MK ... -  《MOLECULAR PLANT-MICROBE INTERACTIONS》

Identification of a large cluster of coiled coil-nucleotide binding site--leucine rich repeat-type genes from the Rps1 region containing Phytophthora resistance genes in soybean.

Fifteen Rps genes confer resistance against the oomycete pathogen Phytophthora sojae, which causes root and stem rot disease in soybean. We have isolated a disease resistance gene-like sequence from the genomic region containing Rps1-k. Four classes of cDNA of the sequence were isolated from etiolated hypocotyl tissues that express the Rps1-k-encoded Phytophthora resistance. Sequence analyses of a cDNA clone showed that the sequence is a member of the coiled coil-nucleotide binding site-leucine rich repeat (CC-NBS-LRR)-type of disease resistance genes. It showed 36% identity to the recently cloned soybean resistance gene Rpg1-b, which confers resistance against Pseudomonas syringae pv. glycinea, and 56% and 38% sequence identity to putative resistance gene sequences from lotus and Medicago truncatula, respectively. The soybean genome contains about 38 copies of the sequence. Most of these copies are clustered in approximately 600 kb of contiguous DNA of the Rps1-k region. We have identified a recombinant that carries both rps1-k- and Rps1-k-haplotype-specific allelomorphs of two Rps1-k-linked molecular markers. An unequal crossover event presumably led to duplication of alleles for these two physically linked molecular markers. We hypothesize that the unequal crossing over was one of the mechanisms involved in tandem duplication of CC-NBS-LRR sequences in the Rps1-k region.

Bhattacharyya MK ，Narayanan NN ，Gao H ，Santra DK ，Salimath SS ，Kasuga T ，Liu Y ，Espinosa B ，Ellison L ，Marek L ，Shoemaker R ，Gijzen M ，Buzzell RI ... -  《THEORETICAL AND APPLIED GENETICS》

Convergent evolution of disease resistance gene specificity in two flowering plant families.

Plant disease resistance (R) genes that mediate recognition of the same pathogen determinant sometimes can be found in distantly related plant families. This observation implies that some R gene alleles may have been conserved throughout the diversification of land plants. To address this question, we have compared R genes from Glycine max (soybean), Rpg1-b, and Arabidopsis thaliana, RPM1, that mediate recognition of the same type III effector protein from Pseudomonas syringae, AvrB. RPM1 has been cloned previously, and here, we describe the isolation of Rpg1-b. Although RPM1 and Rpg1-b both belong to the coiled-coil nucleotide binding site (NBS) Leu-rich repeat (LRR) class of R genes, they share only limited sequence similarity outside the conserved domains characteristic of this class. Phylogenetic analyses of A. thaliana and legume NBS-LRR sequences demonstrate that Rpg1-b and RPM1 are not orthologous. We conclude that convergent evolution, rather than the conservation of an ancient specificity, is responsible for the generation of these AvrB-specific genes.

Ashfield T ，Ong LE ，Nobuta K ，Schneider CM ，Innes RW ... -  《-》