Downy Mildew and Rust Resistance Genes Are Interspersed in a Large Highly Duplicated Family of NBS-LRR Encoding Genes On Linkage Groups 1 and 13 of Sunflower.

The largest class of race-specific plant disease resistance (R) genes encodes proteins containing nucleotide binding site (NBS) and leucine rich repeat (LRR) domains.  Nearly 800 NBS-LRR encoding resistance gene candidates (RGCs) have been identified from partial cDNA or genomic DNA sequences in sunflower (Helianthus annuus L.).  Nearly one-fourth have been genetically mapped and several are tightly linked to downy mildew R genes found on linkage groups 1 (Pl₁₄) and 13 (Pl₈) and a rust R gene found on linkage group 13 (R_Adv) 8 cM upstream of Pl₈.  The phylogenetic identities of many of the NBS-LRR loci found on linkage groups 1 and 13 are unknown, and R_Adv, Pl₈, and Pl₁₄ have not been cloned.  To lay the groundwork for positionally cloning R_Adv, Pl₈, and Pl₁₄, we isolated, genetically and physically mapped, and phylogenetically classified several NBS-LRR encoding genes tightly linked to Pl₈, Pl₁₄, and R_Adv.  Using overgo probes targeting candidate NBS-LRR sequences, numerous bacterial artifical chromosome (BAC) clones were isolated, end-sequenced, fingerprinted, assembled into contigs, and genetically mapped using DNA markers developed from BAC end sequences.  Contigs cosegregated or were very tightly linked to the NBS-LRR sequences used for BAC isolation.  Selected BAC clones from each of the mapped contigs were fully sequenced and structurally and functionally annotated.  Several NBS-LRR encoding genes were identified in contigs tightly linked to R_Adv, Pl₈, and Pl₁₄ and were phylogenetically classified as members of a single highly duplicated NBS-LRR encoding gene family found in large clusters on linkage groups 1 and 13^__the former spanning at least 12 cM and the latter spanning at least 26 cM and each harboring several family members.  DNA markers for NBS-LRR loci from clusters on linkage groups 1 and 13 mapped within 0.3-0.6 cM of R_Adv, Pl₈, and Pl₁₄ and supply resources for marker-assisted breeding.