1: Theor Appl Genet. 2008 Nov 13. [Epub ahead of print]

The genomic architecture of disease resistance in lettuce.

McHale LK, Truco MJ, Kozik A, Wroblewski T, Ochoa OE, Lahre KA, Knapp SJ,
Michelmore RW.

The Genome Center and Department of Plant Sciences, University of California,
Davis, CA, 95616, USA, lkmchale@ucdavis.edu.

Genbank and The Compositae Genome Project database, containing over 42,000
lettuce unigenes from Lactuca sativa cv. Salinas and L. serriola accession
UC96US23 were mined to identify 702 candidate genes involved in pathogen
recognition (RGCs), resistance signal transduction, defense responses, and
disease susceptibility. In addition, to identify sequences representing
additional sub-families of nucleotide binding site (NBS)-leucine-rich repeat
encoding genes; the major classes of resistance genes (R-genes), NBS-encoding
sequences were amplified by PCR using degenerate oligonucleotides designed to NBS
sub-families specific to the subclass Asteridae, which includes the Compositae
family. These products were cloned and sequenced resulting in 18 novel NBS
sequences from cv. Salinas and 15 novel NBS sequences from UC96US23. Using a
variety of marker technologies, 294 of the 735 candidate disease resistance genes
were mapped in our primary mapping population, which consisted of 119 F(7)
recombinant inbred lines derived from an interspecific cross between cv. Salinas 
and UC96US23. Using markers shared across multiple genetic maps, 36 resistance
phenotypic loci, including two new loci for resistance to downy mildew and two
quantitative trait loci for resistance to anthracnose were positioned onto the
reference map to provide a global view of the genomic architecture of disease
resistance in lettuce and to identify candidate genes for resistance phenotypes. 
The majority but not all of the resistance phenotypes were genetically associated
with RGCs.

PMID: 19005638 [PubMed - as supplied by publisher]

Supplemental Data

supplementary_info.xls - This file contains information for resistance candidate genes.
Columns A-B: map coordinates
Columns C-E: marker/sequence names
Columns F-G: functional annotations
Columns H-M: enabling details for markers, oligonucleotide sequence
Column N: for single nucleotide polymorphism (SNP) markers, the assayed SNP displayed in brackets and surrounding sequence
Columns O-P: oligonucleotides to amplify and sequence products


Figure_1.tif - Neighbor-joining tree constructed with Phylip v 3.65 (Felsenstein 2004). of a 240 nucleotide fragment of the NBS-encoding region of 91 sequences. Only bootstrap values greater than 75% are indicated.

LsNBS.nt.aln - Alignment of 240 nucleotide fragment of the NBS-encoding region used to build the tree displayed in figure 1. All Lactuca NBS sequences (novel, Genbank, and CGPDB derived) were translated into protein sequences and aligned using ClustalX v 1.83 with default options (Thompson et al. 1997). Nucleotide sequences were aligned based on protein alignments.

Figure_2.tif - Neighbor-joining tree constructed with Phylip v 3.65 (Felsenstein 2004) of a 80 amino acid fragment of the NBS region encoded by each gene family in L. sativa, Helianthus spp. (Radwan et al. 2008); Cichorium spp. (Plocik et al. 2004), NBS sequences mined from the CGPDB representing Taraxacum officionale, L. perennis and L. virosa, and NBS sequences functioning in resistance from other non-Compositae species. Sequences from L. sativa and L. serriola are labeled in green, other Compositae species are labeled in red, non-Compositae species are labeled in black.

NBS.aa.aln - For Figure_2, a protein alignment was constructed (ClustalX v 1.83; Thompson et al. 1997) from a representative NBS sequence from each gene family for Lactuca, Helianthus (Radwan et al. 2008), and Cichorium (Plocik et al. 2004), NBS sequences mined from the CGPDB for Taraxacum officinale, L. perennis and L. virosa, and NBS sequences functioning in resistance from other non-Compositae species.

map.txt - Tab-delimited map file: Chromosome/Linkage_Group, marker_ID, centimorgan.

lgvm_marker_scores_RIL_NOV_2008.txt - raw marker scores

resistance_gene_candidates.fasta - Fasta file for all resistance gene candidates.