Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments

Abstract

BackgroundQuantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum) has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes.ResultsTo obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome) contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF) in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5.ConclusionComparative sequence analysis revealed highly conserved collinear regions that flank regions showing high variability and tandem duplicated genes. Sequence annotation revealed that the majority of the ORFs were members of multiple gene families. Comparing potato to Arabidopsis thaliana annotated proteins suggested fragmented structural conservation between these distantly related plant species.

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

“…Reduced recombination between homeologous chromosomes caused, for example, by inversions in the introgressed S. vernei segment relative to S. tuberosum, may also have contributed to the maintenance of a large haplotype block in the breeding populations. The existence of a 70-kbp inversion between S. demissum and S. tuberosum in this genome segment has been demonstrated (Ballvora et al 2007). Suppression of recombination depending on the source and size of the introgression from wild species has been shown in tomato (Liharska et al 1996;Kaloshian et al 1998).…”

“…1, sequences in supplementary material). The loci ORF3, ORF12, ORF20, BA87d17t3 and BA213c14t7 were part of a contiguous genomic sequence of 417 kilobase pairs located in the 3 cM GP21-GP179 interval (Ballvora et al 2007). The loci BA87d17t3 and BA213c14t7 are insertion ends of the BAC clones BA87d17 and BA213c14 and have been previously analysed in the QRL linkage study of Sattarzadeh et al (2006).…”

“…With the assumption that the QRL is controlled by one gene with multiple alleles, the association gradient observed in LD group E places this gene within or physically close to the genomic region delimited by BACs BA87d17 and BA213c14. This region harbours the R1 resistance gene and two paralogous members of the R1 gene family (Ballvora et al 2007). When the alternative model is true, meaning that several genes in this genomic region control nematode resistance, at least one of these genes should be located within or physically close to the genomic region delimited by BACs BA87d17 and BA213c14.…”

“…These properties make such populations less suitable for candidate gene veriWcation due to lack of genetic resolution. Candidate genes for the QRL on potato chromosome V are, among other genes (Ballvora et al 2007), the members of the R1 gene family. However, for identifying among all possible candidates the causal gene(s) for the observed nematode resistance phenotype in this genomic region, the full genome sequence of potato (http://www.…”

“…This region of the potato genome is known as a hot spot for qualitative and quantitative resistance factors to various pathogens (reviewed in Gebhardt and Valkonen 2001). One of the resistance factors in the GP21-GP179 interval is the R1 gene for resistance to Phytophthora infestans causing late blight, which is a member of a clustered gene family having a CC (coiled coil), a NB (nucleotide binding) and a LRR (leucine rich repeat) domain (Ballvora et al 2007). Physically close to the R1 locus, in fact, within one of the R1 family members, maps the PCR-based marker 'HC'.…”