Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifolium

Abstract

Resistance (R) genes of plants are responsible for pathogen recognition and encode proteins that trigger a cascade of responses when a pathogen invades a plant. R genes are assumed to be under strong selection, but there is limited knowledge of the processes affecting R gene diversity in the wild. In this study, DNA sequence variation of Cf-2 homologs was surveyed in populations of Solanum pimpinellifolium, a wild relative of the cultivated tomato. The Cf-2 locus is involved in resistance to strains of the fungus Cladosporium fulvum. At least 26 different Cf-2 homologs were detected in natural populations of S. pimpinellifolium. These homologs differ by single base pair substitutions as well as indels in regions coding for leucine-rich repeats. Molecular population genetic analyses suggest that natural selection has acted heterogeneously on Cf-2 homologs, with selection against amino acid substitutions occurring in the 5' portion of the genes, and possible restricted positive selection in the 3' end. Balancing selection may have maintained haplotypes at the 5' end of the genes. Limited sequence exchange between genes has also contributed to sequence variation. S. pimpinellifolium individuals differ in the number of Cf-2 homologs they contain, obscuring the relationships of orthology and paralogy. This survey of Cf-2 variation in S. pimpinellifolium illustrates the wealth of R gene diversity that exists in wild plant populations, as well as the complexity of interacting genetic and evolutionary processes that generate such diversity.

Fig. 1.

Schematic representation of the Cf-2 homolog size classes within S. pimpinellifolium. All genes are represented aligned to the Cf-2 size class. Regions left of the left vertical dashed line and right of the right vertical dashed line were used in sequence comparisons.

Fig. 2.

Gene networks of the alignable areas among homologs. Each step represents a mutational change between haplotypes. Connections exceeding the limits of parsimony were made based on parsimony analysis. Sites are numbered with respect to the Cf-2 size class ORF. The numbering scheme is maintained across deletions present in other haplotypes. Homoplasious mutations are marked with lowercase letters. Mutations leading to an amino acid change are marked with asterisks. Neither network is unique due to alternative placements of homoplasious mutations; alternative networks do not alter topological relationships among haplotypes. (A) Network of the first 654 bp of the 5′ portion of the genes. The limits of parsimony are 11 steps. There are 72 polymorphic sites and 76 mutations; 8 mutations are homoplasious. (B) Network of the 1,045 bp in the 3′ alignable portion of the genes. The spanned region includes the noncoding sequence for genes with early stop codons. The limits of parsimony are 14 steps. There are 55 polymorphic sites and 58 mutations; 8 mutations are homoplasious. A single 3-bp in-frame deletion occurs in size class Hcr2-p1 (position 2656–2658) and was counted as a single mutation for all analyses.