Evolution and Genetic Population Structure of Prickly Lettuce (Lactuca Serriola) and Its RGC2 Resistance Gene Cluster

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ABSTRACT

Genetic structure and diversity of natural populations of prickly lettuce (Lactuca serriola) were studied using AFLP markers and then compared with the diversity of the RGC2 disease resistance gene cluster. Screening of 696 accessions from 41 populations using 319 AFLP markers showed that eastern Turkish and Armenian populations were the most diverse populations and might be located in the origin and center of diversity of L. serriola. Screening 709 accessions using the microsatellite MSATE6 that is located in the coding region of most RGC2 homologs detected 366 different haplotypes. Again, the eastern Turkish and Armenian populations had the highest diversities at the RGC2 cluster. The diversities at the RGC2 cluster in different populations were significantly correlated with their genomewide diversities. There was significant variation of copy number of RGC2 homologs in different populations, ranging from 12 to 22 copies per genome. The nucleotide diversities of two conserved lineages (type II) of RGC2 genes (K and L) were not correlated with diversities calculated using the MSATE6 or AFLP data. We hypothesize that the high genomewide diversity and diversity of the RGC2 cluster in eastern Turkish and Armenian populations resulted from high abiotic and biotic stresses in the regions of origin of L. serriola.

MAXIMAL use of wild genetic resources requires a detailed understanding of the genetic structure, diversity, and divergence of the wild progenitor species. Understanding the nature, organization, geographical structure, and differentiation of a wild species is critical for its biological conservation and is also an important aspect of evolutionary genetics (Nevo 1998). Little is known about these aspects of prickly lettuce (Lactuca serriola; 2x = 2n = 18), the progenitor of cultivated lettuce, L. sativa (Lindqvist 1960; Kesseli et al. 1991; Zohary 1991; Hill et al. 1996).

The wild and cultivated lettuces are sexually compatible and lettuce geneticists and breeders have made extensive use of this wild species, mainly for disease resistance, including resistance against downy mildew caused by Bremia lactucae (Crute 1992; Lebeda et al. 2002; Beharav et al. 2006). At least eight functional resistance genes (R-genes) with different specificities against downy mildew have been mapped to the RGC2 cluster, the major cluster of R-genes in lettuce (Farrara et al. 1987; Kesseli et al. 1994). A functional R-gene, Dm3, conferring resistance against downy mildew, was cloned from the RGC2 cluster (Meyers et al. 1998; Shen et al. 2002). Several other Dm specificities as well as resistance to root aphids have since been shown to be conferred by members of the RGC2 family using RNAi (Wroblewski et al. 2007). The RGC2 cluster varies considerably in copy number, ranging from ~10 to >30 copies in a haplotype (Kuang et al. 2004). The RGC2 cluster in natural populations of L. serriola is very diverse, as shown by the numerous haplotypes identified by a microsatellite marker located in intron 3 of many RGC2 homologs (Sicard et al. 1999).

Fragments from.300 RGC2 homologs from multiple lettuce cultivars and wild Lactuca species were sequenced in previous studies (Kuang et al. 2004, 2006). Sequence analysis indicated that RGC2 homologs exhibit heterogeneous rates of evolution and could be classified into two types: type I and type II R-genes. Type I R-genes are extensive chimeras generated by frequent sequence exchanges among paralogs, while type II R-genes evolve independently and are highly conserved in different genotypes or closely related species (Kuang et al. 2004). The sequence exchanges between type I R-gene homologs generate a large number of distinct R-gene candidates in a plant population or species (Kuang et al. 2006). However, the frequent sequence exchanges between type I R-gene homologs make it difficult to study their evolutionary and population genetics.

Previous studies of evolutionary and population genetics of other R-genes were done mainly on single-copy Rgenes that had no sequence exchange with paralogs (Caicedo et al. …