Molecular Characterization and Evolution of Self-Incompatibility Genes inArabidopsis thaliana:The Case of theScHaplotype

Abstract

The switch from an outcrossing mode of mating enforced by self-incompatibility to self-fertility in the Arabidopsis thaliana lineage was associated with mutations that inactivated one or both of the two genes that comprise the self-incompatibility (SI) specificity-determining S-locus haplotype, the S-locus receptor kinase (SRK) and the S-locus cysteine-rich (SCR) genes, as well as unlinked modifier loci required for SI. All analyzed A. thaliana S-locus haplotypes belong to the SA, SB, or SC haplotypic groups. Of these three, the SC haplotype is the least well characterized. Its SRKC gene can encode a complete open-reading frame, although no functional data are available, while its SCRC sequences have not been isolated. As a result, it is not known what mutations were associated with inactivation of this haplotype. Here, we report on our analysis of the Lz-0 accession and the characterization of its highly rearranged SC haplotype. We describe the isolation of its SCRC gene as well as the subsequent isolation of SCRC sequences from other SC-containing accessions and from the A. lyrata S36 haplotype, which is the functional equivalent of the A. thaliana SC haplotype. By performing transformation experiments using chimeric SRK and SCR genes constructed with SC-and S36-derived sequences, we show that the SRKC and SCRC genes of Lz-0 and at least a few other SC-containing accessions are nonfunctional, despite SCRC encoding a functional full-length protein. We identify the probable mutations that caused the inactivation of these genes and discuss our results in the context of mechanisms of S-locus inactivation in A. thaliana.T HE switch from an outcrossing mode of mating to selffertility was a major transition in the evolutionary history of Arabidopsis thaliana. Recent studies have shown that this switch was accompanied by multiple independent losses of self-incompatibility (SI), the major mechanism that promotes outcrossing in the Brassicaceae Shimizu et al. 2008; Boggs et al. 2009a). In this family, SI is controlled by numerous haplotypes of the S locus. Within each S-locus haplotype (hereafter S haplotype), are two genes that determine specificity in the SI response: one gene encodes the stigma-expressed S-locus receptor kinase (SRK) and the other encodes the pollen coat-localized ligand for SRK, the S-locus cysteine-rich (SCR) protein. The SRK and SCR proteins are highly polymorphic and co-evolving proteins (Sato et al. 2002) and their haplotype-specific interaction is responsible for the specific recognition and inhibition by the stigma epidermis of self-related pollen (i.e., pollen derived from the same flower, other flowers on the same plant, or plants expressing the same S haplotype) (reviewed in Rea and Nasrallah 2008). Consequently, an understanding of the genetic events associated with the switch to self-fertility in the A. thaliana lineage was sought through analysis of SRK and SCR sequences harbored by various A. thaliana geographical accessions (Kusaba et al. 2001;Shimizu et al. 2004Shimizu et al....

The evolution of selfing from outcrossing ancestors in Brassicaceae: what have we learned from variation at the S‐locus?

“…In Brassicaceae SC species, the S‐ locus region has been studied in details only in A. thaliana , where the full sequence of the S‐ locus has been characterized in each of the three different haplogroups as well as in a recombinant haplotype (Kusaba et al ., ; Shimizu et al ., ; Tang et al ., ; Tsuchimatsu et al ., ; Dwyer et al ., ). Here, we further analysed full genome sequences from C. rubella (Slotte et al ., ) and four additional SC species of Brassicaceae ( Eutrema salsugineum , Yang et al ., ; Schrenkiella parvula , Dassanayake et al ., ; Sisymbrium irio and Aethionema arabicum , Haudry et al ., ), in order to identify the S‐ locus region, to search for functional or nonfunctional copies of SRK and SCR , and to characterize patterns of molecular evolution in this region as compared to the S‐ locus region in SI species (methods in Appendix S1).…”

“…Note, however, that these results should be interpreted with caution, as multiple mutations would accumulate at S‐ locus genes after the loss of SI, making it difficult to infer the initial causal mutation except in some exceptional cases (e.g. Tsuchimatsu et al ., ; Dwyer et al ., ). In all SC species investigated here (but with some ambiguity for A. arabicum ), we found remnants of the S‐ locus in the same genomic location as that of the A. thaliana S‐ locus, that is, a region within block U of the linkage group 7 of the ancestral Brassicaceae karyotype (Schranz et al ., ) that is flanked by B80 ( At4g21350 ) and the SRK paralog ARK3 ( Aly8 , At4g21380 ).…”

Pollen-Pistil Interactions and Their Role in Mate Selection

“…In the incompatible response, a key secretory protein, exo70A1 (exocyst complex component 70A1), is destabilized, and secretory vesicles are targeted to a vacuole rather than secreted (Indriolo and Goring, 2014). Since diffusion of the pollen SCR polypeptide ligand to the SRK receptor induces the rejection response in the papillar cell, SC can be caused by a loss-offunction mutations in either pollen-expressed SCR or pistil-expressed SRK (Dwyer et al, 2013).…”

African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

“…In A. thaliana, three S-haplogroups are found, and each contains mutations that obliterate function of the S-locus genes (15)(16)(17). Loss-of-function occurred independently in each S-haplogroup (18)(19)(20)(21), but because these three S-haplogroups were never found together in the same geographic region, self-compatibility is inferred to have evolved separately in multiple locations (16,21,22). However, the hypothesis of geographically distinct origins is difficult to reconcile with the major genomic and phenotypic changes that render A. thaliana incompatible with its out-crossing congeners (9-13).…”