Identification of a candidate self-incompatibility locus in beet (Beta vulgaris)

This study provides the first genomic evidence for a candidate self-incompatibility locus in beets (Beta vulgaris), identifying T2/S-RNase candidate genes and a complex S-locus on beet chromosome 2. A comparison of self-incompatible and self-compatible beet taxa reveals structural degeneration linked to mating system shifts. This work establishes a genomics-first framework for investigating self-incompatibility in understudied taxa and offers important implications for crop breeding and the evolution of plant reproductive systems. The majority of flowering plants maintain various mechanisms to prevent self-fertilization. One such mechanism, the genetic self-incompatibility (SI) system, exists in about half of angiosperms. SI systems have been described for only few taxa, as their diversity and lack of homology renders their study complicated. Yet, an RNase-based SI system (RSI) has emerged as widespread and possibly ancestral to eudicots. RSI has been recognized in at least six plant families and lately also in Caryophyllales. Here, we utilize the accumulated knowledge of RSI systems and high-quality genomic resources to investigate the presence of RSI in beet, Beta vulgaris. The genus Beta encompasses both self-compatible and self-incompatible taxa. We examined the genes of five beet genome assemblies to identify a candidate for the female component of RSI, a T2/S-RNase, and its corresponding candidate S-locus. A locus on beet chromosome 2 met our criteria, supported by phylogenetics data, sequence characteristics, and expression patterns that are unique to S-RNases. The candidate S-locus in Beta was highly repetitive with gene copy number variation observed in different cultivars. By comparing the candidate S-locus of B. vulgaris with that of the self-compatible wild beet B. patula, we hypothesize a potential link between reproductive modes and S-locus architecture. Our analysis suggests that S-RNase genes derived from an ancestral and highly conserved gene family are present and active in Beta, fulfilling a reproductive function. Employing a genomics-first approach, this work contributes insights into T2/S-RNase evolution and lays the groundwork toward elucidating SI in sugar beet and its relatives.