Epigenetic Regulation of the Sex Determination Gene MeGI in Polyploid Persimmon

Abstract

Epigenetic regulation can add a flexible layer to genetic variation, potentially enabling long-term but reversible cis-regulatory changes to an allele while maintaining its DNA sequence. Here, we present a case in which alternative epigenetic states lead to reversible sex determination in the hexaploid persimmon Diospyros kaki. Previously, we elucidated the molecular mechanism of sex determination in diploid persimmon and demonstrated the action of a Y-encoded sex determinant pseudogene called OGI, which produces small RNAs targeting the autosomal gene MeGI, resulting in separate male and female individuals (dioecy). We contrast these findings with the discovery, in hexaploid persimmon, of an additional layer of regulation in the form of DNA methylation of the MeGI promoter associated with the production of both male and female flowers in genetically male trees. Consistent with this model, developing male buds exhibited higher methylation levels across the MeGI promoter than developing female flowers from either monoecious or female trees. Additionally, a DNA methylation inhibitor induced developing male buds to form feminized flowers. Concurrently, in Y-chromosome-carrying trees, the expression of OGI is silenced by the presence of a SINE (short interspersed nuclear element)-like insertion in the OGI promoter. Our findings provide an example of an adaptive scenario involving epigenetic plasticity.

A cross population between D. kaki and D. virginiana shows high variability for saline tolerance and improved salt stress tolerance

“…Arabidopsis genes SOS1 (AF_256224.1), SOS2 (AF_237670.1), SOS3 (HE_802 983.1), NHX1 (AF_106324.1), HKT1 (AK_228564.1) and ALMT9 (NM_112729.4) were blasted against the SRA archive of D. lotus (SRA ID: SRP045872) cv. Kunsenshi [75]. The output fragments were manually assembled to complete putative orthologous genes.…”

Gene networks orchestrated by MeGI: a single‐factor mechanism underlying sex determination in persimmon

“…The OGI gene on the Y chromosome is a non‐coding RNA gene that produces a small‐RNA, and is a genetic determinant of sex in persimmons, while its autosomal counterpart, MeGI , is targeted by the OGI small‐RNA, and is thought to be the integrator of sex expression (Akagi et al ., ). As Oriental persimmon ( Diospyros kaki ) evolved into a hexaploid species, its dioecious sex determination system was transferred into a more plastic system, including monoecious individuals, which are genetically male because they carry a Y chromosome (Akagi et al ., ; Henry et al ., ). Although the fundamental regulatory pathways in the monoecious individuals are likely to be identical to those of diploid dioecious Diospyros species, OGI is substantially silenced by a SINE‐like insertion in the promoter region (Akagi et al ., ).…”

Epigenetic perspectives on the evolution and domestication of polyploid plant and crops

“…In crops, reduced or altered photoperiod response is one of the major ‘domestication syndromes’ [122]. Interestingly, in the hexaploid Persimmon ( Diospyros kaki ), differential methylation patterns of the sexdetermination gene MeGI are associated with developing male and female flowers with the higher DNA methylation levels in the MeGI promoter of the male flower buds [123]. The methylation of MeGI is dependent on small RNAs produced from the Y-encoded sex determinant pseudogene OGI [124].…”