Identification of the genes at S and Z reveals the molecular basis and evolution of grass self-incompatibility

Abstract

Self-incompatibility (SI) is a feature of many flowering plants, whereby self-pollen is recognized and rejected by the stigma. In grasses (Poaceae), the genes controlling this phenomenon have not been fully elucidated. Grasses have a unique two-locus system, in which two independent genetic loci (S and Z) control self-recognition. S and Z are thought to have arisen from an ancient duplication, common to all grasses. With new chromosome-scale genome data, we examined the genes present at S- and Z-loci, firstly in ryegrass (Lolium perenne), and subsequently in ~20 other grass species. We found that two DUF247 genes and a short unstructured protein (SP/ZP) were present at both S- and Z- in all SI species, while in self-compatible species these genes were often lost or mutated. Expression data suggested that DUF247 genes acted as the male components and SP/ZP were the female components. Consistent with their role in distinguishing self- from non-self, all genes were hypervariable, although key secondary structure features were conserved, including the predicted N-terminal cleavage site of SP/ZP. The evolutionary history of these genes was probed, revealing that specificity groups at the Z-locus arose before the advent of various grass subfamilies/species, while specificity groups at the S-locus arose after the split of Panicoideae, Chloridoideae, Oryzoideae and Pooideae. Finally, we propose a model explaining how the proteins encoded at the S and Z loci might function to specify self-incompatibility.

Assessing inbreeding in perennial ryegrass (Lolium perenne) as a step towards F1 hybrid breeding

“…Although some of these alleles will likely be removed by selection, performing further backcrossing prior to inbreeding to reduce the SC genetic contribution would be advisable. Alternatively, identifying the SI components in ryegrass (Herridge et al, 2022) may enable tools such as CRISPR‐Cas site‐directed mutagenesis to introduce self‐fertility into desired elite plants directly.…”

“…Both loci contain genes that encode two DUF247 proteins and a small pistil-expressed protein (SP or ZP), leading to a model where SP and ZP are secreted from the stigma and, upon interactions with matching DUF247 proteins on the pollen tube, form a complex that signals the arrest of pollen-tube growth (Herridge et al, 2022). Interestingly, most SC grass species have deletions or mutations within the S or Z loci genes (Herridge et al, 2022), including the SC darnel ryegrass (Lolium temulentum L.), which contains a frameshift mutation within an S locus DUF247 gene (Manzanares et al, 2016). Thus, mutating the S or Z loci genes using gene editing tools could be a route to SC L. perenne capable of inbreeding (Herridge et al, 2020;Herridge et al, 2022).…”

“…Interestingly, most SC grass species have deletions or mutations within the S or Z loci genes (Herridge et al, 2022), including the SC darnel ryegrass (Lolium temulentum L.), which contains a frameshift mutation within an S locus DUF247 gene (Manzanares et al, 2016). Thus, mutating the S or Z loci genes using gene editing tools could be a route to SC L. perenne capable of inbreeding (Herridge et al, 2020;Herridge et al, 2022). Such an approach has been undertaken in potatoes, where CRISPR/Cas9 was used to mutate a conserved region of the stigma SI component, enabling selffertilization (Ye et al, 2018).…”

Improving abiotic stress tolerance of forage grasses – prospects of using genome editing

“…Forage grasses have a strong gametophytic self-incompatibility (SI) system that makes inbreeding almost impossible. The two multi-allelic S and Z genes have since long been known to govern SI in grasses ( Lundqvist, 1955 ; Cornish et al., 1979 ), and recently it was shown that two DUF247 genes are behind the S and Z loci ( Manzanares et al., 2016 ; Herridge et al., 2022 ). With the sequences and molecular function of these genes known, they would be an obvious target for generating self-fertile knockout lines by genome editing.…”

Improving Abiotic Stress Tolerance of Forage Grasses – Prospects of Using Genome Editing

“…Forage grasses have a strong gametophytic self-incompatibility (SI) system that makes inbreeding almost impossible. The two multi-allelic S and Z genes have since long been known to govern SI in grasses [188,189], and recently it was shown that two DUF247 genes are behind the S and Z loci [190,191]. With the sequences and molecular function of these genes known, they would be an obvious target for generating self-fertile knockout lines by gene editing.…”