Variation among S-locus haplotypes and among stylar RNases in almond

Abstract

in many plant species, self-incompatibility systems limit self-pollination and mating among relatives. this helps maintain genetic diversity in natural populations but imposes constraints in agriculture and plant breeding. in almond [Prunus dulcis (Mill.) D.A. Webb], the specificity of self-incompatibility is mainly determined by stylar ribonuclease (S-Rnase) and S-haplotype-specific F-box (SFB) proteins, both encoded within a complex locus, S. prior to this research, a nearly complete sequence was available for one S-locus haplotype. Here, we report complete sequences for four haplotypes and partial sequences for 11 haplotypes. Haplotypes vary in sequences of genes (particularly S-RNase and SFB), distances between genes and numbers and positions of long terminal repeat transposons. Haplotype variation outside of the S-RNase and SFB genes may help maintain functionally important associations between S-RNase and SFB alleles. fluorescence-based assays were developed to distinguish among some S-RNase alleles. With three-dimensional modelling of five S-RNase proteins, conserved active sites were identified and variation was observed in electrostatic potential and in the numbers, characteristics and positions of secondary structural elements, loop anchoring points and glycosylation sites. A hypervariable region on the protein surface and differences in the number, location and types of glycosylation sites may contribute to determining S-RNase specificity.

A review of plant epigenetics through the lens of almond

“…Subsequently, these results were supported by Goonetilleke et al. (2020), in which the methylation status of a single nucleotide upstream of the coding sequence was found to alter the expression of the self‐compatible ribonuclease ( S f ‐RNase). They also reported that the number and length of long terminal repeat retrotransposons may alter the protein structure of distinct haplotypes of S ‐RNases.…”

“…Fernández i Martí and collaborators (2014) surveyed the DNA sequence at the S f locus in distinct almond cultivars ("Blanquerna," "Vivot," "Soleta," "Ponç") and breeding germplasm (A2-199 and M-2-16) and found differential methylation in several cytosines within regulatory sequences of the S f locus (up to ∼5 kb upstream). Subsequently, these results were supported by Goonetilleke et al (2020), in which the methylation status of a single nucleotide upstream of the coding sequence was found to alter the expression of the self-compatible ribonuclease (S f -RNase). They also reported that the number and length of long terminal repeat retrotransposons may alter the protein structure of distinct haplotypes of S-RNases.…”

“…Almonds, and many other Rosaceous species, are obligate outcrossers due to gametophytic self‐incompatibility (Franklin‐Tong & Franklin, 2003). Exploration of the mechanisms behind this trait has led to the characterization of almond haplotypes (Goonetilleke et al., 2020; Ushijima et al., 2003), biological characteristics like pollen tube growth (Socias i Company et al., 2013), and the role of self‐incompatibility ribonucleases ( S ‐RNAses) (Fernández i Martí et al., 2014) and cross‐compatibility in almond (Gómez, Dicenta, et al., 2019).…”

“…Later research identified the genetic mutations that deactivate the S ‐locus ( S f ; Socias i Company et al., 2015). Subsequently, the distinct epialleles for S f were elucidated (Goonetilleke et al., 2020), as well as the interactions between pollen and the pistil that mediate self‐compatibility (Gómez, Buti, et al., 2019). These tools have allowed breeders to identify and develop self‐compatible cultivars using marker‐assisted selection.…”

Evaluation of the S-locus in Prunus domestica, characterization, phylogeny and 3D modelling

“…It has been proposed that loops in 3D structures serve to link α-helices and β-strands, and that longer loops could be susceptible to proteolytic degradation. The general functional differences among 3D almond SC and SI RNases involved an extended loop in the S f -RNase [60,61]. Furthermore, the main structural difference found in the three-dimensional models generated in this study between the SC and SI P. domestica proteins resided in the presence and length of the loop within the conserved domains RC4 and C5.…”