Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system

Abstract

In Malus × domestica (Rosaceae) the product of each SFBB gene (the pollen component of the gametophytic self-incompatibility (GSI) system) of a S-haplotype (the combination of pistil and pollen genes that are linked) interacts with a sub-set of non-self S-RNases (the pistil component), but not with the self S-RNase. To understand how the Malus GSI system works, we identified 24 SFBB genes expressed in anthers, and determined their gene sequence in nine M. domestica cultivars. Expression of these SFBBs was not detected in the petal, sepal, filament, receptacle, style, stigma, ovary or young leaf. For all SFBBs (except SFBB15), identical sequences were obtained only in cultivars having the same S-RNase. Linkage with a particular S-RNase was further established using the progeny of three crosses. Such data is needed to understand how other genes not involved in GSI are affected by the S-locus region. To classify SFBBs specificity, the amino acids under positive selection obtained when performing intra-haplotypic analyses were used. Using this information and the previously identified S-RNase positively selected amino acid sites, inferences are made on the S-RNase amino acid properties (hydrophobicity, aromatic, aliphatic, polarity, and size), at these positions, that are critical features for GSI specificity determination.

The Genome-Wide Analysis of RALF-Like Genes in Strawberry (Wild and Cultivated) and Five Other Plant Species (Rosaceae)

“…Here, Fragaria vesca, Fragaria × ananassa, and Malus × domestica (only these three species in the present study can be found the available RNA-seq data to analyze the expression profiles about diverse tissues and stresses) were considered when investigating the RALF-like gene expression of diverse tissues, organs, developmental stages, and stresses. The study accessions from NCBI were SRP096282, SRP098567, ERP004230, SRP035308, SRP018410, ERP013896, SRP111905, SRP125281, SRP091754, and SRP139480 [54][55][56][57][58][59][60][61], which were involved in the development of flower tissues, fruit tissues, seed tissues, and fungal stresses. Ultimately, the FPKM (fragments per kilobase per million) [62] of RALF-like genes was extracted from the GTF files and submitted to TBtools [52] to draw the heatmaps with the log 2 translation of FPKM.…”

Finding a Compatible Partner: Self-Incompatibility in European Pear (Pyrus communis); Molecular Control, Genetic Determination, and Impact on Fertilization and Fruit Set

“…As yet, it is still unclear how many SFBB genes are involved in the GSI system. However, based on findings in apple ( Malus domestica ), the currently estimated number of SFBB genes is 17–19 (Pratas et al., 2018). In addition, the S-locus sequence in pear was also found to contain numerous transposon-like sequences which are proposed to generate polymorphisms among S-haplotypes, and which likely contribute to the suppression of meiotic recombination between the S-RNase and SFBBs (Okada et al., 2011).…”

“…In M. domestica , 10 S-haplotypes were screened for the presence of SFBB genes using transcriptome sequencing of anthers. For a given S-haplotype, this resulted in the identification of 17–19 SFBB genes (Pratas et al., 2018). A similar number of SLF genes (namely 16–20 SLF genes, classified into 18 types) was observed in Petunia , which also exhibits a non-self-recognition type GSI system (Matsumoto and Tao, 2016a; Pratas et al., 2018).…”

“…For a given S-haplotype, this resulted in the identification of 17–19 SFBB genes (Pratas et al., 2018). A similar number of SLF genes (namely 16–20 SLF genes, classified into 18 types) was observed in Petunia , which also exhibits a non-self-recognition type GSI system (Matsumoto and Tao, 2016a; Pratas et al., 2018). Several SLFs thereby even appeared to target the same S-RNase (Sun and Kao, 2013; Matsumoto and Tao, 2016a).…”

Self-(In)compatibility Systems: Target Traits for Crop-Production, Plant Breeding, and Biotechnology

“…RNA-seq analysis has emerged as the preferred technique for transcriptome studies (Wang et al, 2009) and it has played an important role in elucidating the non-self recognition GSI system in Solanaceae and Rosaceae. It was used in Petunia to identify all the pollen specificity SLF genes (Williams et al, 2014;Kubo et al, 2015 ), and up to 24 S-locus Fbox Brothers (SFBB) genes were similarly identified in Malus × domestica (Pratas et al, 2018).…”