Data from: No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes

Aguiar, Bruno, University of Porto

Vieira, Jorge, University of Porto

Cunha, Ana E., University of Porto

Vieira, Cristina P., University of Porto

Published Apr 16, 2016 on Dryad. https://doi.org/10.5061/dryad.71rn0

Cite this dataset

Aguiar, Bruno; Vieira, Jorge; Cunha, Ana E.; Vieira, Cristina P. (2016). Data from: No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes [Dataset]. Dryad. https://doi.org/10.5061/dryad.71rn0

Abstract

Background: Fabaceae species are important in agronomy and livestock nourishment. They have a long breeding history, and most cultivars have lost self-incompatibility (SI), a genetic barrier to self-fertilization. Nevertheless, to improve legume crop breeding, crosses with wild SI relatives of the cultivated varieties are often performed. Therefore, it is fundamental to characterize Fabaceae SI system(s). We address the hypothesis of Fabaceae gametophytic (G)SI being RNase based, by recruiting the same S-RNase lineage gene of Rosaceae, Solanaceae or Plantaginaceae SI species. Results: To address if Fabaceae GSI is RNase based we first looked for the presence of SSK1 like genes (described only in species having RNase based GSI), in the Trifolium pratense, Medicago truncatula, Cicer arietinum, Glycine max, and Lupinus angustifolius genomes. Since we find these genes in Fabaceae species, we characterize the S-lineage T2-RNase genes in these genomes. Except for T. pratense, all species are self-compatible (SC). Nevertheless, in T. pratense, but also in M. truncatula and C. arietinum we identify S-RNase lineage genes that in phylogenetic analyses cluster with Pyrinae S-RNases. In M. truncatula and C. arietinum genomes, where large scaffolds are available, these sequences are surrounded by F-box genes that in phylogenetic analyses also cluster with S-pollen genes. In T. pratense the S-RNase lineage genes show, however, expression in tissues not involved in GSI. Moreover, levels of diversity are lower than those observed for other S-RNase genes. The M. truncatula and C. arietinum S-RNase and S-pollen like genes phylogenetically related to Pyrinae S-genes, are also expressed in tissues other than those involved in GSI. To address if other T2-RNases could be determining Fabaceae GSI, here we obtained a style with stigma transcriptome of Cytisus striatus, a species that shows significant difference on the percentage of pollen growth in self and cross-pollinations. Expression and polymorphism analyses of the C. striatus S-RNase like genes revealed that none of these genes, is the S-pistil gene. Conclusion: We find no evidence for Fabaceae GSI being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes. Since none of the C. striatus T2-RNase genes expressed in style with stigma is involved in GSI specificity, there is no evidence that T2-RNase lineage genes could be determining GSI in this species. Therefore, to characterize the Fabaceae S-pistil gene(s), expression analyses, levels of diversity, and segregation analyses in controlled crosses are needed for those genes showing high expression levels in the tissues where GSI occurs.

Usage notes

Sequence data sets used in Aguiar et al. 2015

Sequence data sets used in Aguiar et al. 2015: 1- SSK1 like genes in flowering plants: SSK1 genes(s) have been described only in species having RNase based GSI. Therefore, presence/absence of this gene(s) has been reported as a diagnosis marker for the presence/absence of RNase based GSI (see references in Aguiar et al. 2015). The protein encoded by SSK1 has an unique C-terminus, composed of 5 - 9 amino acid residues, following the conventional "WAFE" motif. In Rosaceae, this amino acid tail shows the conserved sequence “GVDED”. In Solanaceae and Plantaginaceae this motif is not so well conserved but a D residue is always found at the last position of the motif. When using these features and the NCBI flowering plant species database, we retrieved 21 sequences from Solanaceae (three), Plantaginaceae (one), Rosaceae (eight), Fabaceae (five), Malvaceae (one), Rutaceae (one), Euphorbiaceae (one) and Salicaceae (one) species. The two genes from Cytisus striatus were obtained from a style with stigma transcriptome. Oryza sativa [GenBank:AP003824] and Citrus maxima [GenBank:FJ851401] genes that encode proteins not presenting the C-terminus amino acid motif following the conventional "WAFE" motif are here included to root the phylogenetic tree shown in Figure 1 in Aguiar et al. 2015. 2- Fabaceae S-RNase lineage genes: Fabaceae S-RNase lineage genes and Prunus, Pyrinae, Solanaceae and Plantaginaceae S-RNases (Figure 2 and Figure 6A in Aguiar et al. 2015): Sequences used to determine the phylogenetic relationship of M. truncatula, G. max, L. angustifolius, L. corniculatus, L. japonicus, T. pratense, P. sativum, C. cajan, C. tetragonoloba, C. arietinum,and C. striatus S-RNase lineage genes and the Prunus, Pyrinae, Solanaceae and Plantaginaceae S-RNases. 3- CsRNase3: C. striatus CsRNase3 gene and Prunus, Pyrinae, Solanaceae and Plantaginaceae S-RNases (Figure 6 in Aguiar et al. 2015) 4- F-box genes: F-box SFB -SFBB- and SLFL- like genes surrounding the C. arietinum Ca4, M. truncatula Mt3, Mt17, Mt18, and Mt20 S-RNase like genes, and S-pollen genes from Prunus, Malus, Solanaceae and Plantaginaceae, and Prunus S-like genes (genes not involved in GSI specificity; see Aguiar et al. 2015 Figure 5). A. thaliana F-box/kelch-repeat

Aguiar et al 2015.zip