On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae)

Abstract

Polyploidy, or whole-genome duplication, is a common speciation mechanism in plants. An important barrier to polyploid establishment is a lack of compatible mates. Because self-compatibility alleviates this problem, it has long been hypothesized that there should be an association between polyploidy and self-compatibility (SC), but empirical support for this prediction is mixed. Here, we investigate whether the molecular makeup of the Brassicaceae self-incompatibility (SI) system, and specifically dominance relationships among S-haplotypes mediated by small RNAs, could facilitate loss of SI in allopolyploid crucifers. We focus on the allotetraploid species Capsella bursa-pastoris, which formed ~300 kya by hybridization and whole-genome duplication involving progenitors from the lineages of Capsella orientalis and Capsella grandiflora. We conduct targeted long-read sequencing to assemble and analyze eight full-length S-locus haplotypes, representing both homeologous subgenomes of C. bursa-pastoris. We further analyze small RNA (sRNA) sequencing data from flower buds to identify candidate dominance modifiers. We find that C. orientalis-derived S-haplotypes of C. bursa-pastoris harbor truncated versions of the male SI specificity gene SCR and express a conserved sRNA-based candidate dominance modifier with a target in the C. grandiflora-derived S-haplotype. These results suggest that pollen-level dominance may have facilitated loss of SI in C. bursa-pastoris. Finally, we demonstrate that spontaneous somatic tetraploidization after a wide cross between C. orientalis and C. grandiflora can result in production of self-compatible tetraploid offspring. We discuss the implications of this finding on the mode of formation of this widespread weed.

Fig. 1. Capsella bursa-pastoris subgenome B and subgenome A S-haplotypes from four accessions.

S-locus gene exons are shown as arrows in direction of transcription: U-box (red), mirS3 (green), SCR (yellow), SRK (blue), and ARK3 (gray). In C. bursa-pastoris subgenome A, we could not identify a complete SCR gene nor full-length SCR exons, and the bars for SCR here indicate short regions of similarity to C. rubella SCR and A. lyrata AlySCR38.

Fig. 2. SCR amino acid alignment of Arabidopsis halleri AhS12, Capsella grandiflora CgS12, C. orientalis CoS12 in accessions Co1979/09, Co1719/11 and C. bursa-pastoris subgenome B sequences.

There is a single base-pair frame-shift in C. orientalis Co1979/09, Co1719/11 and in C. bursa-pastoris B CbpWEDE and B CbpWESE. There is a larger deletion in C. bursa-pastoris B CbpAQ and B CbpCH.

Fig. 3. SRK-phylogeny.

Maximum likelihood tree based on multiple sequence alignment of SRK exon 1 sequences. Large symbols indicate Capsella alleles. Arabidopsis alleles highly similar to C. bursa-pastoris subgenome B (AlS38 and AlS30) and A (AhS12) and SRK are annotated in the figure. Nodes with >95% bootstrap support are marked with an asterisk (*). The tree is rooted using ARK3 sequences. Labels in the outer circle indicate dominance classes according to Mable et al. (2018) (A1 < B < A2, A3 in order of increasing dominance).

Fig. 4. sRNA precursor CbpBmirS3 identified in the B subgenome of accession CbpWEDE.

a Predicted hairpin structure of CbpBmirS3 with rnafold. b Expression of CbpBmirS3 in C. bursa-pastoris subgenome B S-haplotype. The gray bar marks the length of the precursor, and the green bar shows the location of expressed 24 nt sRNA with a target predicted in subgenome A. c Predicted target of CbpBmirS3 expressed 24 nt sRNA in subgenome A. d Schematic of predicted dominance with C. bursa-pastoris subgenome B expressing CbpBmirS3 sRNA that target C. bursa-pastoris subgenome A.

Fig. 5. Pollen tube counts in newly formed tetraploids with and without manual self-pollination.

Boxplots show the number of pollen tubes after manual self-pollination of emasculated flowers of tetraploid F2 individuals and F3 offspring of tetraploid F2s and in negative controls consisting of unpollinated emasculated tetraploid F2 and F3 flowers.