S-alleles and mating system in natural populations of Capsella grandiflora (Brassicaceae) and its congeneric relatives

Neuffer, Barbara; Bechsgaard, Jesper; Paetsch, Melanie; Titel, Carina; Wesse, Christina; Bona, Enzo; Schimpf, Regina; Čalasan, Anže Žerdoner; Hurka, Herbert

doi:10.1016/j.flora.2022.152206

Cited by 3 publications

(6 citation statements)

References 48 publications

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“…A more complete description of this set of S-alleles is given in the Supplementary Information. Beside these 74 SRK alleles, we also identified five sequences clustering with SRK alleles (H0002, H0003, H0011, H0012 and H0013 in Table S1, named CgrSRK01, CgrSRK06, CgrSRK09, CgrSRK51 and CgrSRK63 in Paetsch et al 2006, andNeuffer et al 2023, see Table S2) that we considered as paralogous sequences unlinked to the S-locus, as already documented in Schierup et al (2001) and Prigoda et al (2005, see Supplementary Information).…”

Section: A Reliable Methodology To Determine S-locus Genotypes and Ph...mentioning

confidence: 59%

“…First, we produced a comprehensive set of S-allele reference sequences in Capsella. For this, we genotyped individuals at the SRK gene using the NGSgenotyp pipeline (Genete et al 2020) (Guo et al 2009;Neuffer et al 2023; see Supplementary Information).…”

Section: A Reliable Methodology To Determine S-locus Genotypes and Ph...mentioning

confidence: 99%

“…To build an extended dataset of reference sequences of SRK from the self-incompatible species Capsella grandiflora, we genotyped 180 individuals of the Cg-9 population of C. grandiflora from Monodendri, Greece (Josephs et al 2015) at the SRK gene with the NGSgenotyp pipeline (Genete et al 2020) using raw Illumina reads available from Sequence Read Archive (SRA, Table S1). For the SRK reference database, we used available sequences of SRK from A. lyrata and A. halleri (Takou et al 2021;Genete et al 2020), and 62 partial sequences from Capsella grandiflora (Guo et al 2009;Neuffer et al 2023; see Table S2). Briefly, this pipeline filters raw reads with a dictionary of k-mers extracted from the reference database, then uses Bowtie2 to align filtered reads against each reference sequence from the database and produces summary statistics with Samtools (v1.4; Danecek et al 2021) allowing it to identify S-alleles present in each individual.…”

Section: Methodological Approach To Type S-alleles In Capsella Experi...mentioning

confidence: 99%

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Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids

Duan

Zhang

Genête

et al. 2023

Preprint

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The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants, and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to impede self-fertilization is controlled by two genes, SCR and SRK, tightly linked within the S-locus. A series of small non-coding RNAs also encoded within the S-locus regulates the transcriptional activity of SCR alleles, resulting in a linear dominance hierarchy between them. Brassicaceae allopolyploid species are often self-compatible (SC) even when one of their parents is self-incompatible, but the causes of the loss of self-incompatibility (SI) in polyploid lineages have generally remained elusive. We used a series of synthetic hybrids obtained between self-fertilizing Capsella orientalis and outcrossing C. grandiflora to test whether the breakdown of SI in allopolyploid species, such as C. bursa-pastoris, could be explained by the dominance interactions between S-haplotypes inherited from the parental lineages. After establishing a database of reference S-allele sequences, we used RNA-sequencing data from young inflorescences to measure allele-specific expression of the SCR and SRK genes in diploid and tetraploid synthetic hybrids. We then compared the observed expression of SCR alleles with the predicted dominance relationship between S-haplotypes in pollen and with the seed set from autonomous self-fertilization in the synthetic hybrids. Our results formally establish that upon hybridization, the immediate effect on the mating system depends on the relative dominance between S-alleles inherited from the parental species. They illustrate that a detailed understanding of the genetic architecture of the control of SI is essential to predict the patterns of association between the mating system and changes in ploidy.

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Section: A Reliable Methodology To Determine S-locus Genotypes and Ph...mentioning

confidence: 59%

Section: A Reliable Methodology To Determine S-locus Genotypes and Ph...mentioning

confidence: 99%

Section: Methodological Approach To Type S-alleles In Capsella Experi...mentioning

confidence: 99%

See 1 more Smart Citation

Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids

Duan

Zhang

Genête

et al. 2023

Preprint

View full text Add to dashboard Cite

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“…A more complete description of this set of S -alleles is given in the Supplementary Information . Beside these 74 SRK alleles, we also identified five sequences clustering with SRK alleles (H0002, H0003, H0011, H0012, and H0013 in Supplementary Table S1 , named CgrSRK01, CgrSRK06, CgrSRK09, CgrSRK51, and CgrSRK63 in Paetsch et al, 2006 ; and Neuffer et al, 2023 , see Supplementary Table S2 ) that we considered as paralogous sequences unlinked to the S -locus, as already documented in Schierup et al (2001) and Prigoda et al (2005 , see Supplementary Information ).…”

Section: Resultsmentioning

confidence: 75%

“…For this, we genotyped individuals at the SRK gene using the NGSgenotyp pipeline ( Genete et al, 2020 ) on publicly available short-read resequencing data of 180 C. grandiflora individuals from Monodendri, Greece (the Cg-9 population in Josephs et al, 2015 ). We started from a database of SRK sequences from A. lyrata and A. halleri that we complemented with 62 partial C. grandiflora SRK sequences previously obtained by Sanger sequencing by Jesper Bechsgaard and Mikkel Schierup ( Guo et al, 2009 ; Neuffer et al, 2023 ; see Supplementary Information ). We obtained a fully resolved S -locus genotype for 177 individuals ( Supplementary Table S1 ), and identified 74 different S -alleles, including 25 previously unknown C. grandiflora S -alleles ( Supplementary Table S2 ).…”

Section: Resultsmentioning

confidence: 99%

Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids

Duan,

Zhang,

Genete

et al. 2024

Evolution Letters

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The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to inhibit self-fertilization is controlled by 2 genes, SCR and SRK, tightly linked within the S-locus. A series of small non-coding RNAs also encoded within the S-locus regulates the transcriptional activity of SCR alleles, resulting in a linear dominance hierarchy between them. In Brassicaceae, natural allopolyploid species are often self-compatible (SC) even when one of the progenitor species is self-incompatible, but the reason why polyploid lineages tend to lose self-incompatibility (SI) and the timing of the loss of SI (immediately after ancestral hybridization between the progenitor species, or at a later stage after the formation of allopolyploid lineages) have generally remained elusive. We used a series of synthetic diploid and tetraploid hybrids obtained between self-fertilizing Capsella orientalis and outcrossing Capsella grandiflora to test whether the breakdown of SI could be observed immediately after hybridization, and whether the occurrence of SC phenotypes could be explained by the dominance interactions between S-haplotypes inherited from the parental lineages. We used RNA-sequencing data from young inflorescences to measure allele-specific expression of the SCR gene and infer dominance interactions in the synthetic hybrids. We then evaluated the seed set from autonomous self-pollination in the synthetic hybrids. Our results demonstrate that self-compatibility of the hybrids depends on the relative dominance between S-alleles inherited from the parental species, confirming that SI can be lost instantaneously upon formation of the ancestral allopolyploid lineage. They also confirm that the epigenetic regulation that controls dominance interactions between S-alleles can function between subgenomes in allopolyploids. Together, our results illustrate how a detailed knowledge of the mechanisms controlling SI can illuminate our understanding of the patterns of co-variation between the mating system and changes in ploidy.

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Multiple polyploidizations inArabidopsis lyratastabilized by long-range adaptive introgression across Eurasia

Scott,

Kolesnikova,

Glushkevich

et al. 2024

Preprint

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Abundance of polyploidy varies across lineages, evolutionary time and geography, suggesting both genetics and environment play a role in polyploid persistence.Arabidopsis lyrataappears to be the most polyploidy-rich species-complex in theArabidopsisgenus, with multiple origins of autotetraploidy. This is revealed by genomic data from over 400 samples across Eurasia. We found over 30 previously undescribed autotetraploid populations in Siberia with a minimum of two separate origins, independent of those previously reported in Central Europe. The establishment of Siberian tetraploids is mediated by meiotic adaptation at the same genes as in European tetraploidA. lyrataandArabidopsis arenosa,despite high divergence and geographical separation. Haplotype analysis based on synthetic long-read assemblies supports the long-range introgression of adaptive alleles from the tetraploid interspecific pool of EuropeanA. lyrataandA. arenosato tetraploid SiberianA. lyrata. Once evolved, adaptation to polyploidy promotes the establishment of new polyploid lineages through adaptive inter– and intraspecific introgression.

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S-alleles and mating system in natural populations of Capsella grandiflora (Brassicaceae) and its congeneric relatives

Cited by 3 publications

References 48 publications

Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids

Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids

Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids

Multiple polyploidizations inArabidopsis lyratastabilized by long-range adaptive introgression across Eurasia

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