Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids
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PROVIDER: S-EPMC11291619 | biostudies-literature | 2024 Mar
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Project description:Background and aimsSporophytic self-incompatibility (SI) prevents inbreeding in many members of the Brassicaceae, and has been well documented in a variety of high-profile species. Arabis alpina is currently being developed as a model system for studying the ecological genetics of arctic-alpine environments, and is the focus of numerous studies on population structure and alpine phylogeography. Although it is highly inbreeding throughout most of its range, populations in central Italy have been identified that show inbreeding coefficients (F(IS)) more typical of self-incompatible relatives. The purpose of this study was to establish whether this variation is due to a functioning SI system.MethodsOutcrossing rate estimates were calculated based on 16 allozyme loci and self-compatibility assessed based on controlled pollinations for six Italian populations that have previously been shown to vary in F(IS) values. Putative SRK alleles (the gene controlling the female component of SI in other Brassicaceae) amplified from A. alpina were compared with those published for other species. Linkage of putative SRK alleles and SI phenotypes was assessed using a diallel cross.Key resultsFunctional avoidance of inbreeding is demonstrated in three populations of A. alpina, corresponding with previous F(IS) values. The presence is described of 15 putative SRK-like alleles, which show high sequence identity to known alleles from Brassica and Arabidopsis and the high levels of synonymous and nonsynonymous variation typical of genes under balancing selection. Also, orthologues of two other members of the S-receptor kinase gene family, Aly8 (ARK3) and Aly9 (AtS1) are identified. Further to this, co-segregation between some of the putative S-alleles and compatibility phenotypes was demonstrated using a full-sibling cross design.ConclusionsThe results strongly suggest that, as with other species in the Brassicaceae, A. alpina has a sporophytic SI system but shows variation in the strength of SI within and between populations.
| S-EPMC3170156 | biostudies-literature
Project description:Self-incompatibility (SI) is conserved among members of the Brassicaceae plant family. This trait is controlled epigenetically by the dominance hierarchy of the male determinant alleles. We previously demonstrated that a single small RNA (sRNA) gene is sufficient to control the linear dominance hierarchy in Brassica rapa and proposed a model in which a homology-based interaction between sRNAs and target sites controls the complicated dominance hierarchy of male SI determinants. In Arabidopsis halleri, male dominance hierarchy is reported to have arisen from multiple networks of sRNA target gains and losses. Despite these findings, it remains unknown whether the molecular mechanism underlying the dominance hierarchy is conserved among Brassicaceae. Here, we identified sRNAs and their target sites that can explain the linear dominance hierarchy of Arabidopsis lyrata, a species closely related to A. halleri. We tested the model that we established in Brassica to explain the linear dominance hierarchy in A. lyrata. Our results suggest that the dominance hierarchy of A. lyrata is also controlled by a homology-based interaction between sRNAs and their targets.
| S-EPMC8268441 | biostudies-literature
Project description:Flowering plants often prevent selfing through mechanisms of self-incompatibility (S.I.). The loss of S.I. has occurred many times independently, because it provides short-term advantages in situations where pollinators or mates are rare. The genus Capsella, which is closely related to Arabidopsis, contains a pair of closely related diploid species, the self-incompatible Capsella grandiflora and the self-compatible Capsella rubella. To elucidate the transition to selfing and its relationship to speciation of C. rubella, we have made use of comparative sequence information. Our analyses indicate that C. rubella separated from C. grandiflora recently ( approximately 30,000-50,000 years ago) and that breakdown of S.I. occurred at approximately the same time. Contrasting the nucleotide diversity patterns of the 2 species, we found that C. rubella has only 1 or 2 alleles at most loci, suggesting that it originated through an extreme population bottleneck. Our data are consistent with diploid speciation by a single, selfing individual, most likely living in Greece. The new species subsequently colonized the Mediterranean by Northern and Southern routes, at a time that also saw the spread of agriculture. The presence of phenotypic diversity within modern C. rubella suggests that this species will be an interesting model to understand divergence and adaptation, starting from very limited standing genetic variation.
| S-EPMC2659713 | biostudies-literature
Project description:BackgroundAllopolyploid speciation requires rapid evolutionary reconciliation of two diverged genomes and gene regulatory networks. Here we describe global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus (Gossypium L.).ResultsEmploying a micro-array platform designed against 40,430 unigenes, we assayed gene expression in two sets of parental diploids and their colchicine-doubled allopolyploid derivatives. Up to half of all genes were differentially expressed among diploids, a striking level of expression evolution among congeners. In the allopolyploids, most genes were expressed at mid-parent levels, but this was achieved via a phenomenon of genome-wide expression dominance, whereby gene expression was either up- or down-regulated to the level of one of the two parents, independent of the magnitude of gene expression. This massive expression dominance was approximately equal with respect to direction (up- or down-regulation), and the same diploid parent could be either the dominant or the recessive genome depending on the specific genomic combination. Transgressive up- and down-regulation were also common in the allopolyploids, both for genes equivalently or differentially expressed between the parents.ConclusionOur data provide novel insights into the architecture of gene expression in the allopolyploid nucleus, raise questions regarding the responsible underlying mechanisms of genome dominance, and provide clues into the enigma of the evolutionary prevalence of allopolyploids.
| S-EPMC2684529 | biostudies-literature
Project description:The evolutionary transition to self-compatibility facilitates polyploid speciation. In Arabidopsis relatives, the self-incompatibility system is characterized by epigenetic dominance modifiers, among which small RNAs suppress the expression of a recessive SCR/SP11 haplogroup. Although the contribution of dominance to polyploid self-compatibility is speculated, little functional evidence has been reported. Here we employ transgenic techniques to the allotetraploid plant A. kamchatica. We find that when the dominant SCR-B is repaired by removing a transposable element insertion, self-incompatibility is restored. This suggests that SCR was responsible for the evolution of self-compatibility. By contrast, the reconstruction of recessive SCR-D cannot restore self-incompatibility. These data indicate that the insertion in SCR-B conferred dominant self-compatibility to A. kamchatica. Dominant self-compatibility supports the prediction that dominant mutations increasing selfing rate can pass through Haldane's sieve against recessive mutations. The dominance regulation between subgenomes inherited from progenitors contrasts with previous studies on novel epigenetic mutations at polyploidization termed genome shock.
| S-EPMC10687001 | biostudies-literature
Project description:BackgroundDespite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora.ResultsWe detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species.ConclusionOverall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species.
| S-EPMC4112209 | biostudies-literature
Project description:Background and aimsSelf-fertilization is often associated with ecological traits corresponding to the ruderal strategy, and selfers are expected to be less competitive than outcrossers, either because of a colonization/competition trade-off or because of the deleterious genetic effects of selfing. Range expansion could reduce further competitive ability while polyploidy could mitigate the effects of selfing. If pollinators are not limited, individual fitness is thus expected to be higher in outcrossers than in selfers and, within selfers, in polyploids than in diploids. Although often proposed in the botanical literature and also suggested by meta-analyses, these predictions have not been directly tested yet.MethodsIn order to compare fitness and the competitive ability of four Capsella species with a different mating system and ploidy level, we combined two complementary experiments. First, we carried out an experiment outdoors in north-west Greece, i.e. within the range of the obligate outcrossing species, C. grandiflora, where several life history traits were measured under two different disturbance treatments, weeded plots vs. unweeded plots. To better control competition and to remove potential effects of local adaptation of the outcrosser, we also performed a similar competition experiment but under growth chamber conditions.Key resultsIn the outdoor experiment, disturbance of the environment did not affect the phenotype in any of the four species. For most traits, the obligate outcrossing species performed better than all selfing species. In contrast, polyploids did not survive or reproduce better than diploids. Under controlled conditions, as in the field experiment, the outcrosser had a higher fitness than selfing species and was less affected by competition. Finally, contrary to the outdoor experiment where the two behaved identically, polyploid selfers were less affected by competition than diploid selfes.ConclusionsIn the Capsella genus, selfing induces lower fitness than outcrossing and can also reduce competitive ability. The effect of polyploidy is, however, unclear. These results highlight the possible roles of ecological context in the evolution of selfing species.
| S-EPMC9113120 | biostudies-literature
Project description:The Quince (Cydonia oblonga Mill.), typically known for its self-compatibility, surprisingly presents a degree of self-incompatibility. This research focused on exploring the diversity within the self-incompatibility gene locus (S) in various C. oblonga genotypes. Through meticulous DNA sequencing, the study sought to unearth potential novel S alleles. In the process of genotyping the S gene across multiple quince genotypes, not only were the previously documented S1 and S2 alleles identified, but this investigation also uncovered two previously unrecognized alleles, termed S4 and S5. These alleles, particularly S4, emerged as the most prevalent among the tested genotypes. To corroborate the findings derived from DNA sequencing, the study employed pollen tube growth germination assays. These assays elucidated a higher pollen germination rate in the Ardabil2 genotype in contrast to Behta. Additionally, the study involved assessing pollen tube growth in both Ardabil2 and Behta through cross-pollination techniques, meticulously tracking the development of pollen tubes at various stages. Remarkably, the outcomes demonstrated that the Behta genotype possesses self-incompatibility, whereas the Ardabil2 genotype showcases a notable degree of self-compatibility. This groundbreaking discovery of new S alleles in quince not only affirms the species' self-compatibility but also sheds light on the complexities of allelic diversity and its impact on self-incompatibility. Such insights are invaluable for enhancing the yield of quince orchards through strategic breeding programs.
| S-EPMC10852308 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2013-04-02 | GSE45687 | GEO
Project description:The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis-regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts.
| S-EPMC4576713 | biostudies-literature