Lipid content and fatty acid composition of seeds of Capsella species from different geographical locations

Seeds of natural populations of Capsella bursa-pastoris, collected from temperate regions, weighed less and had a higher lipid content than those from colder regions. The long-chain (16:0, 18:0, 18:1, 18:2 and 18:3) and very long-chain (20:0, 20:1, 20:2 and 20:3) fatty acid compositions were, however, quite similar in the lipids of all the seed samples which indicates a rigid genetic, rather than environmental, control of fatty acid biosynthesis. Characteristics of the seeds of the diploid species C. rubella and C. grandiflora were similar to those of the tetraploid C. bursa-pastoris, with the exception of the distinctly lower lipid content in C. grandiflora seeds.     

Evolution of the tetraploidCapsella bursa-pastoris (Brassicaceae): Isoelectric focusing analysis of Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1.39) and its subunits (large subunits = LSU, small subunits = SSU) were isolated from threeCapsella spp. by gel electrophoresis and polypeptide composition was analyzed by isoelectric focusing (IEF) in the presence of 8M urea. The described techniques are recommended for large scale systematic studies. Multiple IEF banding patterns of the SSU are probably the outcome of a heterogenous multigene family. The two diploid speciesC. rubella andC. grandiflora show an identical IEF pattern and could be differentiated from the putative allotetraploidC. bursa-pastoris only by the SSU banding pattern. Uniqueness of some SSU bands in the tetraploid and in the two diploid species, respectively, may indicate an ancient alloploid origin of tetraploidC. bursa-pastoris followed by events leading to divergences in the genomes of the allotetraploid and its presumed diploid progenitors after the hybridization event (SSU gene elimination, acquisition of new SSU genes).     

Genomic Identification of Founding Haplotypes Reveals the History of the Selfing Species Capsella rubella

The shift from outcrossing to self-fertilization is among the most common evolutionary transitions in flowering plants. Until recently, however, a genome-wide view of this transition has been obscured by both a dearth of appropriate data and the lack of appropriate population genomic methods to interpret such data. Here, we present a novel population genomic analysis detailing the origin of the selfing species, Capsella rubella, which recently split from its outcrossing sister, Capsella grandiflora. Due to the recency of the split, much of the variation within C. rubella is also found within C. grandiflora. We can therefore identify genomic regions where two C. rubella individuals have inherited the same or different segments of ancestral diversity (i.e. founding haplotypes) present in C. rubella''s founder(s). Based on this analysis, we show that C. rubella was founded by multiple individuals drawn from a diverse ancestral population closely related to extant C. grandiflora, that drift and selection have rapidly homogenized most of this ancestral variation since C. rubella''s founding, and that little novel variation has accumulated within this time. Despite the extensive loss of ancestral variation, the approximately 25% of the genome for which two C. rubella individuals have inherited different founding haplotypes makes up roughly 90% of the genetic variation between them. To extend these findings, we develop a coalescent model that utilizes the inferred frequency of founding haplotypes and variation within founding haplotypes to estimate that C. rubella was founded by a potentially large number of individuals between 50 and 100 kya, and has subsequently experienced a twenty-fold reduction in its effective population size. As population genomic data from an increasing number of outcrossing/selfing pairs are generated, analyses like the one developed here will facilitate a fine-scaled view of the evolutionary and demographic impact of the transition to self-fertilization.     

Das Blühverhalten vonCapsella bursa-pastoris (Brassicaceae)

Capsella bursa-pastoris (L.)Med. is a partially self-pollinating, autogamous plant. The selfing-rate depends on ecological factors. High atmospheric humidity at temperatures over 15 °C and low light intensity, i.e. cloudy and rainy weather, lead to almost exclusive self-pollination, while dry and sunny weather favours outcrossing. At low temperatures (about 4–10 °C) anthesis is prolongated up to five-fold, but allogamy is reduced. Day-length distinctly influences the beginning of flowering.Capsella bursa-pastoris is not a day-neutral plant (as was supposed up to now) but behaves as a quantitative long-day plant.

Teil einer Publikationsreihe über die Populationsökologie vonCapsella bursa-pastoris (L.)Med.     

Evolutionary processes in the genusCapsella (Brassicaceae)

Capsella comprises diploid (C. grandiflora andC. rubella) and tetraploid taxa. It is argued that the tetraploidC. bursa-pastoris is of intraspecific origin despite disomic inheritance and fixed heterozygosity. It is of considerable age as evidenced by the fossil record and molecular data. Gene duplication by polyploidization and a mixed mating system provided the genetic flexibility for greatest colonizing success. Pronounced variation patterns at a micro- and macrogeographic scale are observed inC. bursa-pastoris for many characters including life history traits, leaf morphology and allozymes. This variation pattern can be explained by several components comprising phylogenetic age, random processes, ecotypic variation and colonization history. The adaptive strategy ofC. bursa-pastoris cannot be assigned to either ecotypic differentiation or phenotypic plasticity alone. It depends on the trait under study.Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday     

'Missing link' species Capsella orientalis and Capsella thracica elucidate evolution of model plant genus Capsella (Brassicaceae)

To elucidate the evolutionary history of the genus Capsella, we included the hitherto poorly known species C. orientalis and C. thracica into our studies together with C. grandiflora, C. rubella and C. bursa‐pastoris. We sequenced the ITS and four loci of noncoding cpDNA regions (trnL – F, rps16, trnH –psbA and trnQ –rps16). Sequence data were evaluated with parsimony and Bayesian analyses. Divergence time estimates were carried out with the software package BEAST. We also performed isozyme, cytological, morphological and biogeographic studies. Capsella orientalis (self‐compatible, SC; 2n = 16) forms a clade (eastern lineage) with C. bursa‐pastoris (SC; 2n = 32), which is a sister clade (western lineage) to C. grandiflora (self‐incompatible, SI; 2n = 16) and C. rubella (SC; 2n = 16). Capsella bursa‐pastoris is an autopolyploid species of multiple origin, whereas the Bulgarian endemic C. thracica (SC; 2n = 32) is allopolyploid and emerged from interspecific hybridization between C. bursa‐pastoris and C. grandiflora. The common ancestor of the two lineages was diploid and SI, and its distribution ranged from eastern Europe to central Asia, predominantly confined to steppe‐like habitats. Biogeographic dynamics during the Pleistocene caused geographic and genetic subdivisions within the common ancestor giving rise to the two extant lineages.     

Flower morphology and pollen germination in the genus Capsella (Brassicaceae)

Evolutive changes in mating systems are often accompanied by changes in flower morphology, such as the reduction in size or even loss of petals, changes in production of volatiles, pollen/ovule ratio, the position between anthers and stigma and the germination time of pollen after pollination. These changes have been merged under the term “selfing syndrome” and often result in new taxonomic species. The evolutionary shift frequently happens parallel within many families and genera, for example within the Brassicaceae family. Within the genus Capsella, which is closely related to the molecular model species pair Arabidopsis lyrata (SI)/A. thaliana (SC), we studied self-incompatible and self-compatible species. SC species C. rubella and C. bursa-pastoris produce in comparison with the SI species C. grandiflora (i) smaller petals as the result of decreased cell division and only less of decreasing cell volume, (ii) less production of pollen in one flower, (iii) show a lesser incision between the two valves of the fruits, in combination with a shorter style, and (iv) have a much quicker fertilization of SC pollen after pollination. Crossing success between the diploid species, between different provenances of the tetraploid C. bursa-pastoris, and between the two diploid species and particular individuals of the self-incompatible C. grandiflora has been proven.     

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

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.Subject terms: Evolution, Polyploidy in plants, Plant evolution, Haplotypes     

Mating system shifts and transposable element evolution in the plant genus Capsella

Background

Despite 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.

Results

We 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.

Conclusion

Overall, 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.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-602) contains supplementary material, which is available to authorized users.     

Associations of genes encoding allozymes peroxidase and superoxide dismutase in poplar and spruce species

Summary Isozymes of peroxidase (PER) and superoxide dismutase (SOD) were analyzed in vegetative buds or very young leaves of seven species and two interspecific hybrids of Populus, in progenies of seven controlled crosses of three Populus species, and in needles of five Picea species and one putative hybrid. One to three PER, and one or two SOD zones of activity were observed. Electrophoretic mobility (EM) and banding phenotypes of isozymes of one PER locus were identical to those of one SOD locus in vegetative buds of five Populus species and hybrid. In leaves of the four Populus species and hybrid and progenies of controlled crosses, EM and phenotypes of isozymes of two PER loci were identical to those of two SOD loci. In Picea species, EM of isozymes of the only SOD locus was somewhat similar but not identical to that of one PER locus, and isozyme phenotypes of all individuals at the SOD locus were not identical to those at a PER locus. Chi-square tests verified the single-gene Mendelian control of the segregating allozyme variants at each of Per-L1 and Sod-1 in the three Populus species. The results of joint two-locus segregation tests indicated a very tight linkage and no recombination between Per-L1 and Sod-1 in three Populus species. Genes coding for isozymes of one or two PER loci are either presumably the same as, or very tightly linked to, the genes coding for isozymes of one or two SOD loci in the Populus species.     

Biochemical properties of duplicated isozymes of phosphoglucose isomerase in the plant Clarkia xantiana

The structural gene locus specifying subunits of the cytoplasmic isozymes of phosphoglucose isomerase (PGI) is present in duplicate in many diploid species of Clarkia (Onagraceae), a genus of annual plants native to California. We studied the kinetic properties and molecular weights of a large number of genetically defined and highly purified PGIs in C. xantiana, a species with the duplication, as a means of examining the biochemical consequences of the evolution of a new gene locus. This species is primarily outcrossing, but also includes several previously described predominantly self-pollinating populations. Both cytoplasmic PGI loci in the outcrossing populations are polymorphic and their enzyme products are readily separated by electrophoresis. The PGIs from the outcrossing populations were generally closely similar in molecular weight, pH optimum, heat sensitivity, energy of activation, and apparent K _m (fructose-6-phosphate). The PGI loci in the selfing populations are monomorphic and specify enzymes having identical electrophoretic mobilities to those coded by the most frequent alleles of the outcrosser. The PGI isozymes in the selfers differed fivefold in K _m , suggesting that they have a very different catalytic effectiveness. The high K _m of the PGI-3A isozyme (1.1mm) was anomalous among the examined and would likely be disadvantageous in a species which lacked other more normally functioning PGIs. But in the cytoplasm of the selfing plants, it is present with other PGIs that have low K _m values. The PGI-3A enzyme is a good candidate for a gene product coded by a forbidden mutation that could not have been established in the absence of the duplication. The rationale for this suggestion is described and it is also pointed out that the divergence of duplicated genes is influenced by many factors such as the breeding system and other population factors as well as the effect of particular mutations.This research was supported by NSF Grant DEB77-08448.     

Impact of demography on linked selection in two outcrossing Brassicaceae species

Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.     

Germination behaviour in populations ofCapsella bursa-pastoris (Cruciferae)

Germination behaviour of variousCapsella bursa-pastoris populations collected from Scandinavia, Middle Europe and the Alps, was tested in unheated, non-illuminated greenhouses (46 populations) and in growth chambers using 5–7 alternating temperature regimes (16 populations). For all populations, the influence of temperature on germination rate is straightforward: the higher the temperature, the greater the germination. Germination capacity, however, may depend on the geographical region. There is also a strong seed age effect on both, rate and capacity of germination. Once dormancy was broken, seeds from all populations were able to germinate over the entire range of temperatures. Some populations revealed a more or less pronounced temperature optimum for germination capacity, others germinated equally well over the entire temperature range. This indicates genetic heterogeneity between populations. However, no correlation between germinability and any environmental pattern was detected. The data indicate thatCapsella bursa-pastoris has adopted a germination strategy which includes a broad temperature tolerance. Germination of wildCapsella plants seems to be regulated by the factors contributing to the inception and breaking of dormancy which depend on pre- and postharvest conditions. Adaptation in germination behaviour inCapsella bursa-pastoris is different from that in other life history traits (flowering behaviour, growth form parameters).     

Flowering Ecotypes of Capsella bursa-pastoris(L.) Medik. (Brassicaceae) Analysed by a Cosegregation of Phenotypic Characters (QTL) and Molecular Markers

Capsella bursa-pastoris(Brassicaceae) is an annual to biennialpredominantly autogamous species distributed worldwide. Usinga linkage map with RAPDs and isozymes we studied quantitativetrait loci (QTL) controlling phenotypic traits in this invasivespecies. To obtain a mapping population we crossed two plantsoccurring in different climatic regions in California, USA (CentralValley and Sierra Nevada) with the most diverse ecotypes (phenotypicparameters) and genotypes (isozyme multilocus genotypes). Ahundred and thirteen F₂individuals were raised and analysedfor segregation at 107 RAPDs, six isozyme loci, and one locusdetermining leaf type. The number, location and magnitude ofgenes underlying 13 traits were determined by using both intervaland composite interval mapping. Two to five QTL affecting onecharacter have been detected. Altogether the 13 quantitativetraits produced 48 QTL. The inheritance patterns of traits rangedfrom those controlled by one QTL with a major effect to thosecontrolled by several QTL with only minor effects. Closely linkedQTL, e.g. onset of flowering with rosette leaf number, wereinterpreted as pleiotropic. Three major QTL account for onsetof flowering. These loci were linked to at least three isozymeloci and several other QTL responsible for developmental traitslike rosette leaf number. Heritability of quantitative traits,segregation of the leaf type, and segregation of the allozymeswas tested in the F₃generation. We conclude that historicalevents alone are insufficient to explain the distribution patternof isozyme multilocus genotypes during the colonization of newregions and habitats. The present evidence indicates that ecotypicadaptation and genetic linkage of isozyme loci with adaptivecharacters are involved. Copyright 2001 Annals of Botany Company Capsella bursa-pastoris, Shepherd’s purse, Brassicaceae, plant invasions, RAPDs, allozymes, Mediterranean multilocus genotype, flowering ecotypes, leaf type, fruit dimensions, cosegregation analysis, QTL     

Quantitative studies on the mating system of opium poppy (Papaver somniferum L.)

Summary Nearly 400 individuals at two locations and over a number of years were crossed and subsequently scored for selfing versus outcrossing in eight monohybrid populations of opium poppy (Papaver somniferum). Two different marker loci, petal colour (R/r) and capsule size (B/b) were used to determine the male gametes that had effected fertilizations in F₂ recessives (rr and bb). The estimates of the outcrossing parameter were found to vary with year, location and for the marker locus used ( range: 0.0988–0.3704). Study of two dihybrid crosses involving the two loci simultaneously, further confirmed that outcrossing at the R/r locus was significantly greater than that at the B/b locus. The nature of the outcrossing was, in general, nonrandom. Selfmg predominated in this species; however, there was a high frequency of natural outcrossing for generating variations in P. somniferum.CIMAP publication No. 1086     

Isozyme gene markers in Vicia faba L.

Summary This study was conducted to assess the genetic basis of the variability observed for the glutamate oxaloacetate transaminase (GOT), Superoxide dismutase (SOD), esterase (EST), and malate dehydrogenase (MDH) isozyme systems in different open-pollinated Vicia faba varieties. Individual plants showing contrasting zymogram patterns were simultaneously selfed and cross-combined. Crossing was unsuccessful in producing progeny, and only selfed progenies were suitable for genetical analysis of isozyme variability. Three zones of GOT activity were made visible. The isozyme of GOT-2 and GOT-3 zones were dimeric and under the control of three alleles at the Got-2 locus and two alleles at the Got-3 locus, respectively. The isozymes of the GOT-1 zone did not show any variability. Three zones of SOD isozyme activity were made visible. The isozymes occurring in the SOD-1 (chloroplastic isozyme form) and SOD-2 (cytosol isozyme form) zones were dimeric and under the control of two alleles at the Sod-1 and Sod-2 loci. The isozyme visualized in the SOD-3 zone (mitochondrial isozyme form) were tetrameric and under the control of two alleles at the Sod-3 locus. Apparently the isozymes made visible in the most anodal esterase zones EST-1, EST-2, and EST-3 were monomeric, and the occurrence of two alleles at each of two different loci explained the variability observed in the EST-2 and EST-3 zones. For MDH, only two five-banded zymogram pattern types were found, and every selfed progeny showed only one of the two zymogram type, indicating that each individual possessed fixed alleles at the loci controlling MDH isozyme. Got-2, Got-3, Sod-1, Sod-2, and Sod-3 appear to be five new isozyme gene markers that can be useful in Vicia faba breeding for linkage study, varietal fingerprinting, outcrossing rate estimate, and indirect selection for quantitative characters.     

Mapping of RFLP and qualitative trait loci in Brassica rapa and comparison to the linkage maps of B. napus,B. oleracea,and Arabidopsis thaliana

A linkage map of restriction fragment length polymorphisms (RFLPs) was constructed for oilseed, Brassica rapa, using anonymous genomic DNA and cDNA clones from Brassica and cloned genes from the crucifer Arabidopsis thaliana. We also mapped genes controlling the simply inherited traits, yellow seeds, low seed erucic acid, and pubescence. The map included 139 RFLP loci organized into ten linkage groups (LGs) and one small group covering 1785 cM. Each of the three traits mapped to a single locus on three different LGs. Many of the RFLP loci were detected with the same set of probes used to construct maps in the diploid B. oleracea and the amphidiploid B. napus. Comparisons of the linkage arrangements between the diploid species B. rapa and B. oleracea revealed six LGs with at least two loci in common. Nine of the B. rapa LGs had conserved linkage arrangements with B. napus LGs. The majority of loci in common were in the same order among the three species, although the distances between loci were largest on the B. rapa map. We also compared the genome organization between B. rapa and A. thaliana using RFLP loci detected with 12 cloned genes in the two species and found some evidence for a conservation of the linkage arrangements. This B. rapa map will be used to test for associations between segregation of RFLPs, detected by cloned genes of known function, and traits of interest.