Molecular genetic features of polyploidization and aneuploidization reveal unique patterns for genome duplication in diploid Malus

Phylogeny of genera in Maleae (Rosaceae) based on chloroplast genome analysis

In Rosaceae, the replacement of the traditional four-subfamily division (Amygdaloideae or Prunoideae, Maloideae, Rosoideae, and Spiraeoideae) by the three-subfamily division (Dryadoideae, Rosoideae, and Amygdaloideae), the circumscription, systematic position, and phylogeny of genera in Maleae need to be reconsidered. The study aimed to circumscribe Maleae, pinpoint its systematic position, and evaluate the status of all generally accepted genera in the tribe using complete chloroplast genome data. Results indicated that Maleae consisted of pome-bearing genera that belonged to Maloideae as well as four genera (Gillenia, Kageneckia, Lindleya, and Vauquelinia) that were formerly considered to be outside Maloideae. The tribe could be subdivided into four subtribes: Gilleniinae (Gillenia), Lindleyinae (Kageneckia and Lindleya), Vaugueliniinae (Vauquelinia), and Malinae (all other genera; the core Maleae). Among the 36 recognized genera, Aria, Docyniopsis, Chamaemespilus, and Mespilus were not considered distinct and more research is needed to determine the taxonomic status of Rhaphiolepis from Eriobotrya. Within the core Maleae, five groups were revealed, whereas Sorbus L. was split as its members belonged to different groups.

Aneuploids and its increment on diversity of Lippia alba polyploid complex: genetic aspects and origin

BACKGROUND

Aneuploidy is associated with add or lack of individual chromosomes. The knowledge regarding aneuploidy is still rare in wild and tropical populations. Lippia alba is a tropical polyploid complex naturally formed, with 2x, 3x, 4x, 6x, and aneuploid individuals. The species presents pharmacological and medicinal importance, due to its essential oil compounds, which are related to the ploidal level. Considering the singularity of aneuploids emergence and stability, we proposed to investigate putative cytotypes involved in the aneuploids formation.

METHODS AND RESULTS

Molecular, cytogenetic, reproductive, and chemical approaches were adopted. The results showed that the aneuploids possibly have independent origin considering the genetic, chemical and karyotypical profiles. The chemical composition of aneuploids is related to genetic similarity. The aneuploid origin may involve 2x and 3x cytotypes being possible to rise four scenarios of crosses to explain that.

CONCLUSIONS

The results, in general, contribute to the comprehension of the origin of aneuploids and highlight the genetic profile of these accessions as a key element on the understanding of the chemical profile of L. alba accessions.

Molecular karyotypes of loquat (Eriobotrya japonica) aneuploids can be detected by using SSR markers combined with quantitative PCR irrespective of heterozygosity

BACKGROUND

Aneuploidy, a condition caused by an imbalance between the relative dosages of chromosomes, generally produces a novel phenotype specific to the molecular karyotype. Few techniques are currently available for detecting the molecular karyotypes of aneuploids in plants.

RESULTS

Based on this imbalance in chromosome dosage, a new approach (referred to as 'SSR-qPCR') combining simple sequence repeat (SSR) markers and quantitative real-time PCR (qPCR) has been developed and utilized to detect some common aneuploids irrespective of heterozygosity. We screened 17 specific SSR markers covering all loquat linkage groups and redesigned 6 pairs of primers for SSR markers that can detect loquat chromosome aneuploidies. The SSR-qPCR detection results obtained for hybrid progeny and open-pollination progeny of triploid loquat showed diagnostic accuracies of 88.9% and 62.5%, respectively, compared with the chromosome preparation results.

CONCLUSION

SSR-qPCR can detect loquat aneuploids and be used to construct the entire molecular karyotypes of aneuploid individuals. Therefore, this method offers a novel alternative for the detection of chromosome aneuploidies.

Reproductive pathways in Hieracium s.s. (Asteraceae): strict sexuality in diploids and apomixis in polyploids

Background and Aims

Apomixis or asexual seed reproduction is a key evolutionary mechanism in certain angiosperms providing them with reproductive assurance and isolation. Nevertheless, the frequency of apomixis is largely unknown, especially in groups with autonomous apomixis such as the diploid-polyploid genus Hieracium.

Methods

Using flow cytometric analyses, we determined the ploidy level and reproductive pathways (sexual vs. apomictic) for 7616 seeds originating from 946 plants belonging to >50 taxa sampled at 130 sites across Europe.

Key Results

Diploid seeds produced by diploids were formed exclusively by the sexual pathway after double fertilization of reduced embryo sacs. An absolute majority of tri- and tetraploid seeds (99.6 %) produced by tri- and tetrapolyploid taxa were formed by autonomous apomixis. Only 20 polyploid seeds (0.4 %) were formed sexually. These seeds, which originated on seven polyploid accessions of four taxa, were formed after fertilization of either unreduced embryo sacs through a so-called triploid bridge or reduced embryo sacs, and frequently resulted in progeny with an increased ploidy. In addition, the formation of seedlings with increased ploidy (4x and 6x) was found in two triploid plants. This is the first firm evidence on functional facultative apomixis in polyploid members of Hieracium sensu stricto (s.s.).

Conclusions

The mode of reproduction in Hieracium s.s. is tightly associated with ploidy. While diploids produce seeds exclusively sexually, polyploids produce seeds by obligate or almost obligate apomixis. Strict apomixis can increase the reproductive assurance and this in turn can increase the colonization ability of apomicts. Nevertheless, our data clearly show that certain polyploid plants are still able to reproduce sexually and contribute to the formation of new cytotypes and genotypes. The finding of functional facultative apomicts is essential for future studies focused on evolution, inheritance and ecological significance of apomixis in this genus.

Genetic analysis of a major international collection of cultivated apple varieties reveals previously unknown historic heteroploid and inbred relationships

Domesticated apple (Malus x domestica Borkh.) is a major global crop and the genetic diversity held within the pool of cultivated varieties is important for the development of future cultivars. The aim of this study was to investigate the diversity held within the domesticated form, through the analysis of a major international germplasm collection of cultivated varieties, the UK National Fruit Collection, consisting of over 2,000 selections of named cultivars and seedling varieties. We utilised Diversity Array Technology (DArT) markers to assess the genetic diversity within the collection. Clustering attempts, using the software STRUCTURE revealed that the accessions formed a complex and historically admixed group for which clear clustering was challenging. Comparison of accessions using the Jaccard similarity coefficient allowed us to identify clonal and duplicate material as well as revealing pairs and groups that appeared more closely related than a standard parent-offspring or full-sibling relations. From further investigation, we were able to propose a number of new pedigrees, which revealed that some historically important cultivars were more closely related than previously documented and that some of them were partially inbred. We were also able to elucidate a number of parent-offspring relationships that had resulted in a number of important polyploid cultivars. This included reuniting polyploid cultivars that in some cases dated as far back as the 18th century, with diploid parents that potentially date back as far as the 13th century.

Phylogeny of Maleae (Rosaceae) Based on Multiple Chloroplast Regions: Implications to Genera Circumscription

Maleae consists of economically and ecologically important plants. However, there are considerable disputes on generic circumscription due to the lack of a reliable phylogeny at generic level. In this study, molecular phylogeny of 35 generally accepted genera in Maleae is established using 15 chloroplast regions. Gillenia is the most basal clade of Maleae, followed by Kageneckia + Lindleya, Vauquelinia, and a typical radiation clade, the core Maleae, suggesting that the proposal of four subtribes is reasonable. In the core Maleae including 31 genera, chloroplast gene data support that the four Malus-related genera should better be merged into one genus and the six Sorbus-related genera would be classified into two genera, whereas all Photinia-related genera should be accepted as distinct genera. Although the phylogenetic relationships among the genera in Maleae are much clearer than before, it is still premature to make a formal taxonomic treatment for these genera.

Post-polyploid diploidization and diversification through dysploid changes

Whole-genome duplications are widespread across land plant phylogenies and particularly frequent in ferns and angiosperms. Genome duplications spurred the evolution of key innovations associated with diversification in many angiosperm clades and lineages. Such diversifications are not initiated by genome doubling per se. Rather, differentiation of the primary polyploid populations through a range of processes results in post-polyploid genome diploidization. Structural diploidization gradually reverts the polyploid genome to one functionally diploid-like through chromosomal rearrangements which frequently result in dysploid changes. Dysploidies may lead to reproductive isolation among post-polyploid offspring and significantly contribute to speciation and cladogenetic events.

Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication

Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.

How diploidization turned a tetraploid into a pseudotriploid

PREMISE OF THE STUDY

Despite being highly fertile and occupying a large geographic region, the North American heartleaf bittercress (Cardamine cordifolia; Brassicaceae) has a puzzling triploid-like chromosome number (2n = 3x = 24). As most triploids are sterile, we embarked on a detailed analysis of the C. cordifolia genome to elucidate its origin and structure.

METHODS

Mitotic and meiotic chromosome complement of C. cordifolia was analyzed by comparative chromosome painting using chromosome-specific BAC contigs of Arabidopsis thaliana. Resulting chromosome patterns were documented by multicolor fluorescence microscopy and compared with known ancestral and extant Brassicaceae genomes.

KEY RESULTS

We discovered that C. cordifolia is not a triploid hybrid but a diploidized tetraploid with the prevalence of regular, diploid-like meiotic pairing. The ancestral tetraploid chromosome number (2n = 32) was reduced to a triploid-like number (2n = 24) through four terminal chromosome translocations.

CONCLUSIONS

The structure of the pseudotriploid C. cordifolia genome results from a stepwise diploidization process after whole-genome duplication. We showed that translocation-based descending dysploidy (from n = 16 to n = 12) was mediated by the formation of five new chromosomes. The genome of C. cordifolia represents the diploidization process in statu nascendi and provides valuable insights into mechanisms of postpolyploidy rediploidization in land plants. Our data further suggest that chromosome number alone does not need to be a reliable proxy of species' evolutionary past and that the same chromosome number may originate either by polyploidization (hybridization) or due to descending dysploidy.

Seed formation in triploid loquat (Eriobotrya japonica) through cross-hybridization with pollen of diploid cultivars

As the fruits of loquat (Eriobotrya japonica, 2n = 2x = 34) carry large seeds, the breeding of seedless loquat has long been a goal. The recent creation of triploid cultivars (2n = 3x = 51) and the application of gibberellins allow commercial production of seedless loquat, but the possibility of seed formation in triploid loquats has not been carefully investigated. Through crossing experiments and cytological observations of meiosis and pollen tube growth, we found that the triploid line 3N-N28 was essentially self-sterile, but developed seeds on pollination with pollen from diploid cultivars at rates of up to 5.5%. Almost half of the seedlings survived to 5 months, and carried diploid (2n = 34), tetraploid (2n = 68), or aneuploid chromosome numbers. Our results suggest that triploid loquat cultivars might retain the risk of seed formation. Protection from pollination by diploid cultivars or the development of new triploid cultivars will be necessary to ensure the production of seedless loquat fruits.

Epigenetic control of mobile DNA as an interface between experience and genome change

Mobile DNA in the genome is subject to RNA-targeted epigenetic control. This control regulates the activity of transposons, retrotransposons and genomic proviruses. Many different life history experiences alter the activities of mobile DNA and the expression of genetic loci regulated by nearby insertions. The same experiences induce alterations in epigenetic formatting and lead to trans-generational modifications of genome expression and stability. These observations lead to the hypothesis that epigenetic formatting directed by non-coding RNA provides a molecular interface between life history events and genome alteration.

The more the merrier: recent hybridization and polyploidy in cardamine

This article describes the use of cytogenomic and molecular approaches to explore the origin and evolution of Cardamine schulzii, a textbook example of a recent allopolyploid, in its ~110-year history of human-induced hybridization and allopolyploidy in the Swiss Alps. Triploids are typically viewed as bridges between diploids and tetraploids but rarely as parental genomes of high-level hybrids and polyploids. The genome of the triploid semifertile hybrid Cardamine × insueta (2n = 24, RRA) was shown to combine the parental genomes of two diploid (2n = 2x = 16) species, Cardamine amara (AA) and Cardamine rivularis (RR). These parental genomes have remained structurally stable within the triploid genome over the >100 years since its origin. Furthermore, we provide compelling evidence that the alleged recent polyploid C. schulzii is not an autohexaploid derivative of C. × insueta. Instead, at least two hybridization events involving C. × insueta and the hypotetraploid Cardamine pratensis (PPPP, 2n = 4x-2 = 30) have resulted in the origin of the trigenomic hypopentaploid (2n = 5x-2 = 38, PPRRA) and hypohexaploid (2n = 6x-2 = 46, PPPPRA). These data show that the semifertile triploid hybrid can promote a merger of three different genomes and demonstrate how important it is to reexamine the routinely repeated textbook examples using modern techniques.

Production of diploid male gametes in Arabidopsis by cold-induced destabilization of postmeiotic radial microtubule arrays

Whole-genome duplication through the formation of diploid gametes is a major route for polyploidization, speciation, and diversification in plants. The prevalence of polyploids in adverse climates led us to hypothesize that abiotic stress conditions can induce or stimulate diploid gamete production. In this study, we show that short periods of cold stress induce the production of diploid and polyploid pollen in Arabidopsis (Arabidopsis thaliana). Using a combination of cytological and genetic analyses, we demonstrate that cold stress alters the formation of radial microtubule arrays at telophase II and consequently leads to defects in postmeiotic cytokinesis and cell wall formation. As a result, cold-stressed male meiosis generates triads, dyads, and monads that contain binuclear and polynuclear microspores. Fusion of nuclei in binuclear and polynuclear microspores occurs spontaneously before pollen mitosis I and eventually leads to the formation of diploid and polyploid pollen grains. Using segregation analyses, we also found that the majority of cold-induced dyads and triads are genetically equivalent to a second division restitution and produce diploid gametes that are highly homozygous. In a broader perspective, these findings offer insights into the fundamental mechanisms that regulate male gametogenesis in plants and demonstrate that their sensitivity to environmental stress has evolutionary significance and agronomic relevance in terms of polyploidization.