Regeneration of intergeneric somatic hybrid plants between Lycopersicon esculentum and Solanum muricatum

Chromosome-level pepino genome provides insights into genome evolution and anthocyanin biosynthesis in Solanaceae

Pepino (Solanum muricatum, 2n = 2x = 24), a member of the Solanaceae family, is an important globally grown fruit. Herein, we report high-quality, chromosome-level pepino genomes. The 91.67% genome sequence is anchored to 12 chromosomes, with a total length of 1.20 Gb and scaffold N50 of 87.03 Mb. More than half the genome comprises repetitive sequences. In addition to the shared ancient whole-genome triplication (WGT) event in eudicots, an additional new WGT event was present in the pepino. Our findings suggest that pepinos experienced chromosome rearrangements, fusions, and gene loss after a WGT event. The large number of gene removals indicated the instability of Solanaceae genomes, providing opportunities for species divergence and natural selection. The paucity of disease-resistance genes (NBS) in pepino and eggplant has been explained by extensive loss and limited generation of genes after WGT events in Solanaceae. The outbreak of NBS genes was not synchronized in Solanaceae species, which occurred before the Solanaceae WGT event in pepino, tomato, and tobacco, whereas it was almost synchronized with WGT events in the other four Solanaceae species. Transcriptome and comparative genomic analyses revealed several key genes involved in anthocyanin biosynthesis. Although an extra WGT event occurred in Solanaceae, CHS genes related to anthocyanin biosynthesis in grapes were still significantly expanded compared with those in Solanaceae species. Proximal and tandem duplications contributed to the expansion of CHS genes. In conclusion, the pepino genome and annotation facilitate further research into important gene functions and comparative genomic analysis in Solanaceae.

The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

BACKGROUND

Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species.

RESULTS

Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome.

CONCLUSIONS

This study represents the first genomic resource for the pepino. We suggest that the data will be useful not only for improvement of the pepino, but also for potato and tomato breeding and gene transfer. The high quality of the transcriptome presented here also facilitates comparative studies in the genus Solanum. The accurate transcript annotation will enable us to figure out the gene function of particular traits of interest. The high number of markers (SSR and nucleotide-level variants) obtained will be useful for breeding programs, as well as studies of synteny, diversity evolution, and phylogeny.

Plant regeneration from mesophyll protoplasts ofDianthus superbus

Leaf mesophyll protoplasts ofDianthus superbus were cultured at a density of 5 × 10(4) protoplasts/ml and divided at about 18% plating efficiency in MS liquid medium supplemented with 0.5 mg/L BAP, 2.0 mg/L NAA and 9% mannitol after 2 weeks. Protocolonies formed after 3 to 4 weeks of culture in the dark at 27°C. These colonies were transferred to continuous illumination (21.5 μE m(-2) sec(-1)) for 2 weeks where most of the colonies divided to form microcalli, about 2 mm in diameter. Subsequently, green microcalli were transferred to MS solidified medium with 2.0 mg/L 2,4-D that induced shoot-forming calli after 4 weeks. These calli were transferred onto N6-2 medium containing 0.1 mg/L 2,4-D, 0.1 mg/L NAA, 2.0 mg/L kinetin and 2.0 g/L casein hydrolysate and were cultured under light. After 5 weeks the calli gave rise to multiple shoots (10 to 15 per callus). Upon transfer to MS medium containing 2.0 mg/L NAA, individual shoots were rooted in 4 weeks. The regenerants were successfully transplanted into potting soil.

Plant regeneration from protoplast fusion inPassiflora spp

Protoplasts were isolated from leaf explants ofPassiflora edulis var.flavicarpa (the yellow passion fruit) and from cell suspensions of fivePassiflora species. Chemical fusion was performed using polyethylene glycol and the microcolonies obtained were transferred to growth medium to produce calli. Electrophoresis of soluble proteins and analysis of isoenzymes from calli produced from the fusion experiments were performed to select somatic hybrids. Specific polypeptide bands allowed the identification of somatic hybrids betweenP. edulis var.flavicarpa (+)P. alata, P. edulis var.flavicarpa (+)P. amethystina, P. edulis var.flavicarpa (+)P. cincinnata, P. edulis var.flavicarpa (+)P. giberti andP. edulis var.flavicarpa (+)P. coccinea. An average of 3 to 5% hybrid calli were obtained. With the exception of theP. edulis var.flavicarpa (+)P. coccinea, whole plants were recovered from all hybrids. These somatic hybrids showed 4n=36 chromosomes, which represents a further evidence of their hybridity.

Analysis of nuclear and organellar DNA of somatic hybrid calli and plants between Lycopersicon spp. and Nicotiana spp

Protoplast fusion experiments between Lycopersicon esculentum or L. peruvianum and Nicotiana tabacum or N. plumbaginifolia were performed to investigate the possibility of producing symmetric and asymmetric somatic hybrids between these genera. These fusions, which involved 1.7 x 10(8) protoplasts, yielded 35 viable hybrid calli. Plant regeneration was successful with two calli. One of these regenerants flowered, but developed no fruits. Analysis of the nuclear DNA by means of dot blot hybridization with species-specific repetitive DNA probes combined with flow cytometry, revealed that the nuclei of most hybrid calli contained the same absolute amount of Nicotiana DNA as the Nicotiana parent or (much) less, whereas the amount of Lycopersicon DNA per nucleus was 2-5 times that of the parental genotype. Eighteen of the 34 hybrids analyzed possessed Lycopersicon chloroplast DNA (cpDNA), whereas the other 16 had DNA from Nicotiana chloroplasts. The cpDNA type was correlated with the nuclear DNA composition; hybrids with more than 2C Nicotiana nuclear DNA possessed Nicotiana chloroplasts, whereas hybrids with 2C or less Nicotiana nuclear DNA contained Lycopersicon chloroplasts. Mitochondrial DNA (mtDNA) composition was correlated with both nuclear DNA constitution and chloroplast type. Hybrids possessed only or mainly species-specific mtDNA fragments from the parent predominating in the nucleus and often providing the chloroplasts. The data are discussed in relation to somatic incompatibility which could explain the low frequency at which hybrids between Lycopersicon and Nicotiana species are obtained and the limited morphogenetic potential of such hybrids.

Fertile somatic hybrids between Petunia hybrida and a wild species, Petunia variabilis

Somatic hybrid plants were regenerated following electrofusion between leaf mesophyll protoplasts of P. hybrida (2n = 14) and a wild sexually incompatible species, P. variabilis (2n = 18). The selection of hybrids was based on the hybrid vigour, expressed both in the growth of the callus and at the shoot formation stage, resulting from the combination of parental genomes. Calli exhibiting vigorous growth were selected, and upon transfer to regeneration medium gave rise to shoots. Four regenerated plants from three calli had morphological characteristics intermediate between those of the parents. The hybrid nature of these plants was confirmed by chromosome counts as well as isozyme and DNA analyses. They had amphidiploid chromosome numbers (2n = 32) and were fertile. Following self-pollination and backcrossing with P. variabilis, large numbers of F2 and BC1 seedlings were obtained.

Sexual and somatic hybridization in the genusLycopersicon

In recent years, a large number of reports have been published on the recovery of somatic hybrids in the genusLycopersicon and their potential use as a tool in plant breeding programs. Somatic hybridization as a way of enabling the incompatibility barriers which exist within the genusLycopersicon to be bypassed has attracted great interest. WildLycopersicon species harbor numerous interesting agronomic characteristics, which could be transferred to tomato by somatic hybridization. In particular, the production of asymmetric hybrids is explored as an approach to obtain the transfer of only a part of the nuclear genome of wildLycopersicon species. Considerable information is available on the fate of chloroplasts and mitochondria in fusion products inLycopersicon, and unfortunately, cybridization (transfer of chloroplasts and/or mitochondria) seems often difficult to achieve.

Establishment of somatic hybrid cell lines between Zea mays L. (maize) and Triticum sect, trititrigia MacKey (trititrigia)

Somatic hybrid cell lines were constructed by the fusion of protoplasts isolated from cell suspensions of Zea mays L. (maize, 2n = 20) and Triticum sect, trititrigia MacKey (trititrigia, 2n = 35), a perennial hybrid of T. durum Desf. and Elytrigia intermedium (Host) Nevski. Iodoacetamide-inactivated protoplasts of maize were fused with trititrigia protoplasts, which were sensitive to the PEG/DMSO fusion treatment at high pH and high calcium. Based on physiological complementation, approximately 0.002% of the total protoplasts cultured following fusion treatment developed into cell colonies, and 79 lines of them, almost a half, were singled out and subcultured. Among the subcultured lines three were, in comparison with the parents, identified as somatic hybrids by their coupled XbaI restriction patterns of total DNAs probed with the ribosomal DNA of rice. Southern analysis of the digested total DNAs with a mitochondrial gene, atpA., from pea, or a chloroplast gene, trnK, from rice, revealed that all the hybrids carried only the organellar DNAs of trititrigia, which excluded the possibilities of a chimeric callus or any DNA contamination. Cytogenetically, one hybrid was mixoploid with a 2n of 46-67 in which chromosomal endoreduplication, characterized by the appearance of diplochromosomes, was occasionally observed. Its hybridity was reconfirmed by the fact that it bore the satellite chromosomes of both maize and trititrigia, which were distinguishable from each other by size. In contrast, the other two hybrids were aneuploids. The potential of gene transfer between Zea and Triticum species was thus conclusively established.

Somatic hybridization between Dianthus chinensis and D. barbatus through protoplast fusion

Protoplasts isolated from leaf mesophyll cells of Dianthus chinensis and D. barbatus were fused by polyethylene glycol (PEG). Calli exhibiting vigorous growth were selected from the PEG-treated protoplasts and shoots were regenerated from one of these calli after 5 months of culture. These shoots readily rooted and continuously produced flowers in the in-vitro condition. The data on flower color, chromosome number, and esterase isozyme patterns indicated that this plantlet was an interspecific somatic hybrid. The hybridity of the plantlet was also confirmed by nuclear rDNA analysis. This report provides the possibility of applying the somatic hybridization technique for the genetic improvement of the genus Dianthus.