Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding.

BACKGROUND: Solanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatible with S. melongena. Despite their great interest in S. melongena breeding programs, the genomic resources for these species are scarce. RESULTS: RNA-Seq was performed with NGS from pooled RNA of young leaf, floral bud and young fruit tissues, generating more than one hundred millions raw reads per species. The transcriptomes were assembled in 83,905 unigenes for S. incanum and in 87,084 unigenes for S. aethiopicum with an average length of 696 and 722 bp, respectively. The unigenes were structurally and functionally annotated based on comparison with public databases by using bioinformatic tools. The single nucleotide variant calling analysis (SNPs and INDELs) was performed by mapping our S. incanum and S. aethiopicum reads, as well as reads from S. melongena and S. torvum available on NCBI database (National Center for Biotechnology Information), against the eggplant genome. Both intraspecific and interspecific polymorphisms were identified and subsets of molecular markers were created for all species combinations. 36 SNVs were selected for validation in the S. incanum and S. aethiopicum accessions and 96 % were correctly amplified confirming the polymorphisms. In addition, 976 and 1,278 SSRs were identified in S. incanum and S. aethiopicum transcriptomes respectively, and a set of them were validated. CONCLUSIONS: This work provides a broad insight into gene sequences and allelic variation in S. incanum and S. aethiopicum. This work is a first step toward better understanding of target genes involved in metabolic pathways relevant for eggplant breeding. The molecular markers detected in this study could be used across all the eggplant genepool, which is of interest for breeding programs as well as to perform marker-trait association and QTL analysis studies.

Spectral comparison of diffuse PAR irradiance under different tree and shrub shading conditions and in cloudy days.

Spectral Solar Photosynthetically Photon Flux Density (PPFD) (380 to 780 nm) reaching the surface of a plant in different lighting conditions has been analyzed in order to better understand the different photosynthetic performance of plants depending on their spatial situation and the vegetation surrounding. A comparison between the shadow of several trees in a sunny day and the case of a cloudy day in an open space has been studied. Three isolated trees (a palm tree, an olive tree and a shrub oleander) and a tipuana grove have been studied. The study has been developed in Valencia (Spain) during January and February 2017. A portable Asensetek Standard ALP-01 spectrometer with a measurement wavelength range of 380 to 780 nm, has been used. Conditions with higher PPFD received are found to be, apart from those of a sunny day, those for cloudy day (with a spectral maximum in the Green region of the spectrum), and those for individual trees and shrub shadows in a sunny day (with a spectral maximum in the Blue region). The case in which less amount of PPFD is received is that under the shadow of tipuana grove (with a spectral maximum in the Infrared region of the spectrum). In fact the order of magnitude in which the PPFD in a cloudy day exceeds the PPFD under the tipuana grove shade is up to 20.

Tomato Mosaic Tobamovirus, Causal Agent of a Severe Disease of Pepino (Solanum muricatum).

Pepino (Solanum muricatum Aiton), a vegetatively propagated herbaceous crop from the Andes, is esteemed for its edible, juicy, and fragrant fruits. Its cultivation as a crop for diversification is increasing in many frost-free areas throughout the world (2). In 1994, a severe viruslike disease, previously undescribed, was observed on pepino plants in Valencia, Spain. The disease has continued to cause economic losses in pepino plantings in subsequent years. Symptoms, which are exacerbated at temperatures above 30°C, include dark and light green mosaic predominantly in young leaves, leaf puckering and distortion, short internodes, fruit deformation, delay in ripening, and yield reduction. Samples from affected plants were analyzed by enzyme-linked immunosorbent assay (ELISA). All samples displaying viruslike symptoms reacted positively with antiserum made against tomato mosaic tobamovirus (ToMV) but not with antisera made against alfalfa mosaic alfamovirus, cucumber mosaic cucumovirus, potato Y potyvirus, tobacco mosaic tobamovirus, tomato spotted wilt tospovirus, or tomato yellow leaf curl bigeminivirus. A leaf extract from diseased plants was heated at 72°C for 10 min. This treatment inactivates most plant viruses but does not eliminate infectivity of ToMV (1). Inoculation of a collection of pepino clones resulted in the development of symptoms in most clones. Symptomatic clones were also ELISA-positive for ToMV. A few clones showed a hypersensitive reaction, which consisted of the development of necrotic lesions in the inoculated area. New growth on these clones was asymptomatic and ELISA-negative for ToMV. These results clearly point to a causal relationship between ToMV infection and the observed disease. The initial source of the infection should be eliminated from commercial plantings, as ToMV is easily transmitted when the pepino plants are trellised and pruned. Special care must also be taken to ensure that mother plants from which cuttings are taken are free from this virus. In addition, ToMV is usually found in meristematic tissues, even after thermotherapy and chemotherapy treatments are applied, making the regeneration of virus-free plants from infected clones by meristem tip culture difficult. Therefore, it seems that the best strategy against this disease is the development of resistant cultivars. References: (1) H. Laterrot. Ann. Amélior. Plant. 23:287, 1973; (2) J. Prohens et al. Econ. Bot. 50:355, 1996.

Application of genomic tools in plant breeding.

Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, 'breeding by design', or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the 'superdomestication' of crops and the genetic dissection and breeding for complex traits.