Elena Zuriaga

Classification and phylogenetic relationships in Solanum section Lycopersicon based on AFLP and two nuclear gene sequences

The classification and phylogeny of the species belonging to Solanum section Lycopersicon is a complex issue that has not yet reached a widely accepted consensus. These species diverged recently, are still closely related and, in some cases, are still even capable of interspecific hybridization, thereby blurring the difference between intra- and interspecific variation. To help resolve these issues, in the present study, several accessions covering the natural range for each species were used. In addition, to avoid biases due to the molecular method employed, both AFLP markers and two nuclear-gene sequences, CT179 and CT66, were used to characterize the plant materials. The data obtained suggest a classification similar to those previously proposed by other authors, although with some significant changes. Twelve species were recognized as distinct based on this dataset. According to the data presented, the recently proposed species, S. corneliomulleri, is indistinguishable from S. peruvianum s.str. In addition, both the sequence and the AFLP trees suggest that S. arcanum could represent a complex of populations composed of two cryptic species. With regard to phylogenetic relationships among these species, some clear groups were found: the Lycopersicon group formed by S. pimpinellifolium, S. lycopersicum, S. cheesmaniae and S. galapagense; the Arcanum group constituted by S. chmielewskii, S. neorickii, S. arcanum and S. huaylasense; and the Eriopersicon group made up of S. peruvianum and S. chilense. Solanum pennellii and S. habrochaites are not included in any group, but are the closest to the S. lycopersicoides outgroup.

Development and characterization of microsatellite markers in pomegranate (Punica granatum L.)

The pomegranate (Punica granatum L.) is a temperate climate species requiring high temperatures for proper and complete ripening. The species is consumed as a fresh fruit, but also can be used to obtain transformed products such as juice, jam, or preserve. It is a fruit tree species with a high degree of diversity, but the identification of cultivars by morphological traits is very difficult. Thus, the characterization of genotypes through molecular markers is of great value for germplasm preservation, genetic studies, and plant breeding. The number of simple sequence repeat (SSR or microsatellite) markers developed for this genus is too low, so in this work we report the development of 117 microsatellite loci from a CT/AG-enriched pomegranate genomic library. In order to check their utility, eleven accessions were analyzed. The polymorphism information content (PIC) value across all loci ranged between 0.09 and 0.71, with an average of 0.37. These markers will facilitate genetic diversity studies, mapping, and genotyping of pomegranate.

Analysis of genetic diversity among persimmon cultivars using microsatellite markers

In the Mediterranean area, the production of persimmon (Diospyros kaki Thumb) [2n = 6x = 90] has increased recently as an alternative to the major fruit crops. In Spain, production relies almost exclusively on the cultivar “Rojo Brillante” which accounts for 83% of the crop. A crop based on a monovarietal culture implies several commercial risks that can compromise the future of the crop. Although the species was introduced in Europe very recently, it is well adapted to the climate of southern Europe. However, the recent introduction from Japan, the mistakes on the identity of varieties in the collections due to a bad translation of variety names from Japanese, and the lack of genetic characterization of many varieties have caused difficulties for effective management of the available genetic resources. The present paper was aimed at exploring the genetic diversity among different persimmon cultivars, including those collected in the European survey as well as Japanese cultivars. Seventy-one persimmon cultivars coming from two European collections that included accessions from Japan, Italy, and Spain were analyzed using 19 polymorphic microsatellite markers. A total of 206 alleles were obtained, with a mean value of 10.8 alleles per locus. A neighbor joining dendrogram and a principal coordinate analysis arranged the cultivars according to their genetic relationships. Analysis of molecular variance revealed significant genetic variability between and within groups, 73.3% and 85.2% for astringent-type and country origin, respectively. The simple sequence repeat markers classified the persimmon cultivars according to their genetic relationship.

AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): implications for evolution and domestication

The pepino (Solanum muricatum) is a vegetatively propagated, domesticated native of the Andes, where it grows with wild relatives. We used AFLPs and a 1-kb sequence of the 3-methylcrotonyl-CoA carboxylase gene to study variation of 27 accessions of S. muricatum and 35 collections of 10 species of wild relatives (Solanum section Basarthrum). A total of 298 AFLP fragments and 29 DNA sequence haplotypes were detected. Cluster and principal coordinate analyses and other genetic parameters estimated from both types of markers, show that S. muricatum is closely related to the species from one of the series (Caripensia) of section Basarthrum and that >90% of the variation of the cultigen is also represented in that series. Pepino is highly diverse, either because it is not monophyletic or it has been subjected to regular introgression with wild species, or both. Although a continuous distribution of the genetic variation occurred within the cultivated species, three genetic clusters were recognized. Cluster 1 is mostly centered in Ecuador, cluster 2 in Ecuador and Peru, and cluster 3 in Colombia and Ecuador. Cluster 3 also includes all modern cultivars studied. These results and other evidence suggest that northern Ecuador/southern Colombia is the main center of pepino diversity and the center of origin. The high genetic variation of this cultigen indicates that domestication does not always produce a genetic bottleneck.

Identification of simple sequence repeat markers tightly linked to plum pox virus resistancein apricot

Sharka disease, caused by the plum pox virus (PPV), is one of the major limiting factors for stone fruit production in Europe and America. Attempts to stop the disease through the eradication of infected trees have been unsuccessful. Introgression of PPV resistance for crop improvement is therefore the most important goal in Prunus breeding programs. Due to time- and labour-consuming protocols, phenotyping for sharka is still the major bottleneck in the breeding pipeline. In this context, screening of seedlings at early stages of development and marker-assisted selection (MAS) provide the best solution for enhancing breeding efficiency. In this study, we generated 42 simple sequence repeat (SSR) markers from the peach genome assembly v1.0 and an apricot bacterial artificial chromosome clone identified in the physical map of the PPV resistance locus previously defined in apricot. Using a linkage mapping approach, we found SSR markers tightly linked to PPV resistance trait in all our progenies. Three SSR markers, PGS1.21 PGS1.23 and PGS1.24, showed allelic variants associated with PPV resistance with no recombinants in the crosses analysed. These markers unambiguously discriminated resistant from susceptible accessions in different genetic backgrounds. The results presented here are the first successful application of their use in MAS for breeding resistance in Prunus species.

An S-locus independent pollen factor confers self-compatibility in 'Katy' apricot.

Loss of pollen-S function in Prunus self-compatible cultivars has been mostly associated with deletions or insertions in the S-haplotype-specific F-box (SFB) genes. However, self-compatible pollen-part mutants defective for non-S-locus factors have also been found, for instance, in the apricot (Prunus armeniaca) cv. ‘Canino’. In the present study, we report the genetic and molecular analysis of another self-compatible apricot cv. termed ‘Katy’. S-genotype of ‘Katy’ was determined as S 1 S 2 and S-RNase PCR-typing of selfing and outcrossing populations from ‘Katy’ showed that pollen gametes bearing either the S 1- or the S 2-haplotype were able to overcome self-incompatibility (SI) barriers. Sequence analyses showed no SNP or indel affecting the SFB 1 and SFB 2 alleles from ‘Katy’ and, moreover, no evidence of pollen-S duplication was found. As a whole, the obtained results are compatible with the hypothesis that the loss-of-function of a S-locus unlinked factor gametophytically expressed in pollen (M’-locus) leads to SI breakdown in ‘Katy’. A mapping strategy based on segregation distortion loci mapped the M’-locus within an interval of 9.4 cM at the distal end of chr.3 corresponding to ∼1.29 Mb in the peach (Prunus persica) genome. Interestingly, pollen-part mutations (PPMs) causing self-compatibility (SC) in the apricot cvs. ‘Canino’ and ‘Katy’ are located within an overlapping region of ∼273 Kb in chr.3. No evidence is yet available to discern if they affect the same gene or not, but molecular markers seem to indicate that both cultivars are genetically unrelated suggesting that every PPM may have arisen independently. Further research will be necessary to reveal the precise nature of ‘Katy’ PPM, but fine-mapping already enables SC marker-assisted selection and paves the way for future positional cloning of the underlying gene.

The Implications of AFLP Data for the Systematics of the Wild Species of Solanum Section Basarthrum

Abstract The wild species associated with the Andean domesticate, the pepino, and closely associated with the wild and cultivated potatoes, are morphologically and ecologically variable. We studied 10 of the 11 known species, represented by 35 accessions, of Solanum section Basarthrum, plus material of two putative new species. Given the morphological variability, and cryptic species, molecular studies were appropriate. Amplified Fragment Length Polymorphisms (AFLP) were utilized because they are highly polymorphic, and cover most of the genome. Some 98% of the 292 fragments recovered proved informative. A neighbour joining cluster analysis and principal coordinates analysis largely supported previous taxonomic distinctions based on decades of morphological and biosystematic study. However, two new distinct molecular elements were identified, one autogamous, the other self incompatible, that will be described as new species, and that mimic a species pair of wild tomatoes native to the same region of Peru. The most diverse taxonomic group, the series Caripensia, also proved to be the most diverse genetically (85% of loci polymorphic), allowing morphologically similar species to be distinguished. The AFLP data and species distributions in this series support an hypothesis of rapid evolution and peripheral isolation as evolutionary mechanisms in the geographically and ecologically diverse series Caripensia.

Genetic variation and diversity among loquat accessions

Loquat (Eriobotrya japonica (Thunb.) Lindl., Maloideae, Rosaceae) is a subtropical evergreen fruit tree indigenous of China, where the center of origin of the species is located. Loquat is grown in all subtropical areas and was introduced in the Mediterranean basin in late eighteenth century. In Europe, the largest germplasm bank is located at Instituto Valenciano de Investigaciones Agrarias (IVIA; Valencia, Spain). Thirteen microsatellites and a conserved region of S-allele were used to assess the genetic diversity of 102 accessions of the IVIA collection. A total of 38 SSR alleles and 11 putative S-alleles were used to study the genetic structure of the loquat germplasm bank using the STRUCTURE software, Factorial Correspondence Analysis (FCA), and unweighted pair-group method (UPGMA) cluster analyses. The total diversity was HT = 0.5682, the genetic differentiation GST = 0.1660, and the standardized GST reached a much higher value of G′ST = 0.4948. The Evanno’s test indicated that the most informative number of populations was five, with accessions distributed according to their geographic origin in two, one, and two groups of Spanish, Italo-Spanish, and non-European origin, respectively. Knowledge of the substructure and diversity of the IVIA loquat collection and the self-incompatibility genotype data will allow us to select and incorporate useful materials into the loquat breeding program.

A disulfide bond A-like oxidoreductase is a strong candidate gene for self-incompatibility in apricot (Prunus armeniaca) pollen

A disulfide bond A-like oxidoreductase encoded by a pollen modifier candidate gene is required for gametophytic self-incompatibility in apricot (Prunus armeniaca) as supported by loss-of-function mutations.

SODIUM AZIDE INDUCED MORPHOLOGICAL AND MOLECULAR CHANGES IN PERSIMMON (DIOSPYROS LOTUS L.)

Sodium Azide Induced Morphological and Molecular Changes in Persimmon (Diospyros Lotus L.) Persimmon Diospyros lotus L. is an underutilized species, used as rootstock for Japanese persimmon (Diospyros kaki Thunb.) in many European countries. It has a potential for ornamental uses due to its diploid genome that suggests an easy mutation induction. This study was aimed at unravelling the effects of mutagenic sodium azide (in concentrations of 0.1% and 0.5%) on morphological characters (plant height, maximal leaf blade length, maximal leaf blade width and leaf petiole length) and molecular relations of treated accessions, based on AFLP (amplified fragment length polymorphism). In the M1 generation, the analysed characters of two-year old plants differed among the treatments. Sodium azide influenced persimmon stem and leaves in the opposite way, with increase up to 31.57% in plant height and decrease up to 30.33% in leaf petiole length. Changes in morphological characters were significant, that implies the importance of azide influence on the persimmon. Most genotypes treated with 0.1% azide were without significant differences among them and clustered together. The results suggest that the higher azide concentration of 0.5% is more suitable for persimmon seeds azide treatment to form genotypes, significantly different from the control, at the molecular level.