Integration of morphometrics and machine learning enables accurate distinction between wild and farmed common carp

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Genetic Mapping of Blooming Time in 'Marcona' × 'Fragness' Population with Using Molecular Markers

Abstract Flowering time is an important horticultural trait in almond since it is essential to avoid the late frosts that affect production in early flowering cultivars. Evaluation of this complex trait is a long process because of the prolonged juvenile period of trees and the influence of environmental conditions affecting gene expression year by year. In this research flowering time was studied in an F1 almond progeny of 90 seedlings from the cross between the Marcona and the Fragness. In addition, a set of 63 co-dominant microsatellites or simple-sequence repeat (SSR) markers developed from peach, cherry and almond were used for the molecular characterization of the progeny. A genetic linkage map was created with 17 of these SSRs. Molecular studies at the DNA level confirmed this polygenic nature by identifying several genome regions (Quantitative Trait Loci, QTL) involved. QTL mapping detected two loci for flowering time (Ft-Q1 and Ft Q4) in Linkage groups 1 and 4 that close with BPPCT011 and UDP96-021 respectively. Finally, the development of efficient MAS strategies applied to almond and other Prunus breeding programs are also discussed

Saffron (Crocus sativus L.), a monomorphic or polymorphic species?

Saffron (Crocus sativus L.) which contains exceptional anti-cancer properties is presently the world�s most expensive spice. Iran is known as the original habitat of Crocus L. and a significant source of high-quality cultivated saffron production and export. Considering the importance of this species, we used 27 microsatellite markers to assess molecular variability and discriminating capacity of markers regarding their effectiveness in establishing genetic relationships in Iranian Crocus ecotypes. Thirty eight Iranian cultivated saffron ecotypes and 29 wild allies were evaluated in this research. The results from molecular analyses, including a molecular phylogenetic network and RB analysis, revealed two major groups and five subgroups, regardless of their geographical origins. Also, the results showed a clear distinction between C. sativus and other species of Crocus genus, taking into account their close relationship with C. speciosus and C. hausknechtii, which are assumed to be the two closest relatives of Iranian cultivated saffron among species studied. In this paper, we observed for the first time extensive genetic diversity among Iranian C. sativus despite their asexual reproduction. Considering suitable climatic conditions in Iran for cultivating saffron and the country�s leading high-quality production of Crocus sativus worldwide, studies on great genetic variability among Iranian C. sativus ecotypes as well as wild relatives native to Iran will further highlight the value of this crop. In addition, our results provide valuable information for genetic improvement, reduction of strong genetic erosion, and conservation of costly heritable resources of C. sativus in future breeding program

Development of an SSR-based identification key for Tunisian local almonds

19 Pags., 4 Figs., 2 Tabls.Ten simple sequence repeat (SSR) loci were used to study polymorphism in 54 almond genotypes. All genotypes used in this study originated from almond-growing areas in Tunisia with different climatic conditions ranging from the sub-humid to the arid and are preserved in the national collection at Sidi Bouzid. Using ten SSR, 130 alleles and 250 genotypes were revealed. In order to develop an identification key for each accession, the data were analysed separately for each microsatellite marker. The most polymorphic microsatellite (CPDCT042) was used as a first marker. Two microsatellite loci (CPDCT042 and CPDCT025) were sufficient to discriminate among all accessions studied. Neighbour-joining clustering and principal coordinate analysis were performed to arrange the genotypes according to their genetic relationships and origin. The results are discussed in the context of almond collection management, conformity checks, identification of homonyms, and screening of the local almond germplasm. Furthermore, this microsatellite-based key is a first step toward a marker-assisted identification almond database.Financial support was provided in part by the Tunisian Ministry of Higher Education, Scientific Research and Technology, the Spanish Ministry of Science and Innovation (AGL2008-00283/AGR co-financed by FEDER), the Aragon Government (Group A44), and the Agencia Española de Cooperación Internacional (A/5339/06 and A/8334/07).Peer reviewe

Molecular characterization of almond cultivars and related wild species using nuclear and chloroplast DNA markers

6 pages.The genetic diversity of different accessions of several wild almond species including P. eleagnifolia, P. hausknechtii, P. scoparia and P. lycioides, endemic to Irano-Afghan plate, was investigated using nuclear and chloroplast DNA markers. In addition, five cultivated almond cultivars (Marta from Spain; Nonpareil and Mission from USA; Ferrangnes from France and Tuono from Italy) were included in the study. Diversity was analysed at the DNA level by means of 16 nuclear and 5 chloroplast pairs of primers flanking SSR sequences. In 45 accessions, the number of alleles per locus in nuclear microsatellites ranged from 7 to 16, and expected heterozygosity varied between 0.54 and 0.93 with average PIC value of 0.81. It showed that they represent rather polymorphic species. In the case of chloroplast SSR, the polymorphism observed was much lesser in agreement with higher level of conservation of the chloroplast DNA. Therefore, nuclear microsatellites have been the most abundant markers with a high polymorphism and level of transference across closely related species in comparison with the others. In addition, results indicated the high variability present in the S-locus. Hierarchical analysis using integrated nuclear and chloroplastic microsatellite data yielded best clustering with six logical clusters or groupings corresponding to the different subgenus and sections.Peer reviewe

Integration of morphometrics and machine learning enables accurate distinction between wild and farmed common carp

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Use of biotechnology for preserving rare fruit germplasm

15 pages.The application of recent biotechnological tools for conservation of rare fruit species from developing countries, including in vitro and hydroponic culture protocols, improved propagation techniques and molecular marker application, is described. Promising propagation methods include forcing germination of seeds, in-vitro protocols well adapted to these rare fruit species that allow the introduction, micropropagation and rooting of plant material, and developing hydroponic culture protocols that allow the early propagation of high-risk genotypes. In addition, the growth of seedlings in controlled environmental conditions in greenhouse and cold chamber provides a useful strategy for obtaining vigorously growing plants from seeds year round. A standard karyotyping protocol has been described working in several species as preliminary tool to start molecular (DNA) studies. In addition, different protocols for DNA isolation and quantification have been assayed in these rare fruit species. Molecular markers based on PCR amplification of the DNA have also become an essential tool for the characterization and conservation of these species. Regarding this PCR amplification of the DNA, two main strategies, RAPD (if the DNA sequence is unknown) and SSR markers (if the DNA sequence is known), have been assayed. These markers have been applied in the genetic characterization of this germplasm, the establishment of genetic relationships between cultivars and species, and the future construction of genetic maps of these rare fruit species. Additional advantages encouraging the utilization of these new technologies in breeding programs include the high levels of synteny between genomes of related species, and a well-established international network of cooperation among researchers.Peer reviewe

Assessment of genetic diversity and relatedness among Tunisian almond germplasm using SSR markers

10 Pag., 3 Tabl., 2 Fig.Genetic diversity of 50 Tunisian almond (Prunus dulcis Mill.) genotypes and their relationships to European and American cultivars were studied. In total 82 genotypes were analyzed using ten genomic SSRs. A total of 159 alleles were scored and their sizes ranged from 116 to 227 bp. The number of alleles per locus varied from 12 to 23 with an average of 15.9 alleles per locus. Mean expected and observed heterozygosities were 0.86 and 0.68, respectively. The total value for the probability of identity was 4 × 10−13. All SSRs were polymorphic and they were able all together to distinguish unambiguously the 82 genotypes. The Dice similarity coefficient was calculated for all pair wise and was used to construct an UPGMA dendrogram. The results demonstrated that the genetic diversity within local almond cultivars was important, with clear geographic divergence between the northern and the southern Tunisian cultivars. The usefulness of SSR markers for almond fingerprinting, detection of synonyms and homonyms and evaluation of the genetic diversity in the Tunisian almond germplasm was also discussed. The results confirm the potential value of genetic diversity preservation for future breeding programs.This research was supported in part by the Tunisian Ministry of Higher Education, Scientific Research and Technology, the Spanish Agency for International Cooperation (A/5339/06 and A/8334/07), the Spanish MICINN (Ministry of Science and Innovation) grants AGL2008-00283/AGR, and the Regional Government of Aragon funds (A44).Peer reviewe