Standardization and application of microsatellite markers for variety identification in tomato and wheat

The present study is part of a EU project that aims to demonstrate the technical viability of STMS markers for variety identification. As examples two important European crop species, tomato and wheat were chosen. Initially, about 30-40 STMS markers were used to identify a set of 20 good markers per crop and to standardise the methodology and the interpretation of the results in different laboratories. Several systems were used for the detection of STMS polymorphisms. The selected STMS markers are being tested on 500 varieties of each species and databases are being constructed. The first comparisons of data generated by the different laboratories revealed a high degree of agreement. The causes of discrepancies between duplicate samples analysed in different laboratories and precautions to prevent them, are discussed

Determinants of complications in liver transplant patients

Abstract The aims of this thesis were to identify risk factors for the occurrence of complications in patients with end-stage liver disease (ESLD), both before and after liver transplantation (LTx), and to develop strategies to optimize immunosuppression after LTx in order to reduce immunosuppression-related complications. Important complications in LTx patients are acute rejection and side effects of immunosuppressive drugs, such as infections

Abscisic acid effects on activity and expression of barley (Hordeum vulgare) plastidial glucose-6-phosphate dehydrogenase

Total glucose-6-phosphate dehydrogenase (G6PDH) activity, protein abundance, and transcript levels of G6PDH isoforms were measured in response to exogenous abscisic acid (ABA) supply to barley (Hordeum vulgare cv Nure) hydroponic culture. Total G6PDH activity increased by 50% in roots treated for 12 h with exogenous 0.1 mM ABA. In roots, a considerable increase (35%) in plastidial P2-G6PDH transcript levels was observed during the first 3 h of ABA treatment. Similar protein variations were observed in immunoblotting analyses. In leaves, a 2-fold increase in total G6PDH activity was observed after ABA treatment, probably related to an increase in the mRNA level (increased by 50%) and amount of protein (increased by 85%) of P2-G6PDH. Together these results suggest that the plastidial P2-isoform plays an important role in ABA-treated barley plants

Phenotypic and genetic diversity of Spanish tomato landraces

[EN] The structure of Spanish landraces of tomato (Solanum lycopersicum L) has been analyzed. This diversity has been evaluated using agro-morphological characteristics (43 descriptors), quality parameters (solid soluble contents and individual sugars and organic acids) and DNA markers (amplified fragment length polymorphisms, AFLP). A wide range of variation was found for all traits but in the DNA marker level. Certain common characteristics could be identified in populations of the same landrace in several of the dimensions analyzed, but generally, an overlap of the spectrum of variation of different landraces was found. The results indicate that in each landrace the populations are strongly selected using very basic morphological characteristics such as fruit shape, colour or ribbing, while other traits vary depending on each farmer preferences. Seed mixing and pollen contamination might introduce variation which would be purged by farmers at the morphological level, but would be maintained in quality and yield traits. Despite the introduction of spurious variation it would be still possible to identify certain relations between quality attributes and the morphological traits defining specific landraces. The existence of a wide level of variation in plant yield and quality profiles enables the development of selection programmes targeted to provide farmers with materials with economically viable yield and excellent organoleptic quality. The results also highlight the necessity to stress the efforts in morpho-agronomical and quality characterization over molecular characterization in the ex situ management of these resources, as well as not to underestimate the importance of intra-varietal variability. (C) 2013 Elsevier B.V. All rights reserved.This research was funded by the Generalitat Valenciana with the research projects GV-CAPA00-19 and GV/2007/003.Cebolla Cornejo, J.; Rosello Ripolles, S.; Nuez Viñals, F. (2013). Phenotypic and genetic diversity of Spanish tomato landraces. Scientia Horticulturae. 162:150-164. https://doi.org/10.1016/j.scienta.2013.07.044S15016416

A platform for efficient genotyping in Musa using microsatellite markers

Establishment of a standardized platform for genotyping banana (Musa spp.) using a set of previously published SSR markers is described. The platform will serve a broad Musa research and breeding community and support the conservation and use of genetic diversity

Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes

Within the Dutch genomics initiative the “Centre for Biosystems Genomics” (CBSG) a major research effort is directed at the identification and unraveling of processes and mechanisms affecting fruit quality in tomato. The basis of this fruit quality program was a diverse set of 94 cultivated tomato cultivars, representing a wide spectrum of phenotypes for quality related traits. This paper describes a diversity study performed on these cultivars, using information of 882 AFLP markers, of which 304 markers had a known map position. The AFLP markers were scored as much as possible in a co-dominant fashion. We investigated genome distribution and coverage for the mapped markers and conclude that it proved difficult to arrive at a dense and uniformly distributed coverage of the genome with markers. Mapped markers and unmapped markers were used to investigate population structure. A clear substructure was observed which seemed to coincide with a grouping based on fruit size. Finally, we studied amount and decay of linkage disequilibrium (LD) along the chromosomes. LD was observed over considerable (genetic) distances. We discuss the feasibility of marker-trait association studies and conclude that the amount of genetic variation in our set of cultivars is limited, but that there exists scope for association studies

Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers

<p>Abstract</p> <p>Background</p> <p>Sugar beet is an obligate outcrossing species. Varieties consist of mixtures of plants from various parental combinations. As the number of informative morphological characteristics is limited, this leads to some problems in variety registration research.</p> <p>Results</p> <p>We have developed 25 new microsatellite markers for sugar beet. A selection of 12 markers with high quality patterns was used to characterise 40 diploid and triploid varieties. For each variety 30 individual plants were genotyped. The markers amplified 3-21 different alleles. Varieties had up to 7 different alleles at one marker locus. All varieties could be distinguished. For the diploid varieties, the expected heterozygosity ranged from 0.458 to 0.744. The average inbreeding coefficient F_iswas 0.282 ± 0.124, but it varied widely among marker loci, from F_is= +0.876 (heterozygote deficiency) to F_is= -0.350 (excess of heterozygotes). The genetic differentiation among diploid varieties was relatively constant among markers (F_st= 0.232 ± 0.027). Among triploid varieties the genetic differentiation was much lower (F_st= 0.100 ± 0.010). The overall genetic differentiation between diploid and triploid varieties was F_st= 0.133 across all loci. Part of this differentiation may coincide with the differentiation among breeders' gene pools, which was F_st= 0.063.</p> <p>Conclusions</p> <p>Based on a combination of scores for individual plants all varieties can be distinguished using the 12 markers developed here. The markers may also be used for mapping and in molecular breeding. In addition, they may be employed in studying gene flow from crop to wild populations.</p

Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing

Molecular markers linked to phenotypically important traits are of great interest especially when traits are difficult and/or costly to be observed. In tomato where a strong focus on resistance breeding has led to the introgression of several resistance genes, resistance traits have become important characteristics in distinctness, uniformity and stability (DUS) testing for Plant Breeders Rights (PBR) applications. Evaluation of disease traits in biological assays is not always straightforward because assays are often influenced by environmental factors, and difficulties in scoring exist. In this study, we describe the development and/or evaluation of molecular marker assays for the Verticillium genes Ve1 and Ve2, the tomato mosaic virusTm1 (linked marker), the tomato mosaic virus Tm2 and Tm22 genes, the Meloidogyne incognita Mi1-2 gene, the Fusarium I (linked marker) and I2 loci, which are obligatory traits in PBR testing. The marker assays were evaluated for their robustness in a ring test and then evaluated in a set of varieties. Although in general, results between biological assays and marker assays gave highly correlated results, marker assays showed an advantage over biological tests in that the results were clearer, i.e., homozygote/heterozygote presence of the resistance gene can be detected and heterogeneity in seed lots can be identified readily. Within the UPOV framework for granting of PBR, the markers have the potential to fulfil the requirements needed for implementation in DUS testing of candidate varieties and could complement or may be an alternative to the pathogenesis tests that are carried out at present

Development of microsatellite markers for identifying Brazilian Coffea arabica varieties

Microsatellite markers, also known as SSRs (Simple Sequence Repeats), have proved to be excellent tools for identifying variety and determining genetic relationships. A set of 127 SSR markers was used to analyze genetic similarity in twenty five Coffea arabica varieties. These were composed of nineteen commercially important Brazilians and six interspecific hybrids of Coffea arabica, Coffea canephora and Coffealiberica. The set used comprised 52 newly developed SSR markers derived from microsatellite enriched libraries, 56 designed on the basis of coffee SSR sequences available from public databases, 6 already published, and 13 universal chloroplast microsatellite markers. Only 22 were polymorphic, these detecting 2-7 alleles per marker, an average of 2.5. Based on the banding patterns generated by polymorphic SSR loci, the set of twenty-five coffee varieties were clustered into two main groups, one composed of only Brazilian varieties, and the other of interspecific hybrids, with a few Brazilians. Color mutants could not be separated. Clustering was in accordance with material genealogy thereby revealing high similarity