Development of Sequence Tagged Microsatellite Site (STMS) markers in Azalea

A genomic library was constructed from DNA of two azalea genotypes: a Belgian pot azalea R. simsii hybrid Mevr. Van Belle and a Chinese R. simsii from Daoxian. An enrichment of microsatellite containing sequences was performed as in Van de Wiel et al. (1999). Fragments were sequenced and primers were designed that allow the amplification of the microsatellite repeat. About 220 microsatellite containing clones were selected from the enrichment procedure. Mainly dinucleotide repeats and some trinucleotide repeats were found. The selected primers were tested in a small set of reference varieties to check their value (specificity and polymorphic rate) and to set up the PCR-conditions. Five primer pairs have been tested, two of them gave a specific and polymorphic pattern. They were further screened by radioactive PCR on a selection of 5 plants from the azalea breeders gene pool which included the two genotypes used library construction. These 2 STMS markers uniquely identified the 5 plants

Influence of damaging and wilting red clover on lipid metabolism during ensiling and in vitro rumen incubation

This paper describes the relationship between protein-bound phenols in red clover, induced by different degrees of damaging before wilting and varying wilting duration, and in silo lipid metabolism. The ultimate effect of these changes on rumen biohydrogenation is the second focus of this paper For this experiment, red clover, damaged to different degrees (not damaged (ND), crushing or frozen/thawing (FT)) before wilting (4 or 24 h) was ensiled. Different degrees of damaging and wilting duration lead to differences in polyphenol oxidase (PPO) activity, measured as increase in protein-bound phenols. Treatment effects on fatty acid (FA) content and composition, lipid fractions (free FAs, membrane lipids (ML) and neutral fraction) and lipolysis were further studied in the silage. In FT, red clover lipolysis was markedly lower in the first days after ensiling, but this largely disappeared after 60 days of ensiling, regardless of wilting duration. This suggests an inhibition of plant lipases in FT silages. After 60 days of ensiling no differences in lipid fractions could be found between any of the treatments and differences in lipolysis were caused by reduced FA proportions in ML of wilted FT red clover Fresh, wilted (24 h) after damaging (ND or FT) and ensiled (4 or 60 days; wilted 24 h; ND or FT) red clover were also incubated in rumen fluid to study the biohydrogenation of C18:3n-3 and C18:2n-6 in vitro. Silages (both 60 days and to a lower degree 4 days) showed a lower biohydrogenation compared with fresh and wilted forages, regardless of damaging. This suggests that lipids in ensiled red clover were more protected, but this protection was not enhanced by a higher amount of protein-bound phenols in wilted FT compared with ND red clover The reduction of rumen microbial biohydrogenation with duration of red clover ensiling seems in contrast to what is expected, namely a higher biohydrogenation when a higher amount of FFA is present. This merits further investigation in relation to strategies to activate PPO toward the embedding of lipids in phenol protein complexes

Breeding of CMS-F1-Hybrids in \u3cem\u3eLolium Perenne\u3c/em\u3e With Improved Nitrogen Use Efficiency

The environmental pollution by nitrogen losses from dairy farms can be reduced by improving the nitrogen use efficiency (NUE) of grass varieties. The main goal is to develop varieties with a better nitrogen utilisation. These low input varieties can produce acceptable yields at a low level of N-fertilisation. High input varieties express their high yield potential only at high N-supply. These varieties are less preferable, because N- losses increase at higher levels of nitrogen application. The breeding of CMS-F1-Hybrids can be a successful strategy for developing varieties with a higher NUE. In F1-Hybrid varieties higher heterosis effects can be achieved than in populations or synthetic varieties

Identification of quantitative trait loci controlling root and shoot traits associated with drought tolerance in a lentil (Lens culinaris Medik.) recombinant inbred line population

Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL) analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL (QRSratioIX-2.30) related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 and 28.9% for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL (QLRNIII-98.64) related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL (QSRLIV-61.63) associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labor-intensive conventional breeding methods

Analyses of Genetic Change in Grass-Clover Based Systems Over Time

Since the use of nitrogen fertilisers is reduced, swards based on grass-clover mixtures regain importance in grassland production. Management of these swards is more complicated than the management of pure grass swards. The population structure will develop in response to abiotic and biotic stresses. In this study we will test the genetic change in the clover components of grass-clover mixtures

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

Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L.

While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific

In the name of the rose: a roadmap for rose research in the genome era

The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: ‘Now that we have “the” genome, what’s next?’. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions

Strongly Correlated Quantum Fluids: Ultracold Quantum Gases, Quantum Chromodynamic Plasmas, and Holographic Duality

Strongly correlated quantum fluids are phases of matter that are intrinsically quantum mechanical, and that do not have a simple description in terms of weakly interacting quasi-particles. Two systems that have recently attracted a great deal of interest are the quark-gluon plasma, a plasma of strongly interacting quarks and gluons produced in relativistic heavy ion collisions, and ultracold atomic Fermi gases, very dilute clouds of atomic gases confined in optical or magnetic traps. These systems differ by more than 20 orders of magnitude in temperature, but they were shown to exhibit very similar hydrodynamic flow. In particular, both fluids exhibit a robustly low shear viscosity to entropy density ratio which is characteristic of quantum fluids described by holographic duality, a mapping from strongly correlated quantum field theories to weakly curved higher dimensional classical gravity. This review explores the connection between these fields, and it also serves as an introduction to the Focus Issue of New Journal of Physics on Strongly Correlated Quantum Fluids: from Ultracold Quantum Gases to QCD Plasmas. The presentation is made accessible to the general physics reader and includes discussions of the latest research developments in all three areas.Comment: 138 pages, 25 figures, review associated with New Journal of Physics special issue "Focus on Strongly Correlated Quantum Fluids: from Ultracold Quantum Gases to QCD Plasmas" (http://iopscience.iop.org/1367-2630/focus/Focus%20on%20Strongly%20Correlated%20Quantum%20Fluids%20-%20from%20Ultracold%20Quantum%20Gases%20to%20QCD%20Plasmas