Fine genetic mapping of the Co locus controlling columnar growth habit in apple

Tree architecture is an important, complex and dynamic trait affected by diverse genetic, ontogenetic and environmental factors. ‘Wijcik McIntosh', a columnar (reduced branching) sport of ‘McIntosh' and a valuable genetic resource, has been used intensively in apple-breeding programs for genetic improvement of tree architecture. The columnar growth habit is primarily controlled by the dominant allele of gene Co (columnar) on linkage group-10. But the Co locus is not well mapped and the Co gene remains unknown. To precisely map the Co locus and to identify candidate genes of Co, a sequence-based approach using both peach and apple genomes was used to develop new markers linked more tightly to Co. Five new simple sequence repeats markers were developed (C1753-3520, C18470-25831, C6536-31519, C7223-38004 and C7629-22009). The first four markers were obtained from apple genomic sequences on chromosome-10, whereas the last (C7629-22009) was from an unanchored apple contig that contains an apple expressed sequence tag CV082943, which was identified through synteny analysis between the peach and apple genomes. Genetic mapping of these five markers in four F1 populations of 528 genotypes and 290 diverse columnar selections/cultivars (818 genotypes in total) delimited the Co locus in a genetic interval with 0.37% recombination between markers C1753-3520 and C7629-22009. Marker C18470-25831 co-segregates with Co in the 818 genotypes studied. The Co region is estimated to be 193kb and contains 26 predicted gene in the ‘Golden Delicious' genome. Among the 26 genes, three are putative LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) containing transcription factor genes known of essential roles in plant lateral organ development, and are therefore considered as strong candidates of Co, designated MdLBD1, MdLBD2, and MdLBD3. Although more comprehensive studies are required to confirm the function of MdLBD1-3, the present work represents an important step forward to better understand the genetic and molecular control of tree architecture in appl

Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa

<p>Abstract</p> <p>Background</p> <p>'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip^®microarrays to profile the response of the banana (<it>Musa </it>spp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed <it>Musa </it>transcripts.</p> <p>Results</p> <p>Following cross-hybridisation of <it>Musa </it>gDNA to the Rice GeneChip^®Genome Array, ~33,700 gene-specific probe-sets had a sufficiently high degree of homology to be retained for transcriptomic analyses. In a proof-of-concept approach, pooled RNA representing a single biological replicate of control and drought stressed leaves of the <it>Musa </it>cultivar 'Cachaco' were hybridised to the Affymetrix Rice Genome Array. A total of 2,910 <it>Musa </it>gene homologues with a >2-fold difference in expression levels were subsequently identified. These drought-responsive transcripts included many functional classes associated with plant biotic and abiotic stress responses, as well as a range of regulatory genes known to be involved in coordinating abiotic stress responses. This latter group included members of the ERF, DREB, MYB, bZIP and bHLH transcription factor families. Fifty-two of these drought-sensitive <it>Musa </it>transcripts were homologous to genes underlying QTLs for drought and cold tolerance in rice, including in 2 instances QTLs associated with a single underlying gene. The list of drought-responsive transcripts also included genes identified in publicly-available comparative transcriptomics experiments.</p> <p>Conclusion</p> <p>Our results demonstrate that despite the general paucity of nucleotide sequence data in <it>Musa </it>and only distant phylogenetic relations to rice, gDNA probe-based cross-hybridisation to the Rice GeneChip^®is a highly promising strategy to study complex biological responses and illustrates the potential of such strategies for gene discovery in non-model species.</p

Considerations to prevent the breakdown and loss of fruit carotenoids during extraction and analysis in Musa

The impact of treatments aimed at improving the robustness of protocols for the analysis of carotenoids in fruit of banana and plantain were examined. Neither the inclusion of polyvinylpolypyrrolidine in the extraction buffer, nor vigorous homogenisation with glass beads influenced recoveries or chromatographic profiles. By contrast, heating lead to losses of up to 53% and to the formation of degradation products that are no longer detectable on our RP-HPLC system. Carotenoid extracts are unstable and most sensitive to exposure to light. However, even in the dark at -20 degrees C and in the presence of antioxidants breakdown rates of around 5% per day were observed.status: publishe

Effect of polyploidisation on the response of apple (Malus x domestica Borkh.) to Venturia inaequalis infection

© 2018, Koninklijke Nederlandse Planteziektenkundige Vereniging. Development of new and durable strategies to improve the apple plant’s resistance against apple scab (Venturia inaequalis) remains a major challenge. Polyploids or organisms with three or more complete chromosome sets often possess properties superior to their diploid counterparts. Studies reported that polyploidy confers an increased resistance to biotic and abiotic stress factors. However, the potential use of polyploidy to increase disease resistance is still insufficiently investigated. We determined the influence of artificial genome doubling on the response of three Malus × domestica genotypes, with a variable level of susceptibility to apple scab. Based on visual symptom evaluation and real-time PCR quantification of the V. inaequalis DNA in apple leaves, an increased resistance was observed in the neotetraploid form of the monogenic resistant genotype compared to its diploid progenitor. No pronounced effects were observed comparing ploidy levels of the susceptible genotypes. These results suggest a potential role for polyploidisation in apple scab resistance, but it seems to depend on the degree of disease susceptibility of the genotype. Still, further research on the effects of polyploidy might offer potential in the development of new and durable resistance strategies.status: publishe

Genetic Control of Fruit Vitamin C Contents

An F(1) progeny derived from a cross between the apple (Malus x domestica) cultivars Telamon and Braeburn was used to identify quantitative trait loci (QTL) linked to the vitamin C (l-ascorbate [l-AA]) contents of fruit skin and flesh (cortex) tissues. We identified up to three highly significant QTLs for both the mean l-AA and the mean total l-AA contents of fruit flesh on both parental genetic linkage maps, confirming the quantitative nature of these traits. These QTLs account for up to a maximum of 60% of the total population variation observed in the progeny, and with a maximal individual contribution of 31% per QTL. QTLs common to both parents were identified on linkage groups (LGs) 6, 10, and 11 of the Malus reference map, while each parent also had additional unique QTLs on other LGs. Interestingly, one strong QTL on LG-17 of the Telamon linkage map colocalized with a highly significant QTL associated with flesh browning, and a minor QTL for dehydroascorbate content, supporting earlier work that links fruit l-AA contents with the susceptibility of hardfruit to postharvest browning. We also found significant minor QTLs for skin l-AA and total l-AA (l-AA + dehydroascorbate) contents in Telamon. Currently, little is known about the genetic determinants underlying tissue l-AA homeostasis, but the presence of major, highly significant QTL in both these apple genotypes under field conditions suggests the existence of common control mechanisms, allelic heterozygosity, and helps outline strategies and the potential for the molecular breeding of these traits

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status: publishe

Predicting the Surface Plasmon Resonance Wavelength of Gold-Silver Alloy Nanoparticles

Gold-silver alloy nanoparticles display surface plasmon resonance (SPR) over a broad range of the UV-vis spectrum. We propose a model to predict the SPR wavelength of gold-silver alloy colloids based on the combined effect of alloy composition and particle size. The SPR wavelength is derived from extinction spectra simulated using available experimental dielectric constant data and accounts for particle size by applying Mie theory. Comparison of calculated values with experimental data evidences the accuracy of the model. The new SPR wavelength estimation tool will be of particular interest for developing dedicated bimetallic plasmonic nanostructures. © 2013 American Chemical Society.status: publishe