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The availability of a high quality linkage map is essential for the detection and the analysis of quantitative traits. Such a map should cover a significant part of the genome, should be densely populated with markers, and in order to gain the maximum advantage should be transferable to populations or cultivars other than the ones on which it has been constructed. An apple genetic linkage map has been constructed on the basis of a segregating population of the cross between the cultivars Fiesta and Discovery. A total of 840 molecular markers, 475 AFLPs, 235 RAPDs, 129 SSRs and 1 SCAR, were used for the two parental maps constructed with JoinMap and spanning 1,140 cM and 1,450 cM, respectively. Large numbers of codominant markers, like SSRs, enable a rapid transfer of the map to other populations or cultivars, allowing the investigation of any chosen trait in another genetic background. This map is currently the most advanced linkage map in apple with regard to genome coverage and marker density. It represents an ideal starting point for future mapping projects in Malus since the stable and transferable SSR frame of the map can be saturated quickly with dominant AFLP markers.

Apple scab caused by Venturia inaequalis has evoked the interest for quite different reasons of scientists, agronomists, producers and consumers since over a century. Consumers select spotless apples, producers want to avoid damage, agronomists are asked to develop and implement control measures mostly based on fungicides, scientists are challenged to find cheaper and less questioned control measures. Under these premises a high number of publications have appeared dealing with almost all aspects of the interaction V. inaequalis-Malus. This review considers the advances of the past 10 years due to new genetic tools. It tries to reevaluate and value earlier works. The complex genetic of scab resistance in Malus is viewed in the context of single resistance genes, QTLs and functional interactions at molecular level. Consequences for breeding and for the creation of genetically modified apples are discussed.

The F1 population “Harostar” × “Rouge de Mauves” was used to perform a quantitative trait loci (QTL) mapping for tree architecture traits (i.e., tree diameter, total branch number, tree shape); time to initial reproductive bud break; and fruit quality traits (i.e., ground color, fruit form, soluble solid content) using data collected from 2010 to 2012. For architectural traits, interval mapping detected QTLs only in “Rouge de Mauves” on linkage group 1 for trunk diameter in 2010, on LG6 for total branch number in 2010, and on LG1 and LG5 for tree shape for both years 2010 and 2011 combined. QTLs were detected only in “Harostar” for time to initial reproductive bud break on LG1 and LG4 in 2011. For fruit quality traits, data were collected in 2011 and 2012. QTLs were identified on LG1 in 2011 and on LG4 in 2012 for soluble solid content, on LG3 for ground color in both years, on LG7 only in 2011, and on LG3 for fruit form in both years. The QTLs that we identified were compared to those previously identified in other Prunus spp.

Efficient breeding and selection of high-quality apple cultivars requires knowledge and understanding of the underlying genetics. The availability of genetic linkage maps constructed with molecular markers enables the detection and analysis of major genes and quantitative trait loci contributing to the quality traits of a genotype. A segregating population of the cross between the apple varieties 'Fiesta' (syn. 'Red Pippin') and 'Discovery' has been observed over three years at three different sites in Switzerland and data on growth habit, blooming behaviour, juvenile period and fruit quality has been recorded. QTL analyses were performed, based on a genetic linkage map consisting of 804 molecular markers and covering all 17 apple chromosomes. With the maximum likelihood based interval mapping method, the investigated complex traits could be dissected into a number of QTLs affecting the observed characters. Genomic regions participating in the genetic control of stem diameter, plant height increment, leaf size, blooming time, blooming intensity, juvenile phase length, time of fruit maturity, number of fruit, fruit size and weight, fruit flesh firmness, sugar content and fruit acidity were identified and compared with previously mapped QTLs in apple. Although 'Discovery' fruit displayed a higher acid content, both acidity QTLs were attributed to the sweeter parent 'Fiesta'. This indicated homozygosity at the acidity loci in 'Discovery' preventing their detection in the progeny due to the lack of segregation.

A new set of 148 apple microsatellite markers has been developed and mapped on the apple reference linkage map Fiesta x Discovery. One-hundred and seventeen markers were developed from genomic libraries enriched with the repeats GA, GT, AAG, AAC and ATC; 31 were developed from EST sequences. Markers derived from sequences containing dinucleotide repeats were generally more polymorphic than sequences containing trinucleotide repeats. Additional eight SSRs from published apple, pear, and Sorbus torminalis SSRs, whose position on the apple genome was unknown, have also been mapped. The transferability of SSRs across Maloideae species resulted in being efficient with 41% of the markers successfully transferred. For all 156 SSRs, the primer sequences, repeat type, map position, and quality of the amplification products are reported. Also presented are allele sizes, ranges, and number of SSRs found in a set of nine cultivars. All this information and those of the previous CH-SSR series can be searched at the apple SSR database (http://www.hidras.unimi.it) to which updates and comments can be added. A large number of apple ESTs containing SSR repeats are available and should be used for the development of new apple SSRs. The apple SSR database is also meant to become an international platform for coordinating this effort. The increased coverage of the apple genome with SSRs allowed the selection of a set of 86 reliable, highly polymorphic, and overall the apple genome well-scattered SSRs. These SSRs cover about 85% of the genome with an average distance of one marker per 15 cM.[PUBLICATION ABSTRACT]

Breeding for scab-resistant apple cultivars by pyramiding several resistance genes in the same genetic background is a promising way to control apple scab caused by the fungus Venturia inaequalis. To achieve this goal, DNA markers linked to the genes of interest are required in order to select seedlings with the desired resistance allele combinations. For several apple scab resistance genes, molecular markers are already available; but until now, none existed for the apple scab resistance gene Vbj originating from the crab apple Malus baccata jackii. Using bulk segregant analysis, three RAPD markers linked to Vbj were first identified. These markers were transformed into more reliable sequence-characterised amplified region (SCAR) markers that proved to be co-dominant. In addition, three SSR markers and one SCAR were identified by comparing homologous linkage groups of existing genetic maps. Discarding plants showing genotype-phenotype incongruence (GPI plants) plants, a linkage map was calculated. Vbj mapped between the markers CH05e03 (SSR) and T6-SCAR, at 0.6 cM from CH05e03 and at 3.9 cM from T6-SCAR. Without the removal of the GPI plants, Vbj was placed 15 cM away from the closest markers. Problems and pitfalls due to GPI plants and the consequences for mapping the resistance gene accurately are discussed. Finally, the usefulness of co-dominant markers for pedigree analysis is also demonstrated.

BACKGROUND AND AIMS: Vineyards harbour a variety of weeds, which are usually controlled since they compete with grapevines for water and nutrients. However, weed plants may host groups of fungi and bacteria exerting important functions. METHODS: We grew three different common vineyard weeds (Taraxacum officinalis, Trifolium repens and Poa trivialis) in four different soils to investigate the effects of weeds and soil type on bacterial and fungal communities colonising bulk soil, rhizosphere and root compartments. Measurements were made using the cultivation-independent technique Automated Ribosomal Intergenic Spacer Analysis (ARISA). RESULTS: Weeds have a substantial effect on roots but less impact on the rhizosphere and bulk soil, while soil type affects all three compartments, in particular the bulk soil community. The fungal, but not the bacterial, bulk soil community structure was affected by the plants at the late experimental stage. Root communities contained a smaller number of Operational Taxonomic Units (OTUs) and different bacterial and fungal structures compared with rhizosphere and bulk soil communities. CONCLUSIONS: Weed effect is localised to the rhizosphere and does not extend to bulk soil in the case of bacteria, although the structure of fungal communities in the bulk soil may be influenced by some weed plants.

Guignardia bidwellii is the etiological agent of grape black rot, a disease affecting Vitis and other Vitaceae that can cause heavy crop losses in vineyards. Its identification is based mainly on morphological characters and the symptoms on plants but, due to their variability, they may be difficult to interpret to reliably distinguish the pathogen to species. To date, despite the economic importance of G. bidwellii, no molecular investigations have been carried out on Vitis isolates and few sequence data are available for cultures derived from ornamental host plants. We analyzed samples of G. bidwellii collected from grapevine cultivars and ornamental plants of various geographic origins by morphological, molecular and proteomic techniques, including ITS1-ITS2 regions and calmodulin gene sequencing, as well as matrix-assisted laser desorption/ionization analysis by time-of-flight mass spectrometry (MALDI-TOF MS). This polyphasic approach allowed assessing the phylogenetic relationships among the different isolates and suggested the existence of two distinct species. The advantages of a polyphasic approach for the identification of G. bidwellii are highlighted.

The availability of suitable genetic markers is essential to efficiently select and breed apple varieties of high quality and with multiple disease resistances. Microsatellites (simple sequence repeats, SSR) are very useful in this respect since they are codominant, highly polymorphic, abundant and reliably reproducible. Over 140 new SSR markers have been developed in apple and tested on a panel of 7 cultivars and 1 breeding selection. Their high level of polymorphism is expressed with an average of 6.1 alleles per locus and an average heterozygosity (H) of 0.74. Of all SSR markers, 115 have been positioned on a genetic linkage map of the cross 'Fiesta' x 'Discovery'. As a result, all 17 linkage groups, corresponding to the 17 chromosomes of apple, were identified. Each chromosome carries at least two SSR markers, allowing the alignment of any apple molecular marker map both with regard to identification as well as to orientation of the linkage groups. To test the degree of conservation of the SSR flanking regions and the transferability of the SSR markers to other Rosaceae species, 15 primer pairs were tested on a series of Maloideae and Amygdaloideae species. The usefulness of the newly developed microsatellites in genetic mapping is demonstrated by means of the genetic linkage map. The possibility of constructing a global apple linkage map and the impact of such a number of microsatellite markers on gene and QTL mapping is discussed.

The development of highly informative markers, such as simple sequence repeats, for tagging genes controlling agronomic characters is essential for apple breeding. Furthermore the use of these markers is fundamental both for variety identification and for the characterisation and management of genetic resources. We have developed 16 reliable simple sequence repeat (SSR) markers that amplify all alleles from a panel of 19 Malus x domestica (Borkh.) cultivars or breeding selections and from Malus floribunda 821. Those markers show a high level of genetic polymorphism, with on average 8.2 alleles per locus and an average heterozygosity of 0.78. Due to this high level of polymorphism, it was possible using two selected SSRs to distinguish all cultivars except Starking and Red Delicious. Ten of the markers we developed have been mapped on a RAPD linkage map, proving their Mendelian segregation as well as their random distribution in the apple genome. Finally, we discuss the importance of using co-dominant markers in outbreeding species.