Genomic analysis in maritime pine (Pinus pinaster). Comparison of two RAPD maps using selfed and open-pollinated seeds of the same individual

Two genomic maps were constructed for one individual tree of maritime pine, Pinus pinaster Ait., using a common set of 263 RAPD markers (random amplified polymorphic DNA). The RAPD markers were chosen from a larger number of polymorphic RAPD fragments on the basis of repeatability and inheritance in a three-generation pedigree. The maps were constructed from two independent mapping samples of 62 megagametophytes (In) from a self cross and from an open-pollinated cross. The markers were grouped (LOD≥4; θ≤0.25) and assigned to 13 major and 5 minor linkage groups. Two framework maps were constructed using the ordering criterion of interval support≥3. Comparison of the two framework maps suggested that the locus order was incorrect for 2% of the framework markers. A bootstrap analysis showed that this error rate was representative for our data set. The results showed that framework maps constructed using RAPD markers were repeatable and that differences in locus order for maps of different genotypes or species could result from chance. The total map distance was 1380 cM, and the map provided coverage of approximately 90% of the genome.     

Polygenic inheritance of resistance to <Emphasis Type="Italic">Cacopsylla pyri</Emphasis> in a <Emphasis Type="Italic">Pyrus communis</Emphasis> × <Emphasis Type="Italic">P. ussuriensis</Emphasis> progeny is explained by three QTLs involving an epistatic interaction

Pear psylla (Cacopsylla pyri) causes severe damage on European pear cultivars, resulting in high yield losses. Its control has become difficult since it developed resistance to a wide range of pesticides, while the number of authorized molecules for pest control has decreased. Identifying pear psylla resistance factors should help breeding new resistant pear cultivars. We analyzed the quantitative resistance to psylla inherited from the genotype NY 10355 derived from Pyrus ussuriensis. Quantitative trait locus (QTL) analysis was carried out after counting the number of nymphs and estimating the nymphal development rate using a free-choice test performed on a large segregating progeny. We mapped two new loci for pear psylla resistance on linkage groups LG01 and LG04 of NY 10355 and confirmed the QTL previously detected on LG17. A strong epistatic interaction between the two QTLs detected on LG01 and LG17 appeared to be a major factor controlling the psylla infestation in the genotype NY 10355.     

Iron overload in Hepc1(-/-) mice is not impairing glucose homeostasis

Diabetes Mellitus is found with increasing frequency in iron overload patients with hemochromatosis. In these conditions, the pancreas shows predominant iron overload in acini but also islet beta-cells. We assess glucose homeostasis status in iron-overloaded hepcidin-deficient mice. These mice presented with heavy pancreatic iron deposits but only in the acini. The beta-cell function was found unaffected with a normal production and secretion of insulin. The mutant mice were not diabetic, responded as the control group to glucose and insulin challenges, with no alteration of insulin signalling in the muscle and the liver. These results indicate that, beta-cells iron deposits-induced decreased insulin secretory capacity might be of primary importance to trigger diabetes in hemochromatosic patients.     

Estimation of genetic parameters and prediction of breeding values for apple fruit-quality traits using pedigreed plant material in Europe

Genetic parameters for apple (Malus x domestica) fruit external traits (fruit size, ground colour, proportion of over colour and attractiveness) and sensory traits (firmness, crispness, texture, juiciness, flavour, sugar, acidity and global taste) were estimated using 2,207 pedigreed genotypes from breeding programmes in six European countries. Data were scored for 3 years and four periods during storage. Analyses were performed with a restricted maximum likelihood method using VCE 5.1.2 software. Heritability estimates ranged from medium to high for instrumental traits. Genetic correlations between firmness and sugar were medium and low between firmness and acidity. Sensory traits showed low to high heritability, acidity and flavour being, respectively, the most and the less heritable. Global taste was strongly correlated with texture, juiciness, and flavour and relatively less correlated with crispness and acidity. Sensory sugar and acidity showed highly negative correlations whereas their instrumental measurements showed low and increasing positive correlations from harvest to 4 months post-harvest. Sugar exhibited a higher sensory/instrumental divergence. Conversely, instrumental and sensory firmness were highly correlated. Fruit external characteristics had medium heritability. Fruit attractiveness had highest and lowest correlations with fruit size and ground colour, respectively. Best linear unbiased predictors of breeding values were computed for all genotypes with the software PEST. The results were analysed with regard to the dynamic and the reliability of genetic parameters according to the scoring dates. Original issues of the study and the importance of the obtained results for efficient designs of further apple fruit quality breeding programmes were discussed.     

A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase

OBJECTIVE: AppleBreed DataBase (DB) aims to store genotypic and phenotypic data from multiple pedigree verified plant populations (crosses, breeding selections and commercial cultivars) so that they are easily accessible for geneticists and breeders. It will help in elucidating the genetics of economically important traits, in identifying molecular markers associated with agronomic traits, in allele mining and in choosing the best parental cultivars for breeding. It also provides high traceability of data over generations, years and localities. AppleBreed DB could serve as a generic database design for other perennial crops with long economic lifespans, long juvenile periods and clonal propagation. RESULTS: AppleBreed DB is organized as a relational database. The core element is the GENOTYPE entity, which has two sub-classes at the physical level: TREE and DNA-SAMPLE. This approach facilitates all links between plant material, phenotypic and molecular data. The entities TREE, DNA-SAMPLE, PHENOTYPE and MOLECULAR DATA allow multi-annual observations to be stored as individual samples of individual trees, even if the nature of these observations differs greatly (e.g. molecular data on parts of the apple genome, physico-chemical measurements of fruit quality traits, and evaluation of disease resistance). AppleBreed DB also includes synonyms for cultivars and pedigrees. Finally, it can be loaded and explored through the web, and comes with tools to present basic statistical overviews and with validation procedures for phenotypic and marker data to certify data quality. AppleBreed DB was developed initially as a tool for scientists involved in apple genetics within the framework of the European project, 'High-quality Disease Resistance in Apples for Sustainable Agriculture' (HiDRAS), but it is also applicable to many other perennial crops.     

Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome

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 () 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.E. Silfverberg-Dilworth and C. L. Matasci contributed equally to this work.     

Utilization of pedigree information to estimate genetic parameters from large unbalanced data sets in apple

 Genetic parameters (narrow-sense heritabilities and genetic correlations) were estimated for major agronomical traits in apple from large unbalanced data sets, with the help of wide-pedigree information. The software REML VCE (Groeneveld 1996) took into account the complex pedigree of the French apple-breeding population, thanks to the restricted maximum likelihood procedure combined with the construction of the entire relationship matrix between hybrids planted in the field and their ancestors. Narrow-sense heritability estimates ranged from 0.34 to 0.68 for traits exhibiting a normal distribution. Heritability values around 0.35–0.40 were obtained for fruit characteristics (size, texture, flavour, juice content, attractiveness, russeting). Higher values of heritability were obtained for vigour, assessed by the circumference of the trunk (0.51), and powdery mildew resistance (0.68). Additive genetic correlations between traits were also estimated, showing a very high relationship between fruit-quality traits. Vigour and powdery mildew resistance were slightly correlated with the other traits. Utilization of the ‘individual genetic model’ for the estimation of genetic parameters and breeding values in apple is discussed. Received: 14 June 1997 / Accepted: 4 December 1997     

Identification of candidate genes at the <Emphasis Type="Italic">Dp-fl</Emphasis> locus conferring resistance against the rosy apple aphid <Emphasis Type="Italic">Dysaphis plantaginea</Emphasis>

The cultivated apple is susceptible to several pests including the rosy apple aphid (RAA; Dysaphis plantaginea Passerini), control of which is mainly based on chemical treatments. A few cases of resistance to aphids have been described in apple germplasm resources, laying the basis for the development of new resistant cultivars by breeding. The cultivar ‘Florina’ is resistant to RAA, and recently, the Dp-fl locus responsible for its resistance was mapped on linkage group 8 of the apple genome. In this paper, a chromosome walking approach was performed by using a ‘Florina’ bacterial artificial chromosome (BAC) library. The walking started from the available tightly linked molecular markers flanking the resistance region. Various walking steps were performed in order to identify the minimum tiling path of BAC clones covering the Dp-fl region from both the “resistant” and “susceptible” chromosomes of ‘Florina’. A genomic region of about 279 Kb encompassing the Dp-fl resistance locus was fully sequenced by the PacBio technology. Through the development of new polymorphic markers, the mapping interval around the resistance locus was narrowed down to a physical region of 95 Kb. The annotation of this sequence resulted in the identification of four candidate genes putatively involved in the RAA resistance response.