Teresa Barreneche

A genetic linkage map of Quercus robur L. (pedunculate oak) based on RAPD, SCAR, microsatellite, minisatellite, isozyme and 5S rDNA markers

Abstract A genetic map of Pedunculate oak (Quercus robur) was constructed based on one 5S rDNA, 271 RAPD, ten SCAR, 18 microsatellite, one minisatellite, and six isozyme markers. A total of 94 individuals from a full-sib family was genotyped. Two maps, including 307 markers, were constructed according to the “two-way pseudo-testcross” mapping strategy. Testcross markers segregating in the 1 : 1 ratio were first used to establish separate maternal (893.2 cM, 12 linkage groups) and paternal (921.7 cM, 12 linkage groups) maps. Both maps provided 85–90% genome coverage. Homologies between the male and female linkage groups were then identified based on 74 intercross markers segregating in the 3 : 1, 1 : 2 : 1 and 1 : 1 : 1 : 1 ratios (RAPDs, SCARs, SSRs, 5S rDNA and isozymes) in the hybrid progeny. In each map, approximately 18% of the studied markers showed segregation distortion. More than 60% of the skewed markers were due to an excess of heterozygote genotypes. This map will be used for: (1) studying the molecular organisation of genomic regions involved in inter- and intraspecific differentiation in oaks and (2) identification of QTLs for adaptive traits.

Comparative mapping between Quercus and Castanea using simple-sequence repeats (SSRs)

Simple sequence repeat (SSR) markers from Quercus and Castanea were used for comparative mapping between Quercus robur (L.) and Castanea sativa (Mill.). We tested the transferability of SSRs developed in Quercus to Castanea and vice-versa. In total, 47% (25) of the Quercus SSRs and 63% (19) of the Castanea SSRs showed a strong amplification product in the non-source species. From these 44 putative comparative anchor tags, 19 (15 from Quercus and 4 from Castanea) were integrated in two previously established genetic linkage maps for the two genera. SSR loci were sequenced to confirm the orthology of the markers. The combined information from both genetic mapping and sequence analysis were used to determine the homeology between seven linkage groups, aligned on the basis of pairs or triplets of common markers, while two additional groups were matched using a single microsatellite marker. Orthologous loci identified between Q. robur and C. sativa will be useful as anchor loci for comparative mapping studies within the Fagaceae family.

Distribution of genomic regions differentiating oak species assessed by QTL detection

Pedunculate oak and sessile oak are two sympatric interfertile species that exhibit leaf morphological differences. We aimed to detect quantitative trait loci (QTLs) of these traits in order to locate genomic regions involved in species differentiation. A total of 15 leaf morphological traits were assessed in a mixed forest stand composed of Quercus petraea and Q. robur and in a full-sib pedigree of Q. robur. The progeny of the full-sib family were vegetatively propagated in two successive experiments comprising 174 and 216 sibs, and assessments were made on two leaves collected on each of the 1080 and 1530 cuttings corresponding to the two experiments. Traits that exhibited strong species differences in the mixed stand tended also to have higher repeatability values in the mapping population, thus indicating higher genetic control. A genetic map was constructed for QTL detection. Composite interval mapping with the one QTL model was used for QTL detection. From one to three QTLs were detected for 13 traits. In-depth analysis of the QTLs, controlling the five morphological traits that exhibited the highest interspecific differences in the mixed stand, indicated that they were distributed on six linkage groups, with two clusters comprising QTLs of at least two discriminant traits. These results were reinforced when error 1 for QTL detection was set at 5% at the chromosome level, as up to nine clusters could be identified. In conclusion, traits involved in interspecific differentiation of oaks are under polygenic control and widespread in clusters across the genome.

Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm.

Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.

Variation in grafted European chestnut and hybrids by microsatellites reveals two main origins in the Iberian Peninsula

This is the first known large-scale molecular study of simple sequence repeats (SSR) loci based on samples from grafted trees found in the Iberian Peninsula and Canary Islands and hybrids. Interspecific hybrids resistant to ‘ink disease’ (Phytophthora spp.) were obtained in France, Portugal and Spain, although difficult to distinguish by morphology. This study focuses on genetic variation using 10 SSRs (11 unlinked loci) from clonally propagated cultivars (574 accessions) of European chestnut (Castanea sativa) and hybrids (71 accessions). They were compared with a representative sample of exotic chestnut species present in the Atlantic area, 47 accessions of Castanea crenata, 37 of Castanea mollissima and 33 of Castanea henryi. Accessions were analysed using a model-based Bayesian procedure (Structure), factorial correspondence analysis and analysis of molecular variance. The main chestnut species, hybrids and alien introgressions were differentiated. Two main origins of variability in European cultivated chestnut were found in the Iberian Peninsula, one in the North and a second in the Centre. Andalusian and Canary Island accessions could be assigned to both of these zones, which indicate that they could have been colonised with cultivars originating from either zone, in the case of the Canary Islands from the sixteenth century on.

Linkage mapping of osmotic stress induced genes of oak

Water stress affecting long-lived trees is an important challenge in forestry. Due to global climate change, forest trees will be threatened by extreme conditions like flooding or drought. It is necessary to understand differences in stress tolerance within certain species and to investigate putative relations on genomic level. In this study, osmotic stress induced genes of Quercus ssp. were positioned on two genetic linkage maps of oak. An intra-specific cross 3P*A4 of Quercus robur consisting of 88 offspring and an inter-specific cross 11P*QS29 of Q. robur and Q. petraea comprising 72 full-sibs were analyzed for the inheritance of 14 loci represented by 34 individual single nucleotide polymorphisms. Seven genes in the intra-cross, as well as other six genes in the inter-cross could be mapped and one gene could not be localised due to the severe distortion of the segregation. The collection of expressed sequences involved ribosomal proteins, members of the oxylase/oxygenase gene family, betaine aldehyde dehydrogenase, Dc3 promoter-binding factor, a putative member of the nodulin family, glutathione-S-transferase and proteins with unknown functions. In the inter-cross, two linked markers exhibited 89% deficiency of heterozygosity. Thirteen genes were positioned on ten different oak chromosomes and can serve as orthologous markers in comparative mapping studies within Fagaceae.

Mapping of Candidate Genes Involved in Bud Dormancy and Flowering Time in Sweet Cherry (Prunus avium).

The timing of flowering in perennial plants is crucial for their survival in temperate climates and is regulated by the duration of bud dormancy. Bud dormancy release and bud break depend on the perception of cumulative chilling during endodormancy and heat during the bud development. The objectives of this work were to identify candidate genes involved in dormancy and flowering processes in sweet cherry, their mapping in two mapping progenies ‘Regina’ × ‘Garnet’ and ‘Regina’ × ‘Lapins’, and to select those candidate genes which co-localized with quantitative trait loci (QTLs) associated with temperature requirements for bud dormancy release and flowering. Based on available data on flowering processes in various species, a list of 79 candidate genes was established. The peach and sweet cherry orthologs were identified and primers were designed to amplify sweet cherry candidate gene fragments. Based on the amplified sequences of the three parents of the mapping progenies, SNPs segregations in the progenies were identified. Thirty five candidate genes were genetically mapped in at least one of the two progenies and all were in silico mapped. Co-localization between candidate genes and QTLs associated with temperature requirements and flowering date were identified for the first time in sweet cherry. The allelic composition of the candidate genes located in the major QTL for heat requirements and flowering date located on linkage group 4 have a significant effect on these two traits indicating their potential use for breeding programs in sweet cherry to select new varieties adapted to putative future climatic conditions.

New Insights into Fruit Firmness and Weight Control in Sweet Cherry

Fruit firmness and weight are among the most important fruit quality traits in fruit species. Understanding the control of fruit firmness and weight is essential for the development of domestication research approaches and for the implementation of new breeding strategies. A forward genetic study for these traits was performed using two F1 sweet cherry (Prunus avium) progenies derived from modern cultivars. Quantitative trait locus (QTL) analysis allowed the identification of genomic regions accounting for most of the phenotypic variation in both families. In addition, screening the Prunus persica genome v1.0 permitted the identification of putative candidate genes underlying the QTL with the major effect for fruit weight (LG5) and the one for firmness (LG6). A colocalization of QTLs and candidate genes was found in peach, apple, and tomato. These results give new insights of the interaction between fruit firmness and fruit weight and provide new cues for the identification of genes implicated in the control of these traits. The colocalization of genomic regions between progenies issued from modern cultivars and from modern cultivars × wild individuals suggests the absence of allele fixation within genes controlling fruit firmness and size, two traits potentially involved in domestication/diversification in sweet cherry.

Database of European chestnut cultivars and definition of a core collection using simple sequence repeats

We have evaluated 271 accessions corresponding to 118 European cultivars, 96 from Spain, 16 from Italy, four from France and two from Portugal with the following objectives: (1) to provide a European database based on reference simple sequence repeats (SSRs) and (2) to define a core collection. A set of 24 highly polymorphic SSRs were used for the genetic analysis. Two main clusters were identified using a model-based Bayesian procedure, which correspond to Spanish and Italian cultivar clusters, with the latter showing a higher genetic diversity. An additional genetic substructure was observed among five different groups of cultivars. A core collection with a minimum of 37 cultivars was selected. We provided a database including 132 European accessions with unique genotypes evaluated with 24 SSRs as a reference for distinction, registering and traceability. Finally, we found that a core collection based on 14% of the total accessions conserves all allelic diversity.

Integration of cryopreservation in French plant genetic resource collections: the CRYOVEG project

This book represents contributions, oral as well as posters, of the final meeting of COST Action 871, CRYOPLANET (Cryopreservation of crop species in Europe) held in Angers. Local organizers of the meeting were Dr. Agnes Grapin (AGROCAMPUS OUEST – Angers) and Dr. Florent Engelmann (Institut de Recherche pour le Developpement). COST Action 871 started in December 2006 with a Kick-off meeting at the COST office in Brussels and officially ended in December 2010. Twenty-one COST Action Countries (see figure 1) and 3 non-COST institutes (New Zealand Institute for Crop & Food Research (New Zealand), Vavilov Institute of Plant Industry (Russian Federation), Faculte des Sciences de Sfax (Tunisia) participated actively in this initiative. The Action was created because plant cryobiologists realized that plant cryopreservation was hardly applied in Europe. This was mainly due to the fact that efficient and robust cryopreservation protocols applicable to many plant species and diverse germplasm types were not available, plant researchers were unacquainted to recent developments in cryogenic storage methods and there was a lack of coordinated research in Europe on plant cryopreservation. The main objective of this action was therefore “to improve and apply technologically advanced techniques for plant genetic resources conservation of crops that are grown/ and or conserved in Europe with main emphasis on long-term conservation through cryopreservation”. In order to achieve this, 2 working groups (WGs) were established