Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitièresIn temperate trees, growth resumption in spring time results from chilling and heat requirements, and is an adaptive trait under global warming. Here, the genetic determinism of budbreak and flowering time was deciphered using five related full-sib apple families. Both traits were observed over 3 years and two sites and expressed in calendar and degree-days. Best linear unbiased predictors of genotypic effect or interaction with climatic year were extracted from mixed linear models and used for quantitative trait locus (QTL) mapping, performed with an integrated genetic map containing 6849 single nucleotide polymorphisms (SNPs), grouped into haplotypes, and with a Bayesian pedigree-based analysis. Four major regions, on linkage group (LG) 7, LG10, LG12, and LG9, the latter being the most stable across families, sites, and years, explained 5.6–21.3% of trait variance. Co-localizations for traits in calendar days or growing degree hours (GDH) suggested common genetic determinism for chilling and heating requirements. Homologs of two major flowering genes, AGL24 and FT, were predicted close to LG9 and LG12 QTLs, respectively, whereas Dormancy Associated MADs-box (DAM) genes were near additional QTLs on LG8 and LG15. This suggests that chilling perception mechanisms could be common among perennial and annual plants. Progenitors with favorable alleles depending on trait and LG were identified and could benefit new breeding strategies for apple adaptation to temperature increase

Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi-family Population Based on Statistical Indices and Simplified Phenotyping

Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales. They were used to predict tree behavior and detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of a Biennial Bearing Index (BBI) with an autoregressive coefficient (γg) efficiently predicted and classified the genotype behaviors, despite few misclassifications. Four QTLs common to BBIs and γg and one for synchronicity were highlighted and revealed the complex genetic architecture of the traits. Irregularity resulted from high AS synchronism, whereas regularity resulted from either asynchronous locally alternating or continual regular AS flowering. A relevant and time-saving method, based on a posteriori sampling of axes and statistical indices is proposed, which is efficient to evaluate the tree breeding values for flowering regularity and could be transferred to other species

Circulating tumor cells: approaches to isolation and characterization

Circulating tumor cells (CTCs) shed from primary and metastatic cancers are admixed with blood components and are thus rare, making their isolation and characterization a major technological challenge. CTCs hold the key to understanding the biology of metastasis and provide a biomarker to noninvasively measure the evolution of tumor genotypes during treatment and disease progression. Improvements in technologies to yield purer CTC populations amenable to better cellular and molecular characterization will enable a broad range of clinical applications, including early detection of disease and the discovery of biomarkers to predict treatment responses and disease progression

Minimal residual disease and circulating tumor cells in breast cancer

Tumor cell dissemination in bone marrow or other organs is thought to represent an important step in the metastatic process. The detection of bone marrow disseminated tumor cells is associated with worse outcome in early breast cancer. Moreover, the detection of peripheral blood circulating tumor cells is an adverse prognostic factor in metastatic breast cancer, and emerging data suggest that this is also true for early disease. Beyond enumeration, the characterization of these cells has the potential to improve risk assessment, treatment selection and monitoring, and the development of novel therapeutic agents, and to advance our understanding of the biology of metastasis

Character integration, breeding goals compatibility and selection indexes using genome wide breeding values: a study case

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitièresBreeding in apple is characterized by a high number of characters concerned, related to several biological processes. The main characters are fruit quality, disease resistance and yield. In addition, the will to reduce the use of chemical products in agriculture and the changing climatic context causes the need to breed for new complex characters such as yield regularity and adaptation to temperature increase. This work is a study case of trait integration for fruit quality, yield level and regularity, and bud phenology related traits. Compatibility of breeding objectives, according to one fixed ideotype, were analysed and a strategy for the introduction of new characters in breeding schemes using molecular markers, breeding values estimation, and selection indexes was proposed. Two unrelated families were phenotyped, QTL analyses were run with the Bayesian software FlexQTLTM and the individual genetic breeding values were computed trait by trait by adding the genetic effect of loci estimated during the QTL mapping process. An ideotype integrating all traits was fixed and principal component analyses were realized in order to study the breeding goals compatibility. Traits were integrated in two selection indexes computed with breeding values. Synergistic correlations between fruit size and yield regularity was identified and antagonistic correlation was observed between fruit size and yield level, and yield regularity and level and partially explained by colocalization of QTLs with high opposite effects according to the ideotype. In case of antagonistic correlation between important traits, a genetic ideotype could be a tool to monitor precisely the choice of genitors and identification of progenies compatible with the ideotype. Principal component analyses and selection indexes values revealed a differential genetic potential of the two families depending on traits and their correlations, and interesting individuals could be identified in both families even if selection indexes values were in favor of one of the families. In conclusion, the use of molecular markers, genetic effects estimation in a genomic selection approach, combined with a selection index strategy would be an efficient way to introduce simultaneously new complex characters in breeding schemes