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

QTL analysis on a lemon population provides novel insights on the genetic regulation of the tolerance to the two-spotted spider mite attack

Background: Among the Citrus species, lemon (Citrus limon Burm f.) is one of the most affected by the two-spotted spider mite (Tetranychus urticae Koch). Moreover, chemical control is hampered by the mite's ability to develop genetic resistance against acaricides. In this context, the identification of the genetic basis of the host resistance could represent a sustainable strategy for spider mite control. In the present study, a marker-trait association analysis was performed on a lemon population employing an association mapping approach. An inter-specific full-sib population composed of 109 accessions was phenotyped through a detached-leaf assays performed in modified Huffaker cells. Those individuals, complemented with two inter-specific segregating populations, were genotyped using a target-sequencing approach called SPET (Single Primer Enrichment Technology), the resulting SNPs were employed for the generation of an integrated genetic map. Results: The percentage of damaged area in the full-sib population showed a quantitative distribution with values ranging from 0.36 to 9.67%. A total of 47,298 SNPs were selected for an association mapping study and a significant marker linked with resistance to spider mite was detected on linkage group 5. In silico gene annotation of the QTL interval enabled the detection of 13 genes involved in immune response to biotic and abiotic stress. Gene expression analysis showed an over expression of the gene encoding for the ethylene-responsive transcription factor ERF098-like, already characterized in Arabidopsis and in rice for its involvement in defense response. Conclusion: The identification of a molecular marker linked to the resistance to spider mite attack can pave the way for the development of marker-assisted breeding plan for the development of novel selection coupling favorable agronomical traits (e.g. fruit quality, yield) with a higher resistance toward the mit

High feasibility and antileukemic efficacy of fludarabine, cytarabine, and idarubicin (FLAI) induction followed by risk-oriented consolidation: A critical review of a 10-year, single-center experience in younger, non M3 AML patients

About 105 consecutive acute myeloid leukemia (AML) patients treated with the same induction-consolidation program between 2004 and 2013 were retrospectively analyzed. Median age was 47 years. The first induction course included fludarabine (Flu) and high-dose cytarabine (Ara-C) plus idarubicin (Ida), with or without gemtuzumab-ozogamicin (GO) 3 mg/m2 (FLAI-5). Patients achieving complete remission (CR) received a second course without fludarabine but with higher dose of idarubicin. Patients not achieving CR received an intensified second course. Patients not scheduled for early allogeneic bone marrow transplantation (HSCT) where planned to receive at least two courses of consolidation therapy with Ara-C. Our double induction strategy significantly differs from described fludarabine-containing regimens, as patients achieving CR receive a second course without fludarabine, to avoid excess toxicity, and Ara-C consolidation is administrated at the reduced cumulative dose of 8 g/m2 per cycle. Toxicity is a major concern in fludarabine containing induction, including the recent Medical Research Council AML15 fludarabine, cytarabine, idaraubicin and G-CSF (FLAG-Ida) arm, and, despite higher anti-leukemic efficacy, only a minority of patients is able to complete the full planned program. In this article, we show that our therapeutic program is generally well tolerated, as most patients were able to receive subsequent therapy at full dose and in a timely manner, with a 30-day mortality of 4.8%. The omission of fludarabine in the second course did not reduce efficacy, as a CR rate of 83% was achieved and 3-year disease-free survival and overall survival (OS) were 49.6% and 50.9%, respectively. Our experience shows that FLAI-5/Ara-C + Ida double induction followed by risk-oriented consolidation therapy can result in good overall outcome with acceptable toxicity. Am. J. Hematol. 91:755\u2013762, 2016. \ua9 2016 Wiley Periodicals, Inc

miR-146a-5p impairs melanoma resistance to kinase inhibitors by targeting COX2 and regulating NFkB-mediated inflammatory mediators

BACKGROUND: Targeted therapy with BRAF and MEK inhibitors has improved the survival of patients with BRAF-mutated metastatic melanoma, but most patients relapse upon the onset of drug resistance induced by mechanisms including genetic and epigenetic events. Among the epigenetic alterations, microRNA perturbation is associated with the development of kinase inhibitor resistance. Here, we identified and studied the role of miR-146a-5p dysregulation in melanoma drug resistance.METHODS: The miR-146a-5p-regulated NFkB signaling network was identified in drug-resistant cell lines and melanoma tumor samples by expression profiling and knock-in and knock-out studies. A bioinformatic data analysis identified COX2 as a central gene regulated by miR-146a-5p and NFkB. The effects of miR-146a-5p/COX2 manipulation were studied in vitro in cell lines and with 3D cultures of treatment-resistant tumor explants from patients progressing during therapy.RESULTS: miR-146a-5p expression was inversely correlated with drug sensitivity and COX2 expression and was reduced in BRAF and MEK inhibitor-resistant melanoma cells and tissues. Forced miR-146a-5p expression reduced COX2 activity and significantly increased drug sensitivity by hampering prosurvival NFkB signaling, leading to reduced proliferation and enhanced apoptosis. Similar effects were obtained by inhibiting COX2 by celecoxib, a clinically approved COX2 inhibitor.CONCLUSIONS: Deregulation of the miR-146a-5p/COX2 axis occurs in the development of melanoma resistance to targeted drugs in melanoma patients. This finding reveals novel targets for more effective combination treatment. Video Abstract

Fertility specialists’ views, behavior, and attitudes towards the use of endometrial scratching in Italy

Background: Endometrial scratching (ES) or injury is intentional damage to the endometrium performed to improve reproductive outcomes for infertile women desiring pregnancy. Moreover, recent systematic reviews with meta-analyses and randomized controlled trials demonstrated that ES is not effective, data on the safety are limited, and it should not be recommended in clinical practice. The aim of the current study was to assess the view and behavior towards ES among fertility specialists throughout infertility centers in Italy, and the relationship between these views and the attitudes towards the use of ES as an add-on in their commercial setting. Methods: Online survey among infertility centers, affiliated to Italian Society of Human Reproduction (SIRU), was performed using a detailed questionnaire including 45 questions with the possibility to give "closed" multi-choice answers for 41 items and "open" answers for 4 items. Online data from the websites of the infertility centers resulting in affiliation with the specialists were also recorded and analyzed. The quality of information about ES given on infertility centers websites was assessed using a scoring matrix including 10 specific questions (scored from 0 to 2 points), and the possible scores ranged from 0 to 13 points ('excellent' if the score was 9 points or more, 'moderate' if the score was between 5 and 8, and 'poor' if it was 4 points or less). Results: The response rate was of 60.6% (43 questionnaires / 71 infertility SIRU-affiliated centers). All included questionnaires were completed in their entirety. Most physicians (~ 70%) reported to offer ES to less than 10% of their patients. The procedure is mainly performed in the secretory phase (69.2%) using pipelle (61.5%), and usually in medical ambulatory (56.4%) before IVF cycles to improve implantation (71.8%) without drugs administration (e.g., pain drugs, antibiotics, anti-hemorrhagics, or others) before (76.8%) or after (64.1%) the procedure. Only a little proportion of infertility centers included in the analysis proposes formally the ES as an add-on procedure (9.3%), even if, when proposed, the full description of the indications, efficacy, safety, and costs is never addressed. However, the overall information quality of the websites was generally "poor" ranging from 3 to 8 and having a low total score (4.7 ± 1.6; mean ± standard deviation). Conclusions: In Italy, ES is a procedure still performed among fertility specialists for improving the implantation rate in IVF patients. Moreover, they have a poor attitude in proposing ES as an add-on in the commercial setting

Investigating the fruit texture genetic control in apple and its interplay with the production of volatile compounds using multi-family based analysis and genome wide association mapping

Although varying with context, quality of fresh fruits includes several properties such as color, texture, flavor and health promoting compounds. This thesis focused on two important quality aspects, namely texture and aroma in apple, and defining the genomic regions involved in the control of these two features. The genetic control of texture and VOCs production have been investigated using two marker-trait association analysis approaches: Pedigree Based Analysis (PBA) and Genome Wide Association Study (GWAS). In chapter 2, ASSIsT (Automatic SNP ScorIng Tool), a software dedicated for the efficient calling and filtering of SNPs from Illumina InfiniumÒ arrays is presented. ASSIsT builds on GenomeStudio® derived data and identifies markers showing reliable genotype calls (bi-allelic segregation pattern). In addition, ASSIsT identifies and re-edits SNP calls of markers showing additional alleles (null alleles or additional SNPs in the probe annealing site). Chapter 3 aimed to dissect the genetic control of fruit firmness in apple during storage through PBA and employing 24 bi-parental families (1216 individuals) connected by a common pedigree structure. Ten QTLs were identified encompassing eight linkage groups, which unravelled a QTL dynamics over storage shedding light on the specific genetic control at each time-point. Chapter 4: aimed to comprehensively decipher the genetic control of fruit texture. Two complementing QTL mapping approaches were employed together with a novel and high sophisticated phenotyping device for fruit texture. The PBA was carried out on six full-sib pedigreed families (416 individuals), while the GWAS was performed on a collection of 233 apple accessions. The texture analyser employed (TAXT-AED texture analyser) allowed the measurement of both the mechanical properties (firmness) and the acoustic properties (crispness) of fruit texture. The QTL results indicated chromosome 10 being associated in changes of the mechanical properties of fruit texture, while chromosomes 2 and 14 were more associated to the acoustic response. In Chapter 5 the interplay between texture and volatile organic compounds (VOCs) was investigated in 162 apple accessions. The array of volatile compounds phenotyped was implemented into a GWAS identifying seven chromosomes harbouring important candidate genes for aroma, such as MdAAT1 and MdIGS. Next, volatilome and fruit texture data were integrated revealing a negative correlation between these two features.</p

Prediction of fruit texture with training population optimization for efficient genomic selection in apple

International audienc

Optimizing predictions for applying genomic selection to texture in Apple

International audienceAlthough genomic selection promised to increase drastically breeding efficiency in perennial crops, it is not yet broadly applied in fruit trees. Among the several targets in apple breeding, fruit texture is an essential feature affecting both consumers’ appreciation and storage performance. Due to the fixation of alleles at the major genes underlying texture in modern breeding programs, the available genetic variability for this trait might rely on minor effect alleles, which can be targeted with genomic selection. In this study, we aimed to assess the feasibility of genomic selection for texture in a population of 537 individuals consisting in a collection of 259 individuals and 6 full-sib biparental families, all genotyped with 8,294 SNPs. We dissected the fruit texture complexity by measuring twelve acoustic and mechanical subtraits with a TA.XTplus texture analyzer. We applied different scenarios for the design of the training population with and without taking into account genetic parameters. The use of the entire collection to predict families was not the most efficient strategy, since families were best predicted using training populations composed of the 10 to 202 most related individuals. Training population optimization allowed increasing prediction accuracies by 0.17 on average, reaching a maximum accuracy of 0.78 for predicting the number of force peaks in the family ‘Gala x Pink Lady’. As the two first principal components of texture traits summarized firmness (PC1) and crispiness (PC2), we predicted these two synthetic traits and obtained maximum accuracies of 0.81 and 0.40, respectively. Furthermore, our results indicate that although genetic clustering may be correlated to texture profiles, genetic relatedness might already capture the clustering effect in predictions. Our work sheds light on the high potential for predicting texture in apple. The methods presented here also provide insights for efficiently designing genomic selection trials in fruit trees

Sweet Orange: Evolution, Characterization, Varieties, and Breeding Perspectives

Among Citrus species, the sweet orange (Citrus sinensis (L.) Osbeck) is the most important in terms of production volumes and cultivated areas. Oranges are particularly appreciated for the organoleptic characteristics and the high nutraceutical value of the fruits (thanks especially to their high content of antioxidants). Recent advances in citrus genetic and genomic resources, such as the release of the reference genomes of several sweet orange cultivars, have contributed to (i) understanding the diversification of C. sinensis and its relation with other citrus species, (ii) assessing the molecular mechanisms underlying traits of interest, (iii) identifying and characterizing the candidate genes responsible for important phenotypic traits, and (iv) developing biotechnological methods to incorporate these traits into different citrus genotypes. It has been clarified that all the genetic diversity within the sweet orange species was derived from subsequent mutations starting from a single ancestor and was derived from complex cycles of hybridization and backcrossing between the mandarin (Citrus reticulata Blanco) and the pummelo (Citrus maxima (Burm.) Merr.). This paper provides an overview of the varietal panorama together with a description of the main driving forces in present and future sweet orange breeding. In fact, for the sweet orange, as well as for other citrus species, the release of novel varieties with improved characteristics is being pursued thanks to the employment of conventional and/or innovative (molecular-based) methods. The state of the art methods together with the innovations in genomics and biotechnological tools leading to the so-called new plant breeding technologies were also reviewed and discussed