Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple

Texture is a complex trait and a major component of fruit quality in apple.While the major effect of MdPG1,a gene controlling firmness,has already been exploited in elite cultivars,the genetic basis of crispness remains poorly understood.To further improve fruit texture,harnessing loci with minor effects via genomic selection is therefore necessary.In this study,we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture.Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers.The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance(0.64).Predictions for biparental families using the entire training set varied from low to high accuracy,depending on the family considered.While adding siblings or half-siblings into the training set did not clearly improve predictions,we performed an optimization of the training set size and composition for each validation set.This allowed us to increase prediction accuracies by 0.17 on average,with a maximal accuracy of 0.81 when predicting firmness in the‘Gala’בPink Lady’family.Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple.In particular,we advise to rely on a large training population,with high phenotypic variability from which a‘tailored training population’can be extracted using a priori information on genetic relatedness,in order to predict a specific target population.

Apple whole genome sequences:recent advances and new prospects

In 2010,a major scientific milestone was achieved for tree fruit crops:publication of the first draft whole genome sequence(WGS)for apple(Malus domestica).This WGS,v1.0,was valuable as the initial reference for sequence information,fine mapping,gene discovery,variant discovery,and tool development.A new,high quality apple WGS,GDDH13 v1.1,was released in 2017 and now serves as the reference genome for apple.Over the past decade,these apple WGSs have had an enormous impact on our understanding of apple biological functioning,trait physiology and inheritance,leading to practical applications for improving this highly valued crop.Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly.Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees.High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders.We understand the species,geographical,and genomic origins of domesticated apple more precisely,as well as its relationship to wild relatives.The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable,environmentally sound,productive,and consumer-desirable apple production.This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs.Recommendations for“what’s next”focus on necessary upgrades to the genome sequence data pool,as well as for use of the data,to reach new frontiers in genomics-based scientific understanding of apple.

Wide transcriptional investigation unravel novel insights of the on-tree maturation and postharvest ripening of‘Abate Fetel’pear fruit

To decipher the transcriptomic regulation of the on-tree fruit maturation in pear cv.‘Abate Fetel’,a RNA-seq transcription analysis identified 8939 genes differentially expressed across four harvesting stages.These genes were grouped into 11 SOTA clusters based on their transcriptional pattern,of which three included genes upregulated while the other four were represented by downregulated genes.Fruit ripening was furthermore investigated after 1 month of postharvest cold storage.The most important variation in fruit firmness,production of ethylene and volatile organic compounds were observed after 5 days of shelf-life at room temperature following cold storage.The role of ethylene in controlling the ripening of‘Abate Fetel’pears was furthermore investigated through the application of 1-methylcyclopropene,which efficiently delayed the progression of ripening by reducing fruit softening and repressing both ethylene and volatile production.The physiological response of the interference at the ethylene receptor level was moreover unraveled investigating the expression pattern of 12 candidate genes,initially selected to validate the RNA-seq profile.This analysis confirmed the effective role of the ethylene competitor in downregulating the expression of cell wall(PG)and ethylene-related genes(ACS,ACO,ERS1,and ERS2),as well as inducing one element involved in the auxin signaling pathway(Aux/IAA),highlighting a possible cross-talk between these two hormones.The expression patterns of these six elements suggest their use as molecular toolkit to monitor at molecular level the progression of the fruit on-tree maturation and postharvest ripening.

Investigation of the transcriptomic and metabolic changes associated with superficial scald physiology impaired by lovastatin and 1-methylcyclopropene in pear fruit(cv.“Blanquilla”)

To elucidate the physiology underlying the development of superficial scald in pears,susceptible“Blanquilla”fruit was treated with different compounds that either promoted(ethylene)or repressed(1-methylcyclopropene and lovastatin)the incidence of this disorder after 4 months of cold storage.Our data show that scald was negligible for the fruit treated with 1-methylcyclopropene or lovastatin,but highly manifested in untreated(78%incidence)or ethylenetreated fruit(97%incidence).The comparison between the fruit metabolomic profile and transcriptome evidenced a distinct reprogramming associated with each treatment.In all treated samples,cold storage led to an activation of a cold-acclimation-resistance mechanism,including the biosynthesis of very-long-chain fatty acids,which was especially evident in 1-methylcyclopropane-treated fruit.Among the treatments applied,only 1-methylcyclopropene inhibited ethylene production,hence supporting the involvement of this hormone in the development of scald.However,a common repression effect on the PPO gene combined with higher sorbitol content was found for both lovastatin and 1-methylcyclopropene-treated samples,suggesting also a non-ethylene-mediated process preventing the development of this disorder.The results presented in this work represent a step forward to better understand the physiological mechanisms governing the etiology of superficial scald in pears.

Electrical storm in systemic sclerosis: Inside the electroanatomic substrate

We report the case of a 63-year-old woman affected by a severe form of systemic scleroderma with pul-monary involvement(interstitial fibrosis diagnosed by biopsy and moderate pulmonary hypertension) and cardiac involvement(paroxysmal atrial fibrillation, right atrial flutter treated by catheter ablation, ventricular tachyarrhythmias, previous dual chamber implantable cardioverter defibrillator implant). Because of recurrent electrical storms refractory to iv antiarrhythmic drugs the patient was referred to our institution to undergo catheter ablation. During electrophysiological proce-dure a 3D shell of cardiac anatomy was created with intracardiac echocardiography pointing out a significant right ventricular dilatation with a complex aneurysmal lesion characterized by thin walls and irregular multiple trabeculae. A substrate-guided strategy of catheter ab-lation was accomplished leading to a complete electri-cal isolation of the aneurism and to the abolishment of all abnormal electrical activities. The use of advanced strategies of imaging together with electroanatomical mapping added important information to the complex arrhythmogenic substrate and improved efficacy and safety.

Ethylene-auxin crosstalk regulates postharvest fruit ripening process in apple

The ripening of climacteric fruits,such as apple,is represented by a series of genetically programmed events orchestrated by the action of several hormones.In this study,we investigated the existence of a hormonal crosstalk between ethylene and auxin during the post-harvest ripening of three internationally known apple cultivars:‘Golden Delicious',‘Granny Smith'and‘Fuji'.The normal climacteric ripening was impaired by the exogenous application of 1-methylcyclopropene(1-MCP)that affected the production of ethylene and the physiological behaviour of specific ethylene-related quality traits,such as fruit texture and the production of volatile organic compounds.The application of 1-MCP induced,moreover,a de-novo accumulation of auxin.The RNA-Seq wide-transcriptome analysis evidenced as the competition at the level of the ethylene receptors induced a cultivar-dependent transcriptional re-programming.The DEGs annotation carried out through the KEGG database identified as most genes were assigned to the plant hormone signaling transduction category,and specifically related to auxin and ethylene.The interplay between these two hormones was further assessed through a candidate gene analysis that highlighted a specific activation of GH3 and ILL genes,encoding key steps in the process of the auxin homeostasis mechanism.Our results showed that a compromised ethylene metabolism at the onset of the climacteric ripening in apple can stimulate,in a cultivar-dependent fashion,an initial de-novo synthesis and de-conjugation of auxin as a tentative to restore a normal ripening progression.