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.

Treatment of Retained Fetal Membranes: Comparison of the Postpartum Period after Routine Treatment or Routine Treatment Including an Additional Phytotherapeutic Substance in Dairy Cattle in Switzerland

Background: The therapy of retained fetal membranes (RFM) is a controversial subject. In Switzerland, intrauterine antibiotics are routinely administered although their effect on fertility parameters is questionable. The objective of this study was to compare the post-partal period after a routine treatment of RFM in 2 groups: one group received a placebo additionally (A), whereas the other group received a phytotherapeutic substance (lime bark) (B) additionally. The routine treatment of RFM included an attempt to manually remove the fetal membranes (for a maximum of 5 min), intramuscular administration of oxytetracycline and intrauterine treatment with tetracycline. In case of an elevated rectal temperature (>39.0°C), an additional non-steroidal inflam-matory drug was allowed. Methods: Cows undergoing caesarean section, suffering from prolapse of the uterus, deep cervical or vaginal injuries, hypocalcaemia, and illnesses during the last 14 days before calving were excluded. Cows had to be more than 265 days pregnant. Only cows that were artificially inseminated after RFM were included. Group stratification was done according to the last number on the ear tag (even/uneven) with (n = 50) cows in group A and (n = 55) cows in group B. Results: The number of treatments after the initial treatment of RFM was not significantly different between groups. The median interval from calving to the first insemination was 77 days in group A compared to 82 days in group B (p = 0.72). The number of AI’s until conception was not significantly different between groups. The median number of days open was 89 days in group A compared to 96 days in group B (p = 0.57). The culling rate was not significantly different between groups. Conclusion: There was neither a difference between the groups concerning therapies within the first 50 days after RFM nor concerning the subsequent fertility variables.

Climate Change Favors Grapevine Production in Temperate Zones

Wine production has a long-standing history in Palatinate (Southwestern Germany), dating back to Roman times. Especially “Riesling”, but also several “Pinot” varieties gained major significance. Red wine varieties gained prominence over the last 20 years only, which may be a consequence of climate change. Our objective was to review temperature and rainfall data over the last 40 years, measured “on-winery” in Hainfeld and correlate these data with grapevine growth parameters: the development of bud break, flowering, veraison and harvest dates, yields and grape sugar concentrations of “Pinot Gris”, “Pinot Noir”, “Riesling”, “Silvaner” and “Müller-Thurgau”. Since the 1970s, bud break, flowering and veraison are 11 - 15, 18 - 22 and 16 - 22 days earlier;harvest dates are 25 - 40 days earlier. Sugar concentrations increased significantly, but yields decreased. Annual rainfall has not significantly risen, while the mean annual minimum and maximum air-temperatures rose by ~0.9°C, and by ~3.4°C, respectively, resulting in an average increase of the mean annual temperature of ~2.1°C. Remarkably, both mean monthly minimum and maximum temperatures rose especially in springtime, which should have been the driver for earlier bud break and flowering. A change in the climatic conditions, therefore, appears to be one of the key reasons for more favorable grapevine production in Palatinate, especially for “Pinot Noir”, which showed the highest increase in sugar concentrations. The Huglin-index, a measure for the suitability of growing specific grapevine varieties in given environments, increased from 1685 to 2063. According to this index, the climate change may be favorable already for growing grape varieties so far rarely grown in temperate zones, such as “Cabernet Sauvignon”, “Syrah” and “Tempranillo” that are more suited to warmer, Mediterranean climates.

An integrated approach for increasing breeding efficiency in apple and peach in Europe

Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and breeding.To bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private companies.Three complementary approaches were pursued:(i)tool and software development,(ii)deciphering genetic control of main horticultural traits taking into account allelic diversity and(iii)developing plant materials,tools and methodologies for breeders.Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding,development of new,dense SNP arrays in apple and peach,new phenotypic methods for some complex traits,software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis(PBA).This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies(GWAS)on several European genebank collections.FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities.Through FruitBreedomics,significant progresses were made in the field of apple and peach breeding,genetics,genomics and bioinformatics of which advantage will be made by breeders,germplasm curators and scientists.A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public.This review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond.

The apple REFPOP—a reference population for genomics-assisted breeding in apple

Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates.Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs,and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions.Here we present an apple reference population:the apple REFPOP,a large collection formed of 534 genotypes planted in six European countries,as a unique tool to accelerate apple breeding.The population consisted of 269 accessions and 265 progeny from 27 parental combinations,representing the diversity in cultivated apple and current European breeding material,respectively.A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95.Based on the genotypic data,linkage disequilibrium was low and population structure was weak.Two well-studied phenological traits of horticultural importance were measured.We found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date,respectively.With decreasing SNP density,the detection of significant marker–trait associations varied depending on trait architecture.Regardless of the trait,10,000 SNPs sufficed to maximize genomic prediction ability.We confirm the suitability of the apple REFPOP design for genomics-assisted breeding,especially for breeding programs using related germplasm,and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.

Quality aspects of coffees and teas: Application of electron paramagnetic resonance (EPR) spectroscopy to the elucidation of free radical and other processes.

Coffees and teas are beverages that are both exceptionally rich in antioxidant molecules, and are also both associated with beneficial health effects. Thus although the quality characteristics of these beverages are conventionally assessed on the basis of their sensory properties, their antioxidant contents represent an additional and increasingly valued attribute of quality based on their contributions to healthy diets. Both beverages are prepared by hot water extraction of a pure plant-derived product, and thus their compositions can potentially change quite rapidly as a result of oxidation in contact with air. Oxidative processes often proceed via free radical intermediates, and sometimes also result in the formation of stable radical end-products;thus EPR spectroscopy is a convenient technique for investigating some of the various free radical reactions that occur in these beverages. This paper reviews progress that has been made in elucidating free radical processes that occur during the preparation and storage of coffees and teas, and the results are discussed in terms of quality criteria of the beverages.

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.

What if esca disease of grapevine were not a fungal disease?

Esca disease,which attacks the wood of grapevine,has become increasingly devastating during the past three decades and represents today a major concern in all wine-producing countries.This disease is attributed to a group of systematically diverse fungi that are considered to be latent pathogens,however,this has not been conclusively established.This study presents the first in-depth comparison between the mycota of healthy and diseased plants taken from the same vineyard to determine which fungi become invasive when foliar symptoms of esca appear.An unprecedented high fungal diversity,158 species,is here reported exclusively from grapevine wood in a single Swiss vineyard plot.An identical mycota inhabits wood of healthy and diseased adult plants and presumed esca pathogens were widespread and occurred in similar frequencies in both plant types.Pioneer esca-associated fungi are not transmitted from adult to nursery plants through the grafting process.Consequently the presumed esca-associated fungal pathogens are most likely saprobes decaying already senescent or dead wood resulting from intensive pruning,frost or other mecanical injuries as grafting.The cause of esca disease therefore remains elusive and requires well executive scientific study.These results question the assumed pathogenicity of fungi in other diseases of plants or animals where identical mycota are retrieved from both diseased and healthy individuals.

A multilocus phylogeny for worldwide Cantharellus (Cantharellales, Agaricomycetidae)

After a short historical overview of past systematic studies on Cantharellus,discussing delimitation and species diversity of the genus as well as previous,morphology-based,infrageneric classifications,this paper presents the first molecularly-based infrageneric classification of this genus using a multigene phylogenetic approach(nucLSU,mitSSU,RPB2 and tef-1)on a dataset that covers approximately halve of the described chanterelles worldwide,including many type specimens.Six subgenera are recognized and the recognition of subgenus Afrocantharellus as a separate genus is not accepted.The taxonomic value of individual morphological features is discussed as challenged by this new multigene phylogeny which comprises five new sections,one new subgenus and many emendations for previously recognized infrageneric groups.The paper discusses the observed discrepancy in biodiversity of Cantharellus when comparing between studies that focus either on below-or above-ground presence.A preliminary biogeographic hypothesis suggests an‘out of Africa’Gondwanan origin as a result of vicariance and subsequent migrations.

Molecular evidence for novel Cantharellus (Cantharellales, Basidiomycota) from tropical African miombo woodland and a key to all tropical African chanterelles

The authors present a combined morphological and molecular approach of the genus Cantharellus in Africa.Morphological descriptions and detailed illustrations are provided for five new species from the Zambezian savannah woodlands in tropical Africa:C.afrocibarius,C.gracilis,C.humidicolus,C.miomboensis and C.tanzanicus.A maximum likelihood analysis of tef-1 sequences obtained for 83 collections of Cantharellus that are representative of all major groups in world wide Cantharellus,places a total of 13 African chanterelles,including the five newly described taxa.The recognition of a separate genus Afrocantharellus is rejected.An identification key based on the re-examination of all existing type material is provided for all presently known African Cantharellus.

Sequence data reveal a high diversity of Cantharellus associated with endemic vegetation in Madagascar

This revision of Cantharellus in Madagascar deals with species that are associated with strictly endemic host trees and shrubs.Based on morphological differences and molecular sequence data of the tef-1 gene,five new species are proposed(C.albidolutescens,C.ambohitantelyensis,C.ibityensis,C.paucifurcatus and C.sebosus),as well as one new subspecies,C.subincarnatus ssp.rubrosalmoneus,whereas C.decolorans and C.platyphyllus ssp.bojeriensis are epitypified.A key is provided to all Cantharellus that grow with native vegetation in Madagascar.