Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time

Domestication drastically changed crop genomes,fixing alleles of interest and creating different genetic populations.Genome-wide association studies(GWASs)are a powerful tool to detect these alleles of interest(and so QTLs).In this study,we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond accessions.Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups,all formed by accessions with a common origin.One of these groups was formed exclusively by Spanish accessions,while the rest were mainly formed by accessions from China,Italy,France,and the USA.These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases:Asiatic,Mediterranean,Californian,and southern hemisphere.In total,we found 13 independent QTLs for nut weight,crack-out percentage,double kernels percentage,and blooming time.Of the 13 QTLs found,only one had an additive effect.Through candidate gene analysis,we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage,Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage,and Prudul26A000954 as a candidate gene for the QTL found in blooming time.Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.

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.

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.

Genetic dissection of climacteric fruit ripening in a melon population segregating for ripening behavior

Melon is as an alternative model to understand fruit ripening due to the coexistence of climacteric and non-climacteric varieties within the same species,allowing the study of the processes that regulate this complex trait with genetic approaches.We phenotyped a population of recombinant inbred lines(RILs),obtained by crossing a climacteric(Védrantais,cantalupensis type)and a non-climcteric variety(Piel de Sapo T111,inodorus type),for traits related to climacteric maturation and ethylene production.Individuals in the RIL population exhibited various combinations of phenotypes that differed in the amount of ethylene produced,the early onset of ethylene production,and other phenotypes associated with ripening.We characterized a major QTL on chromosome 8,ETHQV8.1,which is sufficient to activate climacteric ripening,and other minor QTLs that may modulate the climacteric response.The ETHQV8.1 allele was validated by using two reciprocal introgression line populations generated by crossing Védrantais and Piel de Sapo and analyzing the ETHQV8.1 region in each of the genetic backgrounds.A Genome-wide association study(GWAS)using 211 accessions of the ssp.melo further identified two regions on chromosome 8 associated with the production of aromas,one of these regions overlapping with the 154.1 kb interval containing ETHQV8.1.The ETHQV8.1 region contains several candidate genes that may be related to fruit ripening.This work sheds light into the regulation mechanisms of a complex trait such as fruit ripening.

Fine mapping and identification of candidate genes for the peach powdery mildew resistance gene Vr3

Powdery mildew is one of the major diseases of peach(Prunus persica),caused by the ascomycete Podosphaera pannosa.Currently,it is controlled through calendar-based fungicide treatments starting at petal fall,but an alternative is to develop resistant peach varieties.Previous studies mapped a resistance gene(Vr3)in interspecific populations between almond(‘Texas’)and peach(‘Earlygold’).To obtain molecular markers highly linked to Vr3 and to reduce the number of candidate genes,we fine-mapped Vr3 to a genomic region of 270 kb with 27 annotated genes.To find evidence supporting one of these positional candidate genes as being responsible of Vr3,we analyzed the polymorphisms of the resequences of both parents and used near-isogenic lines(NILs)for expression analysis of the positional candidate genes in symptomatic or asymptomatic leaves.Genes differentially expressed between resistant and susceptible individuals were annotated as a Disease Resistance Protein RGA2(Prupe2G111700)or an Eceriferum 1 protein involved in epicuticular wax biosynthesis(Prupe2G112800).Only Prupe2G111700 contained a variant predicted to have a disruptive effect on the encoded protein,and was overexpressed in both heterozygous and homozygous individuals containing the Vr3 almond allele,compared with susceptible individuals.This information was also useful to identify and validate molecular markers tightly linked and flanking Vr3.In addition,the NILs used in this work will facilitate the introgression of this gene into peach elite materials,alone or pyramided with other known resistance genes such as peach powdery mildew resistance gene Vr2.

Selection footprints reflect genomic changes associated with breeding efforts in 56 cucumber inbred lines

Cucumber selective breeding over recent decades has dramatically increased productivity and quality,but the genomic characterizations and changes associated with this breeding history remain unclear.Here,we analyzed the genome resequencing data of 56 artificially selected cucumber inbred lines that exhibit various phenotypes to detect trait-associated sequence variations that reflect breeding improvement.We found that the 56 cucumber lines could be assigned to group 1 and group 2,and the two groups formed a distinctive genetic structure due to the breeding history involving hybridization and selection.Differentially selected regions were identified between group 1 and group 2,with implications for genomic-selection breeding signatures.These regions included known quantitative trait loci or genes that were reported to be associated with agronomic traits.Our results advance knowledge of cucumber genomics,and the 56 selected inbred lines could be good germplasm resources for breeding.

The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon

Melon(Cucumis melo L.)is an important vegetable crop that has an extensive history of cultivation.However,the genome of wild and semi-wild melon types that can be used for the analysis of agronomic traits is not yet available.Here we report a chromosome-level T2T genome assembly for 821(C.melo ssp.agrestis var.acidulus),a semi-wild melon with two haplotypes of∼373 Mb and∼364 Mb,respectively.Comparative genome analysis discovered a significant number of structural variants(SVs)between melo(C.melo ssp.melo)and agrestis(C.melo ssp.agrestis)genomes,including a copy number variation located in the ToLCNDV resistance locus on chromosome 11.Genome-wide association studies detected a significant signal associated with climacteric ripening and identified one candidate gene CM_ac12g14720.1(CmABA2),encoding a cytoplasmic short chain dehydrogenase/reductase,which controls the biosynthesis of abscisic acid.This study provides valuable genetic resources for future research on melon breeding.

Attention sports fans! The far-reaching contributions of bud sport mutants to horticulture and plant biology

A bud sport is a lateral shoot,inflorescence or single flower/fruit with a visibly different phenotype from the rest of the plant.The new phenotype is often caused by a stable somatic mutation in a single cell that is passed on to its clonal descendants and eventually populates part or all of a meristem.In many cases,a bud sport can be vegetatively propagated,thereby preserving the novel phenotype without sexual reproduction.Bud sports provide new characteristics while retaining the desirable qualities of the parent plant,which is why many bud sports have been developed into popular cultivars.We present an overview of the history of bud sports,the causes and methods of detecting somaclonal variation,and the types of mutant phenotypes that have arisen spontaneously.We focus on examples where the molecular or cytological changes causing the phenotype have been identified.Analysis of these sports has provided valuable insight into developmental processes,gene function and regulation,and in some cases has revealed new information about layer-specific roles of some genes.Examination of the molecular changes causing a phenotype and in some cases reversion back to the original state has contributed to our understanding of the mechanisms that drive genomic evolution.

Plant buffering against the high-light stress- induced accumulation of CsGA2ox8 transcripts via alter native splici ng to fi n ely tune gibberelli n levels and maintain hypocotyl elongation

In plants,alternative splicing(AS)is markedly induced in response to environmental stresses,but it is unclear why plants generate multiple transcripts under stress conditions.In this study,RNA-seq was performed to identify AS events in cucumber seedlings grown under different light intensities.We identi fi ed a novel transcript of the gibberellin(GA)-deactivating enzyme Gibberellin 2-beta-dioxygenase 8(CsGA2ox8).Compared with canonical CsGA2ox8.1,the CsGA2ox8.2 isoform presented intron retention between the second and third exons.Functional analysis proved that the transcript of CsGA2ox8.1 but not CsGA2ox8.2 played a role in the deactivation of bioactive GAs.Moreover,expression analysis demonstrated that both transcripts were upregulated by increased light intensity,but the expression level of CsGA2ox8.1 increased slowly when the light intensity was>400μmol-m-2-s-1 PPFD(photosynthetic photon fl ux density),while the CsGA2ox8.2 transcript levels increased rapidly when the light intensity was>200 pmol-m-2-s-1 PPFD.Our fi ndings provide evidence that plants might fi nely tune their GA levels by buffering against the normal transcripts of CsGA2ox8 through AS.

Genomic patterns of homozygosity and inbreeding depression in MurcianoGranadina goats

Background:Inbreeding depression can adversely affect traits related to fitness,reproduction and productive performance.Although current research suggests that inbreeding levels are generally low in most goat breeds,the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data.Results:We genotyped 1040 goats with the Goat SNP50 BeadChip.This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns.We detected38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1,2,4,6,14,16 and 17.Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes.Four regions on chromosomes 8 and 25were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count.Notably,these regions contain several genes related with immunity,such as SYK,IL27,CCL19 and CCL21.Moreover,one region on chromosome 2 was significantly associated with inbreeding depression for milk yield.Conclusions:Although genomic inbreeding levels are low in Murciano-Granadina goats,significant evidence of inbreeding depression for the logarithm of the somatic cell count,a phenotype closely associated with udder health and milk yield,have been detected in this population.Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis,which is one of the main causes of dairy goat culling.

A comprehensive study of the proteins involved in salinity stress response in roots and shoots of the FL478 genotype of rice(Oryza sativa L. ssp. indica)

Rice,a major staple,is the most salt-sensitive cereal.High salinity triggers several adaptive responses in rice to cope with osmotic and ionic stress at the physiological,cellular,and molecular levels.A major QTL for salinity tolerance,named Saltol,is present on chromosome 1 of Indian landraces such as Pokkali and Nona Bokra.The early proteomic and physiological responses to salinity in roots and shoots of FL478,an inbred rice line harboring the Saltol QTL,were characterized.Plantlets were cultured in hydroponic cultures with 100 mmol L^(-1) Na Cl and evaluated at 6,24,and 48 h.At the physiological level,root length significantly increased at 48 h,whereas shoot length was reduced.The Na^(+)/K^(+) ratio was maintained at lower levels in shoots than in roots,suggesting that roots play a protective role.More than 2000 proteins were detected in both tissues.Roots showed a faster and more coordinated proteomic response than shoots,evident after only 6 h of treatment.These responses showed clear correspondence with those of proteins involved in transcription and translation.Maintenance of mitochondrial activity and amino acid metabolism in roots,and activation of stress-responsive proteins such as dehydrins and PLAT in shoots,may play a key role during the response of the plant to salinity stress.Proteomic and physiological responses showed that roots respond in a more highly adaptive manner than shoots to salinity stress,suggesting that this tissue is critical to the tolerance observed in cultivars harboring Saltol.

Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats

Background:In this study,we aimed to investigate the molecular basis of lactation as well as to identify the genetic factors that influence milk yield and composition in goats.To achieve these two goals,we have analyzed how the mRNA profile of the mammary gland changes in seven Murciano-Granadina goats at each of three different time points,i.e.78 d(T1,early lactation),216 d(T2,late lactation)and 285 d(T3,dry period)after parturition.Moreover,we have performed a genome-wide association study(GWAS)for seven dairy traits recorded in the 1st lactation of 822 Murciano-Granadina goats.Results:The expression profiles of the mammary gland in the early(T1)and late(T2)lactation were quite similar(42 differentially expressed genes),while strong transcriptomic differences(more than one thousand differentially expressed genes)were observed between the lactating(T1/T2)and non-lactating(T3)mammary glands.A large number of differentially expressed genes were involved in pathways related with the biosynthesis of amino acids,cholesterol,triglycerides and steroids as well as with glycerophospholipid metabolism,adipocytokine signaling,lipid binding,regulation of ion transmembrane transport,calcium ion binding,metalloendopeptidase activity and complement and coagulation cascades.With regard to the second goal of the study,the performance of the GWAS allowed us to detect 24 quantitative trait loci(QTLs),including three genome-wide significant associations:QTL1(chromosome 2,130.72-131.01 Mb)for lactose percentage,QTL6(chromosome 6,78.90-93.48 Mb)for protein percentage and QTL17(chromosome 17,11.20 Mb)for both protein and dry matter percentages.Interestingly,QTL6 shows positional coincidence with the casein genes,which encode 80%of milk proteins.Conclusions:The abrogation of lactation involves dramatic changes in the expression of genes participating in a broad array of physiological processes such as protein,lipid and carbohydrate metabolism,calcium homeostasis,cell death and tissue remodeling,as well as immunity.We also conclude that genetic variation at the casein genes has a major impact on the milk protein content of Murciano-Granadina goats.

Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply

Background:The role of non-coding RNAs in the porcine muscle metabolism is poorly understood,with few studies investigating their expression patterns in response to nutrient supply.Therefore,we aimed to investigate the changes in microRNAs(miRNAs),long intergenic non-coding RNAs(lincRNAs)and mRNAs muscle expression before and after food intake.Results:We measured the miRNA,lincRNA and mRNA expression levels in the gluteus medius muscle of 12 gilts in a fasting condition(AL-T0)and 24 gilts fed ad libitum during either 5 h.(AL-T1,N=12)or 7 h.(AL-T2,N=12)prior to slaughter.The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced,whereas lincRNA and mRNA expression data were already available.In terms of mean and variance,the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs.Food intake induced the differential expression of 149(AL-T0/AL-T1)and 435(AL-T0/AL-T2)mRNAs,6(AL-T0/AL-T1)and 28(AL-T0/AL-T2)miRNAs and none lincRNAs,while the number of differentially dispersed genes was much lower.Among the set of differentially expressed miRNAs,we identified ssc-miR-148a-3p,ssc-miR-22-3p and ssc-miR-1,which play key roles in the regulation of glucose and lipid metabolism.Besides,co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding.One case example was represented by seven miRNAs(ssc-miR-148a-3p,ssc-miR-151-3p,ssc-miR-30a-3p,ssc-miR-30e-3p,ssc-miR-421-5p,ssc-miR-493-5p and ssc-miR-503)which putatively interact with the PDK4 mRNA,one of the master regulators of glucose utilization and fatty acid oxidation.Conclusions:As a whole,our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability.

Clp Protease and OR Directly Control the Proteostasis of Phytoene Synthase, the Crucial Enzyme for Carotenoid Biosynthesis in Arabidopsis

Phytoene synthase （PSY） is the crucial plastidial enzyme in the carotenoid biosynthetic pathway. However, its post-translational regulation remains elusive. Likewise, Clp protease constitutes a central part of the plastid protease network, but its substrates for degradation are not well known. In this study, we report that PSY is a substrate of the Clp protease. PSY was uncovered to physically interact with various Clp protease subunits （i.e., ClpS1, CIpC1, and CIpD）. High levels of PSY and several other carotenogenic enzyme proteins overac- cumulate in the clpcl, clpp4, and clprl-2 mutants. The overaccumulated PSY was found to be partially enzy- matically active. Impairment of Clp activity in clpcl results in a reduced rate of PSY protein turnover, further supporting the role of Clp protease in degrading PSY protein. On the other hand, the ORANGE （OR） protein, a major post-translational regulator of PSY with holdase chaperone activity, enhances PSY protein stability and increases the enzymatically active proportion of PSY in clpcl, counterbalancing CIp-mediated proteol- ysis in maintaining PSY protein homeostasis. Collectively, these findings provide novel insights into the qual- ity control of plastid-localized proteins and establish a hitherto unidentified post-translational regulatory mechanism of carotenogenic enzymes in modulating carotenoid biosynthesis in plants.

Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes

Deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWRI-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo- lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and repro- ductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses tran- scription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWRI-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.

PLEIOTROPIC REGULATORY LOCUS 1 （PRL1） Integrates the Regulation of Sugar Responses with Isoprenoid Metabolism in Arabidopsis

The biosynthesis of isoprenoids in plant cells occurs from precursors produced in the cytosol by the mevalonate （MVA） pathway and in the plastid by the methylerythritol 4-phosphate （MEP） pathway, but little is known about the mechanisms coordinating both pathways. Evidence of the importance of sugar signaling for such coordination in Arabi- dopsis thaliana is provided here by the characterization of a mutant showing an increased accumulation of MEP-derived isoprenoid products （chlorophylls and carotenoids） without changes in the levels of relevant MEP pathway transcripts, proteins, or enzyme activities. This mutant was found to be a new loss-of-function allele of PRL1 （Pleiotropic Regulatory Locus 1）, a gene encoding a conserved WD-protein that functions as a global regulator of sugar, stress, and hormone responses, in part by inhibition of SNFl-related protein kinases （SnRK1）. Consistent with the reported role of SnRK1 kinases in the phosphorylation and inactivation of the main regulatory enzyme of the MVA pathway （hydroxymethylglutaryl coenzyme-A reductase）, its activity but not transcript or protein levels was reduced in prll seedlings. However, the accumulation of MVA-derived end products （sterols） was unaltered in mutant seedlings. Sucrose supplementation to wild- type seedlings phenocopied the prll mutation in terms of isoprenoid metabolism, suggesting that the observed isoprenoid phenotypes result from the increased sugar accumulation in the prll mutant. In summary, PRL1 appears to coordinate isoprenoid metabolism with sugar, hormone, and stress responses.

New Insights into Plant Isoprenoid Metabolism

Isoprenoids are a hugely diverse family of compounds derived from the C5 precursors isopentenyl diphosphate （IPP） and dimethylallyl diphosphate （DMAPP）. Although all free-living organisms synthesize isoprenoids, they are particularly abun- dant and diverse in plants, with tens of thousands structures known to date. The highest variety of plant isoprenoids are specialized （secondary） metabolites that participate in the interaction of plants with their environment. These include pigments, volatiles, and defense compounds, some of which have applications in industry and agriculture.

Robust transcriptional indicators of immune cell death revealed by spatiotemporal transcriptome analyses

Recognition of a pathogen by the plant immune system often triggers a form of regulated cell death traditionally known as the hypersensitive response(HR).This type of cell death occurs precisely at the site of pathogen recognition,and it is restricted to a few cells.Extensive research has shed light on how plant immune receptors are mechanistically activated.However,two central key questions remain largely unresolved:how does cell death zonation take place,and what are the mechanisms that underpin this phenomenon?Consequently,bona fide transcriptional indicators of HR are lacking,which prevents deeper insight into its mechanisms before cell death becomes macroscopic and precludes early or live observation.In this study,to identify the transcriptional indicators of HR we used the paradigmatic Arabidopsis thaliana–Pseudomonas syringae pathosystem and performed a spatiotemporally resolved gene expression analysis that compared infected cells that will undergo HR upon pathogen recognition with bystander cells that will stay alive and activate immunity.Our data revealed unique and time-dependent differences in the repertoire of differentially expressed genes,expression profiles,and biological processes derived from tissue undergoing HR and that of its surroundings.Furthermore,we generated a pipeline based on concatenated pairwise comparisons between time,zone,and treatment that enabled us to define 13 robust transcriptional HR markers.Among these genes,the promoter of an uncharacterized AAA-ATPase was used to obtain a fluorescent reporter transgenic line that displays a strong spatiotemporally resolved signal specifically in cells that will later undergo pathogen-triggered cell death.This valuable set of genes can be used to define cells that are destined to die upon infection with HR-triggering bacteria,opening new avenues for specific and/or high-throughput techniques to study HR processes at a single-cell level.

Corrigendum to “Automatic Fruit Morphology Phenome and Genetic Analysis: An Application in the Octoploid Strawberry”

In the article titled“Automatic Fruit Morphology Phenome and Genetic Analysis:An Application in the Octoploid Strawberry”[1],some funding information was omitted.The funding DOI“10.13039/501100011033”was missing.The corrected Acknowledgements section is provided below.

Automatic Fruit Morphology Phenome and Genetic Analysis:An Application in the Octoploid Strawberry

Automatizing phenotype measurement will decisively contribute to increase plant breeding efficiency.Among phenotypes,morphological traits are relevant in many fruit breeding programs,as appearance influences consumer preference.Often,these traits are manually or semiautomatically obtained.Yet,fruit morphology evaluation can be enhanced using fully automatized procedures and digital images provide a cost-effective opportunity for this purpose.Here,we present an automatized pipeline for comprehensive phenomic and genetic analysis of morphology traits extracted from internal and external strawberry(Fragaria x ananassa)images.The pipeline segments,classifies,and labels the images and extracts conformation features,including linear(area,perimeter,height,width,circularity,shape descriptor,ratio between height and width)and multivariate(Fourier elliptical components and Generalized Procrustes)statistics.Internal color patterns are obtained using an autoencoder to smooth out the image.In addition,we develop a variational autoencoder to automatically detect the most likely number of underlying shapes.Bayesian modeling is employed to estimate both additive and dominance effects for all traits.As expected,conformational traits are clearly heritable.Interestingly,dominance variance is higher than the additive component for most of the traits.Overall,we show that fruit shape and color can be quickly and automatically evaluated and are moderately heritable.Although we study strawberry images,the algorithm can be applied to other fruits,as shown in the GitHub repository.