Stone fruit phenolic and triterpenoid compounds modulate gene expression of Monilinia spp. in culture media.

Phenolic and triterpenoid compounds are essential components in stone fruit skin and flesh tissues. They are thought to possess general antimicrobial activity. However, regarding brown rot disease, investigations were only confined to a limited number of phenolics, especially chlorogenic acid. The activity of triterpenoids against Monilinia spp., as an essential part of the peach cuticular wax, has not been studied before. In this work, the anti-fungal effect of some phenolics, triterpenoids, and fruit surface compound (FSC) extracts of peach fruit at two developmental stages were investigated on Monilinia fructicola and Monilinia laxa characteristics during in vitro growth. A new procedure for assaying anti-fungal activity of triterpenoids, which are notoriously difficult to assess in vitro because of their hydrophobicity, has been developed. Measurements of colony diameter, sporulation, and germination of second-generation conidia were recorded. Furthermore, the expression of twelve genes of M. fructicola associated with germination and/or appressorium formation and virulence-related genes was studied relative to the presence of the compounds. The study revealed that certain phenolics and triterpenoids showed modest anti-fungal activity while dramatically modulating gene expression in mycelium of M. fructicola on culture medium. MfRGAE1 gene was overexpressed by chlorogenic and ferulic acids and MfCUT1 by betulinic acid, at 4- and 7- days of mycelium incubation. The stage II FSC extract, corresponding to the period when the fruit is resistant to Monilinia spp., considerably up-regulated the MfLAE1 gene. These findings effectively contribute to the knowledge of biochemical compounds effects on fungi on in vitro conditions.

Genetic dissection of fruit maturity date in apricot (P. armeniaca L.) through a Single Primer Enrichment Technology (SPET) approach.

BACKGROUND: Single primer enrichment technology (SPET) is an emerging and increasingly popular solution for high-throughput targeted genotyping in plants. Although SPET requires a priori identification of polymorphisms for probe design, this technology has potentially higher reproducibility and transferability compared to other reduced representation sequencing (RRS) approaches, also enabling the discovery of closely linked polymorphisms surrounding the target one. RESULTS: The potential for SPET application in fruit trees was evaluated by developing a 25K target SNPs assay to genotype a panel of apricot accessions and progenies. A total of 32,492 polymorphic sites were genotyped in 128 accessions (including 8,188 accessory non-target SNPs) with extremely low levels of missing data and a significant correlation of allelic frequencies compared to whole-genome sequencing data used for array design. Assay performance was further validated by estimating genotyping errors in two biparental progenies, resulting in an overall 1.8% rate. SPET genotyping data were used to infer population structure and to dissect the architecture of fruit maturity date (MD), a quantitative reproductive phenological trait of great agronomical interest in apricot species. Depending on the year, GWAS revealed loci associated to MD on several chromosomes. The QTLs on chromosomes 1 and 4 (the latter explaining most of the phenotypic variability in the panel) were the most consistent over years and were further confirmed by linkage mapping in two segregating progenies. CONCLUSIONS: Besides the utility for marker assisted selection and for paving the way to in-depth studies to clarify the molecular bases of MD trait variation in apricot, the results provide an overview of the performance and reliability of SPET for fruit tree genetics.

Less is more: natural variation disrupting a miR172 gene at the di locus underlies the recessive double-flower trait in peach (P. persica L. Batsch).

BACKGROUND: With the domestication of ornamental plants, artificial selective pressure favored the propagation of mutations affecting flower shape, and double-flower varieties are now readily available for many species. In peach two distinct loci control the double-flower phenotype: the dominant Di2 locus, regulated by the deletion of the binding site for miR172 in the euAP2 PETALOSA gene Prupe.6G242400, and the recessive di locus, of which the underlying factor is still unknown. RESULTS: Based on its genomic location a candidate gene approach was used to identify genetic variants in a diverse panel of ornamental peach accessions and uncovered three independent mutations in Prupe.2G237700, the gene encoding the transcript for microRNA miR172d: a ~5.0 Kb LTR transposable element and a ~1.2 Kb insertion both positioned upstream of the sequence encoding the pre-miR172d within the transcribed region of Prupe.2G237700, and a ~9.5 Kb deletion encompassing the whole gene sequence. qRT-PCR analysis confirmed that expression of pre-miR172d was abolished in di/di genotypes homozygous for the three variants. CONCLUSIONS: Collectively, PETALOSA and the mutations in micro-RNA miR172d identified in this work provide a comprehensive collection of the genetic determinants at the base of the double-flower trait in the peach germplasms.

Quantitative Trait Loci Mapping and Identification of Candidate Genes Linked to Fruit Acidity in Apricot (Prunus armeniaca L.).

Apricot breeding programs could be strongly improved by the availability of molecular markers linked to the main fruit quality traits. Fruit acidity is one of the key factors in consumer acceptance, but despite its importance, the molecular bases of this trait are still poorly understood. In order to increase the genetic knowledge on the fruit acidity, an F1 apricot population ('Lito' × 'BO81604311') has been phenotyped for titratable acidity and juice pH for the three following years. In addition, the contents of the main organic acids of the juice (malate, citrate, and quinate) were also evaluated. A Gaussian distribution was observed for most of the traits in this progeny, confirming their quantitative inheritance. An available simple sequence repeat (SSR)-based molecular map, implemented with new markers in specific genomic regions, was used to perform a quantitative trait loci (QTL) analysis. The molecular map was also anchored to the recently published apricot genome sequence of 'Stella.' Several major QTLs linked to fruit acidity-related traits have been identified both in the 'Lito' (no. 21) and 'BO81604311' (no. 13), distributed in five linkage groups (LG 4, 5, 6, 7, and 8). Some of these QTLs show good stability between years and their linked markers were used to identify candidate genes in specific QTLs genomic regions.

Development of an HRMA-Based Marker Assisted Selection (MAS) Approach for Cost-Effective Genotyping of S and M Loci Controlling Self-Compatibility in Apricot (Prunus armeniaca L.).

The apricot species is characterized by a gametophytic self-incompatibility (GSI) system. While GSI is one of the most efficient mechanisms to prevent self-fertilization and increase genetic variability, it represents a limiting factor for fruit production in the orchards. Compatibility among apricot cultivars was usually assessed by either field pollination experiments or by histochemical evaluation of in vitro pollen tube growth. In apricots, self-compatibility is controlled by two unlinked loci, S and M, and associated to transposable element insertion within the coding sequence of SFB and ParM-7 genes, respectively. Self-compatibility has become a primary breeding goal in apricot breeding programmes, stimulating the development of a rapid and cost-effective marker assisted selection (MAS) approach to accelerate screening of self-compatible genotypes. In this work, we demonstrated the feasibility of a novel High Resolution Melting Analysis (HRMA) approach for the massive screening of self-compatible and self-incompatible genotypes for both S and M loci. The different genotypes were unambiguously recognized by HRMA, showing clearly distinguishable melting profiles. The assay was developed and tested in a panel of accessions and breeding selections with known self-compatibility reaction, demonstrating the potential usefulness of this approach to optimize and accelerate apricot breeding programmes.

Genetic and phenotypic analyses reveal major quantitative loci associated to fruit size and shape traits in a non-flat peach collection (P. persica L. Batsch).

Fruit size and shape are critical agronomical and pomological attributes and prime targets in peach breeding programs. Apart from the flat peach type, a Mendelian trait well-characterized at the genetic level, ample diversity of fruit size and shapes is present across peach germplasms. Nevertheless, knowledge of the underlying genomic loci remains limited. In this work, fruit size and shape were assessed in a collection of non-flat peach accessions and selections, under controlled fruit load conditions. The architecture of these traits was then dissected by combining association and linkage mapping, revealing a major locus on the proximal end of chromosome 6 (qSHL/Fs6.1) explaining a large proportion of phenotypic variability for longitudinal shape and also affecting fruit size. A second major locus for fruit longitudinal shape (qSHL5.1), probably also affecting fruit size, was found co-localizing at locus G, suggesting pleiotropic effects of peach/nectarine traits. An additional QTL for fruit longitudinal shape (qSHL6.2) was identified in the distal end of chromosome 6 in a cross with an ornamental double-flower peach and co-localized with the Di2 locus, controlling flower morphology. Besides assisting breeding activities, knowledge of loci controlling fruit size and shape paves the way for more in-depth studies aimed at the identification of underlying genetic variant(s).

The Di2/pet Variant in the PETALOSA Gene Underlies a Major Heat Requirement-Related QTL for Blooming Date in Peach [Prunus persica (L.) Batsch].

Environmental adaptation of deciduous fruit trees largely depends on their ability to synchronize growth and development with seasonal climate change. Winter dormancy of flower buds is a key process to prevent frost damage and ensure reproductive success. Temperature is a crucial environmental stimulus largely influencing the timing of flowering, only occurring after fulfillment of certain temperature requirements. Nevertheless, genetic variation affecting chilling or heat-dependent dormancy release still remains largely unknown. In this study, a major QTL able to delay blooming date in peach by increasing heat requirement was finely mapped in three segregating progenies, revealing a strict association with a genetic variant (petDEL) in a PETALOSA gene, previously shown to also affect flower morphology. Analysis of segregating genome-edited tobacco plants provided further evidence of the potential ability of PET variations to delay flowering time. Potential applications of the petDEL variant for improving phenological traits in peach are discussed.

The Multisite PeachRefPop Collection: A True Cultural Heritage and International Scientific Tool for Fruit Trees.

Plants have evolved a range of adaptive mechanisms that adjust their development and physiology to variable external conditions, particularly in perennial species subjected to long-term interplay with the environment. Exploiting the allelic diversity within available germplasm and leveraging the knowledge of the mechanisms regulating genotype interaction with the environment are crucial to address climatic challenges and assist the breeding of novel cultivars with improved resilience. The development of multisite collections is of utmost importance for the conservation and utilization of genetic materials and will greatly facilitate the dissection of genotype-by-environment interaction. Such resources are still lacking for perennial trees, especially with the intrinsic difficulties of successful propagation, material exchange, and living collection maintenance. This work describes the concept, design, and realization of the first multisite peach (Prunus persica) reference collection (PeachRefPop) located across different European countries and sharing the same experimental design. Other than an invaluable tool for scientific studies in perennial species, PeachRefPop provides a milestone in an international collaborative project for the conservation and exploitation of European peach germplasm resources and, ultimately, as a true heritage for future generations.

Mutations in orthologous PETALOSA TOE-type genes cause a dominant double-flower phenotype in phylogenetically distant eudicots.

The double-flower phenotype has been selected by humans for its attractiveness in various plant species and it is of great commercial value for the ornamental market. In this study we investigated the genetic determinant of the dominant double-flower trait in carnation, petunia, and Rosa rugosa, and identified mutant alleles of TARGET OF EAT (TOE)-type genes characterized by a disruption of the miR172 target sequence and of the C-terminal portion of the encoded protein. Despite the phylogenetic distance between these eudicots, which diverged in the early Cretaceous, the orthologous genes carrying these mutations all belong to a single TOE-type subgroup, which we name as PETALOSA (PET). Homology searches allowed us to identify PET sequences in various other species. To confirm the results from naturally occurring mutations, we used CrispR-Cas9 to induce lesions within the miR172 target site of Nicotiana tabacum PET genes, and this resulted in the development of supernumerary petaloid structures. This study describes pet alleles in economically important ornamental species and provides evidence about the possibility of identifying and engineering PET genes to obtain the desirable double-flower trait in different plants.

Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of 'Lito' Chromosome 1 and Analysis of Candidate Genes.

Sharka, a common disease among most stone fruit crops, is caused by the Plum Pox Virus (PPV). Resistant genotypes have been found in apricot (Prunus armeniaca L.), one of which-the cultivar 'Lito' heterozygous for the resistance-has been used to map a major quantitative trait locus (QTL) on linkage group 1, following a pseudo-test-cross mating design with 231 individuals. In addition, 19 SNP markers were selected from among the hundreds previously developed, which allowed the region to be limited to 236 kb on chromosome 1. A 'Lito' bacterial artificial chromosome (BAC) library was produced, screened with markers of the region, and positive BAC clones were sequenced. Resistant (R) and susceptible (S) haplotypes were assembled independently. To refine the assembly, the whole genome of 'Lito' was sequenced to high coverage (98×) using PacBio technology, enabling the development of a detailed assembly of the region that was able to predict and annotate the genes in the QTL region. The selected cultivar 'Lito' allowed not only to discriminate structural variants between the two haplotypic regions but also to distinguish specific allele expression, contributing towards mining the PPVres locus. In light of these findings, genes previously indicated (i.e., MATHd genes) to have a possible role in PPV resistance were further analyzed, and new candidates were discussed. Although the results are not conclusive, the accurate and independent assembly of R and S haplotypes of 'Lito' is a valuable resource to predict and test alternative transcription and regulation mechanisms underpinning PPV resistance.

High-density multi-population consensus genetic linkage map for peach.

Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars 'Zin Dai' and 'Crimson Lady' (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae.

Deletion of the miR172 target site in a TOE-type gene is a strong candidate variant for dominant double-flower trait in Rosaceae.

Double flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants, including Prunus persica (peach), a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double-flower phenotype in peach, we focused on the dominant Di2 locus. High-resolution linkage mapping in five segregating progenies delimited Di2 to an interval spanning 150 858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic resequencing data from single- and double-flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double-flower trait, and we showed transcript expression for both wild-type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical times for floral development. The indelDi2 molecular marker designed on this sequence variant co-segregated with the phenotype in 621 progenies, accounting for the dominant inheritance of the Di2 locus. Further corroborating the results in peach, we identified a distinct but similar mutation in the ortholog of Prupe.6G242400 in double-flower roses. Phylogenetic analysis showed that these two genes belong to a TARGET OF EAT (TOE)-type clade not represented in Arabidopsis, indicating a divergence of gene functions between AP2-type and TOE-type factors in Arabidopsis and other species. The identification of orthologous candidate genes for the double-flower phenotype in two important Rosaceae species provides valuable information to understand the genetic control of this trait in other major ornamental plants.

Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch).

BACKGROUND: Texture is one of the most important fruit quality attributes. In peach, stony hard (SH) is a recessive monogenic trait (hd/hd) that confers exceptionally prolonged firm flesh to fully ripe fruit. Previous studies have shown that the SH mutation affects the fruit ability to synthesize appropriate amounts of indol-3-acetic acid (IAA), which orchestrates the ripening processes through the activation of system 2 ethylene pathway. Allelic variation in a TC microsatellite located within the first intron of PpYUC11-like (a YUCCA-like auxin-biosynthesis gene) has been recently proposed as the causal mutation of the SH phenotype. RESULTS: The simple genetic determinism of the SH trait has been clarified through genome-wide association and LD analyses in a diverse set of accessions, restricting the hd locus to an interval of about 1.8 Mbp in chromosome 6. The comparison of fruit transcriptome data from non-SH (melting flesh) and SH accessions provided an expression patterns overview of the annotated transcripts within the hd locus, confirming the absence of PpYUC11-like expression in SH fruits. To explore further possible associations between genomic variants at the hd locus and the SH phenotype, re-sequencing data of the SH accession 'D41-62' were compared with several SH and non-SH accessions with different genetic backgrounds. A further step of validation was provided through the evaluation of variant-trait association in two bi-parental F2 populations issued from the SH accession 'D41-62' and a panel of advanced breeding selections, showing perfect co-segregation of the PpYUC11-like intron TC20 allele and the SH phenotype. CONCLUSIONS: In this study, we provide a multi-level validation of the genetic control of the SH trait through the integration of genome-wide association mapping, transcriptome analysis and whole-genome resequencing data for SH and non-SH accessions, and marker-trait association in a panel of advanced breeding selections and segregating progenies. Collectively, our data confirm with high confidence the role of allelic variation at PpYUC11-like locus as the genetic determinant of the SH trait, opening interesting perspectives at both biological and applied research level.

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.

PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data.

Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalog of genetic variants present in peach (Prunus persica L. Batsch) and wild-related species of Prunus genera, annotated from 146 samples publicly released on the Sequence Read Archive (SRA). We designed a user-friendly web-based interface of the database, providing search tools to retrieve single nucleotide polymorphism (SNP) and InDel variants, along with useful statistics and information. PeachVar-DB results are linked to the Genome Database for Rosaceae (GDR) and the Phytozome database to allow easy access to other external useful plant-oriented resources. In order to extend the genetic diversity covered by the PeachVar-DB further, and to allow increasingly powerful comparative analysis, we will progressively integrate newly released data.

Identification of a melting type variant among peach (P. persica L. Batsch) fruit textures by a digital penetrometer.

The increase of peach (Prunus persica L. Batsch) fruit shelf-life is one of the most important objectives of breeding activities, as peach is a highly perishable fruit which undergoes rapid softening during ripening. The loss of fruit firmness is accompanied by a modification of textural properties. At least four distinct textures were described in peach: melting, non-melting, stony-hard, and slow-melting (better defined as "slow-softening"). Flesh textures are usually discriminated using different approaches, specific for each type. Objective of this work was the development of a reliable method to assess flesh texture variants in peach fruit, with special attention to the slow-softening type which is currently scored by sensorial evaluation. A puncture-based test using a digital penetrometer was performed on 20 accessions belonging to the four textural groups, obtaining a series of rheological measures related to mechanical flesh properties and including Young's Modulus, Upper Yield Point, and Slope of Yield Stress. Among the components of elasto-plastic behavior of the fruits, the texture dynamic index (TD) was shown to be a reliable parameter to distinguish the group of melting flesh texture from slow-softening, non-melting, and stony-hard, these last resulting characterized by similar mechanical properties. The TD index can be applied to discriminate slow-softening and melting fruits, although variability within the different texture groups suggests the existence of accessions with intermediate phenotypes and minor quantitative trait variation. The availability of an objective method to clearly distinguish the melting from the slow-softening phenotypes paves the road to phenotype segregating progenies in order to find molecular markers associated to the slow-softening trait. PRACTICAL APPLICATIONS: The TD index could be considered to determine different textures in fleshy fruits in preharvest and postharvest, to support evaluation of quality for the intended use.

Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch).

BACKGROUND: Plum pox virus (PPV), agent of Sharka disease, is the most important quarantine pathogen of peach (P. persica L. Batsch). Extensive evaluation of peach germplasm has highlighted the lack of resistant sources, while suggesting the presence of a quantitative disease resistance, expressed as reduction in the intensity of symptoms. Unravelling the genetic architecture of peach response to PPV infection is essential for pyramiding resistant genes and for developing more tolerant varieties. For this purpose, a genome-wide association (GWA) approach was applied in a panel of accessions phenotyped for virus susceptibility and genotyped with the IPSC peach 9 K SNP Array, and coupled with an high-coverage resequencing of the tolerant accession 'Kamarat'. RESULTS: Genome-wide association identified three highly significant associated loci on chromosome 2 and 3, accounting for most of the reduction in PPV-M susceptibility within the analysed peach population. The exploration of associated intervals through whole-genome comparison of the tolerant accession 'Kamarat' and other susceptible accessions, including the PPV-resistant wild-related species P. davidiana, allow the identification of allelic variants in promising candidate genes, including an RTM2-like gene already characterized in A. thaliana. CONCLUSIONS: The present study is the first effort to identify genetic factors involved in Sharka disease in peach germplasm through a GWA approach. We provide evidence of the presence of quantitative resistant loci in a collection of peach accessions, identifying major loci and highly informative SNPs that could be useful for marker assisted selection. These results could serve as reference bases for future research aimed at the comprehension of genetic mechanism regulating the complex peach-PPV interaction.

Integrated QTL detection for key breeding traits in multiple peach progenies.

BACKGROUND: Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. RESULTS: Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value. CONCLUSIONS: The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality.

Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies.

BACKGROUND: Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. RESULTS: A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3-5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted phenotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average). CONCLUSIONS: This study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes.

The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.

BACKGROUND: The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. RESULTS: Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. CONCLUSIONS: The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.