Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa)

Deciphering the genetic architecture of fruit color in strawberry

Fruits of Fragaria species usually have an appealing bright red color due to the accumulation of anthocyanins, water-soluble flavonoid pigments. Octoploid cultivated strawberry (Fragaria × ananassa) is a major horticultural crop for which fruit color and associated nutritional value are main breeding targets. Great diversity in fruit color intensity and pattern is observed not only in cultivated strawberry but also in wild relatives such as its octoploid progenitor F. chiloensis or the diploid woodland strawberry F. vesca, a model for fruit species in the Rosaceae. This review examines our understanding of fruit color formation in strawberry and how ongoing developments will advance it. Natural variations of fruit color as well as color changes during fruit development or in response to several cues have been used to explore the anthocyanin biosynthetic pathway and its regulation. So far, the successful identification of causal genetic variants has been largely driven by the availability of high-throughput genotyping tools and high-quality reference genomes of F. vesca and F. × ananassa. The current completion of haplotype-resolved genomes of F. × ananassa combined with QTL mapping will accelerate the exploitation of the untapped genetic diversity of fruit color and help translate the findings into strawberry improvement.

Marker-Assisted Selection in Breeding for Fruit Trait Improvement: A Review

Breeding fruit species is time-consuming and expensive. With few exceptions, trees are likely the worst species to work with in terms of genetics and breeding. Most are characterized by large trees, long juvenile periods, and intensive agricultural practice, and environmental variability plays an important role in the heritability evaluations of every single important trait. Although vegetative propagation allows for the production of a significant number of clonal replicates for the evaluation of environmental effects and genotype × environment interactions, the spaces required for plant cultivation and the intensity of work necessary for phenotypic surveys slow down the work of researchers. Fruit breeders are very often interested in fruit traits: size, weight, sugar and acid content, ripening time, fruit storability, and post-harvest practices, among other traits relevant to each individual species. The translation of trait loci and whole-genome sequences into diagnostic genetic markers that are effective and affordable for use by breeders, who must choose genetically superior parents and subsequently choose genetically superior individuals among their progeny, is one of the most difficult tasks still facing tree fruit geneticists. The availability of updated sequencing techniques and powerful software tools offered the opportunity to mine tens of fruit genomes to find out sequence variants potentially useful as molecular markers. This review is devoted to analysing what has been the role of molecular markers in assisting breeders in selection processes, with an emphasis on the fruit traits of the most important fruit crops for which examples of trustworthy molecular markers have been developed, such as the MDo.chr9.4 marker for red skin colour in apples, the CCD4-based marker CPRFC1, and LG3_13.146 marker for flesh colour in peaches, papayas, and cherries, respectively.

QTL analysis for ascorbic acid content in strawberry fruit reveals a complex genetic architecture and association with GDP-L-galactose phosphorylase

Strawberry (Fragaria × ananassa) fruits are an excellent source of L-ascorbic acid (AsA), a powerful antioxidant for plants and humans. Identifying the genetic components underlying AsA accumulation is crucial for enhancing strawberry nutritional quality. Here, we unravel the genetic architecture of AsA accumulation using an F₁ population derived from parental lines 'Candonga' and 'Senga Sengana', adapted to distinct Southern and Northern European areas. To account for environmental effects, the F₁ and parental lines were grown and phenotyped in five locations across Europe (France, Germany, Italy, Poland and Spain). Fruit AsA content displayed normal distribution typical of quantitative traits and ranged five-fold, with significant differences among genotypes and environments. AsA content in each country and the average in all of them was used in combination with 6,974 markers for quantitative trait locus (QTL) analysis. Environmentally stable QTLs for AsA content were detected in linkage group (LG) 3A, LG 5A, LG 5B, LG 6B and LG 7C. Candidate genes were identified within stable QTL intervals and expression analysis in lines with contrasting AsA content suggested that GDP-L-Galactose Phosphorylase FaGGP(3A), and the chloroplast-located AsA transporter gene FaPHT4;4(7C) might be the underlying genetic factors for QTLs on LG 3A and 7C, respectively. We show that recessive alleles of FaGGP(3A) inherited from both parental lines increase fruit AsA content. Furthermore, expression of FaGGP(3A) was two-fold higher in lines with high AsA. Markers here identified represent a useful resource for efficient selection of new strawberry cultivars with increased AsA content.

FvNST1b NAC Protein Induces Secondary Cell Wall Formation in Strawberry

Secondary cell wall thickening plays a crucial role in plant growth and development. Diploid woodland strawberry (Fragaria vesca) is an excellent model for studying fruit development, but its molecular control of secondary wall thickening is largely unknown. Previous studies have shown that Arabidopsis NAC secondary wall thickening promoting factor1 (AtNST1) and related proteins are master regulators of xylem fiber cell differentiation in multiple plant species. In this study, a NST1-like gene, FvNST1b, was isolated and characterized from strawberry. Sequence alignment and phylogenetic analysis showed that the FvNST1b protein contains a highly conserved NAC domain, and it belongs to the same family as AtNST1. Overexpression of FvNST1b in wild-type Arabidopsis caused extreme dwarfism, induced ectopic thickening of secondary walls in various tissues, and upregulated the expression of genes related to secondary cell wall synthesis. In addition, transient overexpression of FvNST1b in wild-type Fragaria vesca fruit produced cells resembling tracheary elements. These results suggest that FvNST1b positively regulates secondary cell wall formation as orthologous genes from other species.

Soil-biodegradable mulch is an alternative to non-biodegradable plastic mulches in a strawberry-lettuce double-cropping system

Double-cropping strawberry (Fragaria × ananassa Duch.) and lettuce (Lactuca sativa L.) could be a sustainable alternative practice for diversified specialty crop growers. Plastic mulch is beneficial for strawberry and lettuce production with soil-biodegradable mulch (BDM) providing opportunities to reduce plastic waste generation and costs of mulch disposal. The objective of this study was to compare non-biodegradable plastic mulches and BDM to bare ground cultivation in a strawberry–lettuce double-cropping system in a Mediterranean climate. A split-plot randomized complete block design experiment with mulch treatment [non-biodegradable polyethylene (PE) film, “weedmat” (woven, PE-based), BDM, and bare ground control] as the main factor and double-cropping rotation scheme (rotation 1 or 2) as the split-plot factor was conducted between 2020 and 2021. Strawberry yield was overall greatest when mulched with BDM, PE, and weedmat compared to the bare ground control. Total soluble solids (TSS), pH, and total titratable acidity (TA) of strawberry differed due to harvest date, but only pH differed due to mulch treatment. For lettuce canopy cover, rotation 2 had greater canopy cover (86%) compared with rotation 1 (66%) 30 days after transplanting. Average head weight (0.4 kg) and head length and diameter (both 20 cm) did not differ due to mulch or rotation. Average soil temperatures under PE and BDM were ~1.5°C higher than under weedmat and 2.5°C higher than the bare ground control. Soil under weedmat had the highest moisture content, whereas the PE, BDM, and bare ground treatments had similar levels. PE, BDM, and weedmat provided equivalent weed suppression, whereas the bare ground control had the most weeds. BDM deterioration estimated as percent soil exposure (PSE) was greatest (59% PSE) by the end of the experiment, whereas PE had 18% PSE and weedmat had no deterioration. Results show that despite high levels of deterioration, BDM performs similarly to PE in terms of soil temperature and moisture modification, weed suppression, and promotion of crop growth and yield in a double-cropped system. Double-cropping strawberry and lettuce is a promising alternative for growers to diversify their crop type and with potential economic benefits by increasing mulch lifespan.

Inheritance of esters and other volatile compounds responsible for the fruity aroma in strawberry

Cultivated strawberry, Fragaria  ×  ananassa, has a complex aroma due to the presence of more than 350 volatile organic compounds (VOCs). However, a mixture of only 19 compounds, called Key Volatile Compounds (KVC), can impart the main strawberry aroma. The octoploid nature of the cultivated strawberry species (2n = 8x = 56) adds complexity to the heritance of the accumulation of the volatiles responsible for aroma. An F1 population cross between two breeding parental lines, FC50 and FD54, was phenotyped for aroma by SPME GCMS during six harvests. A total of 58 compounds were identified: 33 esters, nine terpenes, seven aldehydes, four lactones, two furans, one acid, one alkane and one alcohol, of which 16 were KVCs. A total of 179 QTLs were found, and 85 of these were detected in at least three harvests, of which 50 QTLs were considered major (LOD > 4.0) and detected in five or six analyzed harvests. Several clusters of ester QTLs associated with fruity aroma were discovered, such as QTLs for esters that share hexanoate group that were mapped in LG4A (Hexanoate_4A), those that share acetate and octyl groups in LG6A (Acetate_6A and Octyl_6A) or those with the same methyl group in LG7B (Methyl_7B). Different terpene QTLs associated with floral aroma appear grouped in a cluster in LG3C (Terpene_3C). Some of these clusters of QTLs were validated in a second F2 population, a cross of "Camarosa" and "Dover," that was also phenotyped for three years. Selected SNPs from floral and fruity aroma QTLs were tested in a third population, which will most likely be useful for marker-assisted breeding (MAB).

Analysis of a Multi-Environment Trial for Black Raspberry (Rubus occidentalis L.) Quality Traits

U.S. black raspberry (BR) production is currently limited by narrowly adapted, elite germplasm. An improved understanding of genetic control and the stability of pomological traits will inform the development of improved BR germplasm and cultivars. To this end, the analysis of a multiple-environment trial of a BR mapping population derived from a cross that combines wild ancestors introgressed with commercial cultivars on both sides of its pedigree has provided insights into genetic variation, genotype-by-environment interactions, quantitative trait loci (QTL), and QTL-by-environment interactions (QEI) of fruit quality traits among diverse field environments. The genetic components and stability of four fruit size traits and six fruit biochemistry traits were characterized in this mapping population following their evaluation over three years at four distinct locations representative of current U.S. BR production. This revealed relatively stable genetic control of the four fruit size traits across the tested production environments and less stable genetic control of the fruit biochemistry traits. Of the fifteen total QTL, eleven exhibited significant QEI. Closely overlapping QTL revealed the linkage of several fruit size traits: fruit mass, drupelet count, and seed fraction. These and related findings are expected to guide further genetic characterization of BR fruit quality, management of breeding germplasm, and development of improved BR cultivars for U.S. production.

Genomic prediction of strawberry resistance to postharvest fruit decay caused by the fungal pathogen Botrytis cinerea

Gray mold, a disease of strawberry (Fragaria × ananassa) caused by the ubiquitous necrotroph Botrytis cinerea, renders fruit unmarketable and causes economic losses in the postharvest supply chain. To explore the feasibility of selecting for increased resistance to gray mold, we undertook genetic and genomic prediction studies in strawberry populations segregating for fruit quality and shelf life traits hypothesized to pleiotropically affect susceptibility. As predicted, resistance to gray mold was heritable but quantitative and genetically complex. While every individual was susceptible, the speed of symptom progression and severity differed. Narrow-sense heritability ranged from 0.38 to 0.71 for lesion diameter (LD) and 0.39 to 0.44 for speed of emergence of external mycelium (EM). Even though significant additive genetic variation was observed for LD and EM, the phenotypic ranges were comparatively narrow and genome-wide analyses did not identify any large-effect loci. Genomic selection (GS) accuracy ranged from 0.28 to 0.59 for LD and 0.37 to 0.47 for EM. Additive genetic correlations between fruit quality and gray mold resistance traits were consistent with prevailing hypotheses: LD decreased as titratable acidity increased, whereas EM increased as soluble solid content decreased and firmness increased. We concluded that phenotypic and GS could be effective for reducing LD and increasing EM, especially in long shelf life populations, but that a significant fraction of the genetic variation for resistance to gray mold was caused by the pleiotropic effects of fruit quality traits that differ among market and shelf life classes.

The Intragenesis and Synthetic Biology Approach towards Accelerating Genetic Gains on Strawberry: Development of New Tools to Improve Fruit Quality and Resistance to Pathogens

Under climate change, the spread of pests and pathogens into new environments has a dramatic effect on crop protection control. Strawberry (Fragaria spp.) is one the most profitable crops of the Rosaceae family worldwide, but more than 50 different genera of pathogens affect this species. Therefore, accelerating the improvement of fruit quality and pathogen resistance in strawberry represents an important objective for breeding and reducing the usage of pesticides. New genome sequencing data and bioinformatics tools has provided important resources to expand the use of synthetic biology-assisted intragenesis strategies as a powerful tool to accelerate genetic gains in strawberry. In this paper, we took advantage of these innovative approaches to create four RNAi intragenic silencing cassettes by combining specific strawberry new promoters and pathogen defense-related candidate DNA sequences to increase strawberry fruit quality and resistance by silencing their corresponding endogenous genes, mainly during fruit ripening stages, thus avoiding any unwanted effect on plant growth and development. Using a fruit transient assay, GUS expression was detected by the two synthetic FvAAT2 and FvDOF2 promoters, both by histochemical assay and qPCR analysis of GUS transcript levels, thus ensuring the ability of the same to drive the expression of the silencing cassettes in this strawberry tissue. The approaches described here represent valuable new tools for the rapid development of improved strawberry lines.

Genome-Wide Analysis of MYB10 Transcription Factor in Fragaria and Identification of QTLs Associated with Fruit Color in Octoploid Strawberry

The genus Fragaria encompass fruits with diverse colors influenced by the distribution and accumulation of anthocyanin. Particularly, the fruit colors of strawberries with different ploidy levels are determined by expression and natural variations in the vital structural and regulatory genes involved in the anthocyanin pathway. Among the regulatory genes, MYB10 transcription factor is crucial for the expression of structural genes in the anthocyanin pathway. In the present study, we performed a genome wide investigation of MYB10 in the diploid and octoploid Fragaria species. Further, we identified seven quantitative trait loci (QTLs) associated with fruit color in octoploid strawberry. In addition, we predicted 20 candidate genes primarily influencing the fruit color based on the QTL results and transcriptome analysis of fruit skin and flesh tissues of light pink, red, and dark red strawberries. Moreover, the computational and transcriptome analysis of MYB10 in octoploid strawberry suggests that the difference in fruit colors could be predominantly influenced by the expression of MYB10 from the F. iinumae subgenome. The outcomes of the present endeavor will provide a platform for the understanding and tailoring of anthocyanin pathway in strawberry for the production of fruits with aesthetic colors.

Shape, firmness and fruit quality QTLs shared in two non-related strawberry populations

The cultivated strawberry (Fragaria x ananassa) is an octoploid species (2n = 8x = 56), appreciated widely for its fruit. There have been very few studies on fruit quality traits, which are known to be mostly polygenic and environmentally dependent. To identify higher genetic variability, two non-related populations were genotyped: an F1 population cross between 'FC50' and 'FD54' and an F2 population cross between 'Camarosa' and 'Dover', hybridizing both with IStraw35k and IStraw90k SNP arrays, respectively. The F1 genetic map was constructed with 14595 SNPs and the F2 map with 7977 SNPs. High collinearity was observed when comparing one genetic map with the other and on comparing both with the octoploid genome. To assess fruit variability, both populations were phenotyped for shape, firmness, taste and other fruit traits over the 2016-2019 period. With QTL analyses, 33 stable QTLs were mapped in the 'FC50xFD54' population, and three hotspot regions were found for shape traits in LG3A, LG4D and LG6D. In the '21AF' population, only eight stable QTLs were detected. Despite that, two major and stable QTLs were mapped in the same interval of confidence for both populations. A shared fruit shape ratio QTL which explained around 25 % of trait variance was mapped in LG3A, and a shared firmness QTL explaining 26.9 % of trait variance in LG7C. For the first time, two QTLs were discovered in LG3A and LG4A for a phenotype neck without achenes. When analysing two different mapping populations, in addition to finding specific QTL regions for the studied traits, a narrowing down of the interval of confidence for the shared QTLs is achieved. As a result of this study, a new set of SNPs for fruit firmness and shape is now available for use in MAS in strawberry breeding programs.

Strawberry fruit shape: quantification by image analysis and QTL detection by genome-wide association analysis

Fruit shape of cultivated strawberry (Fragaria × ananassa Duch.) is an important breeding target. To detect genomic regions associated with this trait, its quantitative evaluation is needed. Previously we created a multi-parent advanced-generation inter-cross (MAGIC) strawberry population derived from six founder parents. In this study, we used this population to quantify fruit shape. Elliptic Fourier descriptors (EFDs) were generated from 2 969 two-dimensional binarized fruit images, and principal component (PC) scores were calculated on the basis of the EFD coefficients. PC1-PC3 explained 96% of variation in shape and thus adequately quantified it. In genome-wide association study, the PC scores were used as phenotypes. Genome wide association study using mixed linear models revealed 2 quantitative trait loci (QTLs) for fruit shape. Our results provide a novel and effective method to analyze strawberry fruit morphology; the detected QTLs and presented method can support marker-assisted selection in practical breeding programs to improve fruit shape.

Chromosome Level Assembly of Homozygous Inbred Line 'Wongyo 3115' Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line 'Wongyo 3115', using long- and short-read sequencing technologies. The assembly of 'Wongyo 3115' produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the 'Wongyo 3115' reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the 'BS F₂' populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the 'Wongyo 3115' genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of 'BS F₂' obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.

Genomic Informed Breeding Strategies for Strawberry Yield and Fruit Quality Traits

Over the last two centuries, breeders have drastically modified the fruit quality of strawberries through artificial selection. However, there remains significant variation in quality across germplasm with scope for further improvements to be made. We reported extensive phenotyping of fruit quality and yield traits in a multi-parental strawberry population to allow genomic prediction and quantitative trait nucleotide (QTN) identification, thereby enabling the description of genetic architecture to inform the efficacy of implementing advanced breeding strategies. A negative relationship (r = -0.21) between total soluble sugar content and class one yield was identified, indicating a trade-off between these two essential traits. This result highlighted an established dilemma for strawberry breeders and a need to uncouple the relationship, particularly under June-bearing, protected production systems comparable to this study. A large effect of quantitative trait nucleotide was associated with perceived acidity and pH whereas multiple loci were associated with firmness. Therefore, we recommended the implementation of both marker assisted selection (MAS) and genomic prediction to capture the observed variation respectively. Furthermore, we identified a large effect locus associated with a 10% increase in the number of class one fruit and a further 10 QTN which, when combined, are associated with a 27% increase in the number of marketable strawberries. Ultimately, our results suggested that the best method to improve strawberry yield is through selecting parental lines based upon the number of marketable fruits produced per plant. Not only were strawberry number metrics less influenced by environmental fluctuations, but they had a larger additive genetic component when compared with mass traits. As such, selecting using "number" traits should lead to faster genetic gain.

Comparative transcriptome and metabolome analyses of two strawberry cultivars with different storability

Postharvest storability is an important trait for breeding strawberry (Fragaria × ananassa Duch.). We evaluated the postharvest fruit quality of five strawberry cultivars (‘Durihyang’, ‘Kingsberry’, ‘Maehyang’, ‘Seolhyang’, and ‘Sunnyberry’) and identified differences in their fruit ripening during the transition from the big-green to fully-red stage between two cultivars with the highest (‘Sunnyberry’) and lowest (‘Kingsberry’) storability, using comparative transcriptome and -metabolome analysis. The differentially expressed genes revealed transcriptome changes related to anthocyanin biosynthesis and cell walls. Consistently, the metabolites of both cultivars showed general changes during ripening along with cultivar-specific characteristics in sugar and amino acid profiles. To identify the genes responsible for storability differences, we surveyed the expression of transcription factors, and found that the expression levels of WRKY31, WRKY70, and NAC83 correlated with delayed senescence and increased storability. Among them, the expression levels of NAC83, and its downstream target genes, in the five cultivars suggested that NAC83 expression can be used to predict postharvest strawberry fruit storability.

Genetic analysis of phenylpropanoids and antioxidant capacity in strawberry fruit reveals mQTL hotspots and candidate genes

Phenylpropanoids are a large class of plant secondary metabolites, which play essential roles in human health mainly associated with their antioxidant activity. Strawberry (Fragaria × ananassa) is a rich source of phytonutrients, including phenylpropanoids, which have been shown to have beneficial effects on human health. In this study, using the F. × ananassa '232' × '1392' F₁ segregating population, we analyzed the genetic control of individual phenylpropanoid metabolites, total polyphenol content (TPC) and antioxidant capacity (TEAC) in strawberry fruit over two seasons. We have identified a total of 7, 9, and 309 quantitative trait loci (QTL) for TPC, TEAC and for 77 polar secondary metabolites, respectively. Hotspots of stable QTL for health-related antioxidant compounds were detected on linkage groups LG IV-3, LG V-2 and V-4, and LG VI-1 and VI-2, where associated markers represent useful targets for marker-assisted selection of new varieties with increased levels of antioxidant secondary compounds. Moreover, differential expression of candidate genes for major and stable mQTLs was studied in fruits of contrasting lines in important flavonoids. Our results indicate that higher expression of FaF3'H, which encodes the flavonoid 3'-hydroxylase, is associated with increased content of these important flavonoids.

A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding

A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three regions conserved among apple (Malus × domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) were identified that contained previously detected sweetness-related quantitative trait loci (QTL) in at least two of the crops. Sugar related genes from these conserved regions and 789 sugar-associated apple genes were used to identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the ‘Hillquist’ blackberry (R. argutus) and ORUS 4115-3 black raspberry (R. occidentalis) genomes and tested for their association with soluble solids content (SSC). A total of 173 alleles were identified that were significantly (α = 0.05) associated with SSC. KASP genotyping was conducted for 92 of these alleles on a validation set of blackberries from each breeding program and 48 markers were identified that were significantly associated with SSC. One QTL, qSSC-Ruh-ch1.1, identified in both breeding programs accounted for an increase of 1.5 °Brix and the polymorphisms were detected in the intron space of a sucrose synthase gene. This discovery represents the first environmentally stable sweetness QTL identified in blackberry. The approach demonstrated in this study can be used to develop breeding tools for other crops that have not yet benefited directly from the genomics revolution.

Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses

Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.

ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry (Fragaria x ananassa)

Understanding the genetic determinants are essential for improving the fruit quality traits of strawberry. In this study, we focused on mapping the loci for fruit-length (FL), -diameter (FD), -weight (FW) and -soluble solid content (SSC) using the genome-wide single nucleotide polymorphisms (SNPs) identified via ddRAD-sequencing of the F₁ population raised from Maehyang (♀) X Festival (♂). A total of 12,698 high quality SNPs were identified of which 1554 SNPs that showed significant Mendelian segregation (p < 0.05) were mapped to 53 linkage groups (LG) spanning a total of 2937.93 cM with an average marker density of 2.14 cM/locus. Six QTLs for FL and four QTLs for each of FD, FW and SSC were identified that explained 24–35%, 21–42%, 24–54% and 23–50% of overall phenotypic variations, respectively. The genes that lie within these QTL regions were extracted and discussed thoroughly. In addition, a high resolution melting marker (MF154) were designed based on the SNP A1⁷²³G of the UDP-glucose 4-epimerase GEPI48-like gene FAN_iscf00021287. The marker detected the high vs low sugar containing F₁ plants and commercial cultivars with 81.39% and 86.95% detection accuracy, respectively. These SNPs, linkage map, QTLs and candidate genes will be helpful in understanding and improving the fruit quality traits of strawberry.

Metabolite Quantitative Trait Loci for Flavonoids Provide New Insights into the Genetic Architecture of Strawberry (Fragaria × ananassa) Fruit Quality

Flavonoids are products from specialized metabolism that contribute to fruit sensorial (color) and nutritional (antioxidant properties) quality. Here, using a pseudo full-sibling F₁ progeny previously studied for fruit sensorial quality of cultivated strawberry (Fragaria × ananassa), we explored over two successive years the genetic architecture of flavonoid-related traits using liquid chromatography electrospray ionization tandem mass spectrometry (13 compounds including anthocyanins, flavonols, and flavan-3-ols) and colorimetric assays (anthocyanins, flavonoids, phenolics, and total antioxidant capacity (ferric reducing antioxidant power and Trolox equivalent antioxidant capacity)). Network correlation analysis highlighted the high connectivity of flavonoid compounds within each chemical class and low correlation with colorimetric traits except for anthocyanins. Mapping onto the female and male linkage maps of 152 flavonoid metabolic quantitative trait loci (mQTLs) and of 26 colorimetric QTLs indicated colocalization on few linkage groups of major flavonoid- and taste-related QTLs previously uncovered. These results pave the way for the discovery of genetic variations underlying flavonoid mQTLs and for marker-assisted selection of strawberry varieties with improved sensorial and nutritional quality.

A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination

The first high-resolution genetic linkage map of the ancestral octoploid (2n = 8x = 56) strawberry species, Fragaria virginiana, was constructed using segregation data obtained from a pentaploid progeny population. This novel mapping population of size 178 was generated by crossing highly heterozygous F. virginiana hybrid "LB48" as a paternal parent with diploid (2n = 2x = 14) Fragaria vesca "Hawaii 4". The LB48 linkage map comprises 6055 markers genotyped on the Axiom® IStraw90 strawberry SNP array. The map consists of 28 linkage groups (LGs) organized into seven homoeology groups of four LGs each, and excludes a small 29th LG of undefined homoeology. One member of each homoeology group was assignable to an "A" subgenome associated with ancestral diploid Fragaria vesca, while no other subgenomes were defined. Despite an intriguing discrepancy within homoeology group VI, synteny comparisons with the previously published Fragaria ×ananassa DA × MO linkage map revealed substantial agreement. Following initial map construction, examination of crossover distributions revealed that six of the total 5162 (=29 chromosomes/individual × 178 individuals) chromosomes making up the data set exhibited abnormally high crossover counts, ranging from 15 to 48 crossovers per chromosome, as compared with the overall mean of 0.66 crossovers per chromosome. Each of these six hyper-recombinant (HypR) chromosomes occurred in a different LG and in a different individual. When calculated upon exclusion of the six HypR chromosomes, the canonical (i.e., broadly representative) LB48 map had 1851 loci distributed over a total map length of 1873 cM, while their inclusion increased the number of loci by 130, and the overall map length by 91 cM. Discovery of these hyper-recombinant chromosomes points to the existence of a sporadically acting mechanism that, if identified and manipulable, could be usefully harnessed for multiple purposes by geneticists and breeders.

A roadmap for research in octoploid strawberry

The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant-pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.

Vitamin C Content in Fruits: Biosynthesis and Regulation

Throughout evolution, a number of animals including humans have lost the ability to synthesize ascorbic acid (ascorbate, vitamin C), an essential molecule in the physiology of animals and plants. In addition to its main role as an antioxidant and cofactor in redox reactions, recent reports have shown an important role of ascorbate in the activation of epigenetic mechanisms controlling cell differentiation, dysregulation of which can lead to the development of certain types of cancer. Although fruits and vegetables constitute the main source of ascorbate in the human diet, rising its content has not been a major breeding goal, despite the large inter- and intraspecific variation in ascorbate content in fruit crops. Nowadays, there is an increasing interest to boost ascorbate content, not only to improve fruit quality but also to generate crops with elevated stress tolerance. Several attempts to increase ascorbate in fruits have achieved fairly good results but, in some cases, detrimental effects in fruit development also occur, likely due to the interaction between the biosynthesis of ascorbate and components of the cell wall. Plants synthesize ascorbate de novo mainly through the Smirnoff-Wheeler pathway, the dominant pathway in photosynthetic tissues. Two intermediates of the Smirnoff-Wheeler pathway, GDP-D-mannose and GDP-L-galactose, are also precursors of the non-cellulosic components of the plant cell wall. Therefore, a better understanding of ascorbate biosynthesis and regulation is essential for generation of improved fruits without developmental side effects. This is likely to involve a yet unknown tight regulation enabling plant growth and development, without impairing the cell redox state modulated by ascorbate pool. In certain fruits and developmental conditions, an alternative pathway from D-galacturonate might be also relevant. We here review the regulation of ascorbate synthesis, its close connection with the cell wall, as well as different strategies to increase its content in plants, with a special focus on fruits.

Identification of quantitative trait loci and candidate genes for primary metabolite content in strawberry fruit

Improvement of nutritional and organoleptic quality of fruits is a key goal in current strawberry breeding programs. The ratio of sugars to acids is a determinant factor contributing to fruit liking, although different sugars and acids contribute in varying degrees to this complex trait. A segregating F₁ population of 95 individuals, previously characterized for several fruit quality characters, was used to map during 2 years quantitative trait loci (QTL) for 50 primary metabolites, l-ascorbic acid (L-AA) and other related traits such as soluble solid content (SSC), titratable acidity (TA), and pH. A total of 133 mQTL were detected above the established thresholds for 44 traits. Only 12.9% of QTL were detected in the 2 years, suggesting a large environmental influence on primary metabolite content. An objective of this study was the identification of key metabolites that were associated to the overall variation in SSC and acidity. As it was observed in previous studies, a number of QTL controlling several metabolites and traits were co-located in homoeology group V (HG V). mQTL controlling a large variance in raffinose, sucrose, succinic acid, and L-AA were detected in approximate the same chromosomal regions of different homoeologous linkage groups belonging to HG V. Candidate genes for selected mQTL are proposed based on their co-localization, on the predicted function, and their differential gene expression among contrasting F₁ progeny lines. RNA-seq analysis from progeny lines contrasting in L-AA content detected 826 differentially expressed genes and identified Mannose-6-phosphate isomerase, FaM6PI1, as a candidate gene contributing to natural variation in ascorbic acid in strawberry fruit.

Virus-induced gene silencing and virus-induced flowering in strawberry (Fragaria × ananassa) using apple latent spherical virus vectors

Apple latent spherical virus (ALSV) vector is a convenient alternative to genetic transformation in horticultural plants, especially in species recalcitrant to genetic transformation. ALSV, an RNA virus, can infect a wide variety of plant species including major horticultural plants without inducing symptoms. Here, methodologies were developed for infection of ALSV vectors to strawberry seedlings and plantlets cultured in vitro. A seed-propagated F₁ hybrid strawberry cultivar 'Yotsuboshi' was aseptically grown on half-strength Murashige-Skoog medium for 1 month and true leaves were inoculated with an ALSV RNA preparation by particle bombardment. ALSV vector infection rates varied from 58 to 100% according to the insertion sequences, in 'Yotsuboshi' seedlings. Plantlets ('Dover') propagated in vitro could also be infected with ALSV vector at a similar infection rate. For virus-induced gene silencing (VIGS), we prepared an ALSV vector carrying a 201 nucleotide segment of the strawberry phytoene desaturase gene. 'Yotsuboshi' and 'Dover' plants infected by this vector generated completely white leaves at fifth or sixth true leaves and above. For virus-induced flowering (VIF), we used an ALSV vector expressing the Arabidopsis thaliana flowering locus T gene. Strawberry seedlings infected by this vector started to flower from about 2 months post inoculation and bore fruits with viable seeds. The ALSV vector was no longer detected in any of the seedlings from early-flowered strawberries. Thus, the ALSV vector may be beneficial for examination of gene functions by VIGS in strawberry, and VIF using ALSV vector constitutes an effective new plant breeding technique for the promotion of cross-breeding in strawberry.

Identification and characterization of known and novel microRNAs in strawberry fruits induced by Botrytis cinerea

MicroRNAs are endogenous small non-coding RNAs that negatively regulate mRNAs, mainly at the post-transcriptional level, and play an important role in resistance response of plants. To date, there are few reports on resistance response of strawberry miRNAs to pathogens. In this study, using high-throughput sequencing, 134 conserved and 35 novel miRNAs were identified in six libraries within the treatment of Botrytis cinerea. A total 497 potential target genes were predicted using Fragaria vesca genome. Most of the differential expressed miRNAs in strawberry fruits were up-regulated in early libraries and down-regulated in late libraries. PIRL, the target gene of miR5290a, showed the opposite expressed trend compared with miR5290 from T1 to T3 libraries, and functional analysis of the PIRL gene shows that it has obvious resistance to B. cinerea in the strawberry fruits with overexpressed PIRL gene. We speculate that miR5290a negatively regulates its target gene PIRL to increase resistance to pathogen infection, and further analysis of PIRL function is meaningful for studying the plant-pathogen relationship and improving strawberry fruit quality and yield.

Construction of a SNP-Based High-Density Genetic Map Using Genotyping by Sequencing (GBS) and QTL Analysis of Nut Traits in Chinese Chestnut (Castanea mollissima Blume)

Chinese chestnut is a wildly distributed nut species with importantly economic value. The nut size and ripening period are mainly desired breeding objectives in Chinese chestnut. However, high-density linkage maps and quantitative trait loci (QTL) analyses related to nut traits are less than satisfactory, which hinders progress in the breeding of Chinese chestnut. Here, a single nucleotide polymorphism (SNP)-based high-density linkage map was constructed through genotyping-by-sequencing (GBS) of an F1 cross between the two widely grown Chinese chestnut cultivars 'Yanshanzaofeng' and 'Guanting No. 10'. The genetic linkage map consists of 2,620 SNP markers with a total length of 1078.06 cM in 12 linkage groups (LGs) and an average marker distance of 0.41 cM. 17 QTLs were identified for five nut traits, specifically single-nut weight (SNW), nut width (NW), nut thickness (NT), nut height (NH), and ripening period (RP), based on phenotypic data from two successive years. Of the 17 QTLs, two major QTLs, i.e., qNT-I-1 and qRP-B-1 related to the NT and RP traits, respectively, were exploited. Moreover, the data revealed one pleiotropic QTL at 23.97 cM on LG I, which might simultaneously control SNW, NT, and NW. This study provides useful benchmark information concerning high-density genetic mapping and QTLs identification related to nut size and ripening period, and will accelerate genetic improvements for nuts in the marker-assisted selection (MAS) breeding of Chinese chestnut.

Validation of a PCR test to predict the presence of flavor volatiles mesifurane and γ-decalactone in fruits of cultivated strawberry (Fragaria × ananassa)

Flavor improvement is currently one of the most important goals for strawberry breeders. At the same time, it is one of the most complex traits to improve, involving the balanced combination of several desired characteristics such as high sweetness, moderate acidity, and the appropriate combination of aroma compounds that are beginning to be delineated in consumer tests. DNA-informed breeding will expedite the selection of complex traits, such as flavor, over traditional phenotypic evaluation, particularly when markers linked to several traits of interests are combined during the breeding process. Natural variation in mesifurane and γ-decalactone, two key volatile compounds providing sweet Sherry and fresh peach-like notes to strawberry fruits, is controlled by the FaOMT and FaFAD1 genes, respectively. In this study, we have optimized a simple PCR test for combined analysis of these genes and determined a prediction accuracy above 91% using a set of 71 diverse strawberry accessions. This high accuracy in predicting the presence of these important volatiles combined with the simplicity of the analytical methodology makes this DNA test an efficient tool for its implementation in current strawberry-breeding programs for the selection of new strawberry cultivars with superior flavor.

Development and characterization of a strawberry MAGIC population derived from crosses with six strawberry cultivars

A strawberry Multi-parent Advanced Generation Intercrosses (MAGIC) population, derived from crosses using six strawberry cultivars was successfully developed. The population was composed of 338 individuals; genome conformation was evaluated by expressed sequence tag-derived simple short repeat (EST-SSR) markers. Cluster analysis and principal component analysis (PCA) based on EST-SSR marker polymorphisms revealed that the MAGIC population was a mosaic of the six founder cultivars and covered the genomic regions of the six founders evenly. Fruit quality related traits, including days to flowering (DTF), fruit weight (FW), fruit firmness (FF), fruit color (FC), soluble solid content (SC), and titratable acidity (TA), of the MAGIC population were evaluated over two years. All traits showed normal transgressive segregation beyond the founder cultivars and most traits, except for DTF, distributed normally. FC exhibited the highest correlation coefficient overall and was distributed normally regardless of differences in DTF, FW, FF, SC, and TA. These facts were supported by PCA using fruit quality related values as explanatory variables, suggesting that major genetic factors, which are not influenced by fluctuations in other fruit traits, could control the distribution of FC. This MAGIC population is a promising resource for genome-wide association studies and genomic selection for efficient strawberry breeding.

Improvement in Fruit Quality by Overexpressing miR399a in Woodland Strawberry

Fruit quality is an important trait in strawberry and is determined by many factors. The soluble solid content in strawberry fruits is positively related to the phosphorus content. MicroRNA399 (miR399) is involved in the regulation of phosphate (Pi) homeostasis. However, the effect of miR399 on strawberry quality remains unknown. In this study, miR399a-overexpressing transgenic woodland strawberries (Fragaria vesca) were obtained via an Agrobacterium-mediated transformation. The phosphorus (P) content was 1.1-fold to 2.1-fold higher in the leaves and fruits of the miR399a-overexpressing plants than in the wild type (WT). However, the P content in the miR399a-overexpressing plants was decreased by 25% to 45% in the roots. The primary root length of the transgenic lines in both the high-Pi and low-Pi media was shorter than that of the WT. Interestingly, the transgenic lines in pots under Pi-sufficient conditions grew better than the WT, and the fruit quality, including the contents of fructose and glucose and soluble solid, was significantly higher in the transgenic lines than in the WT. The overexpression of miR399a in strawberry can be used to improve the parameters involved in fruit quality and provides information regarding breeding nutrient-improved strawberry.

Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca.

Pedigree-Based Analysis in a Multiparental Population of Octoploid Strawberry Reveals QTL Alleles Conferring Resistance to Phytophthora cactorum

Understanding the genetic architecture of traits in breeding programs can be critical for making genetic progress. Important factors include the number of loci controlling a trait, allele frequencies at those loci, and allele effects in breeding germplasm. To this end, multiparental populations offer many advantages for quantitative trait locus (QTL) analyses compared to biparental populations. These include increased power for QTL detection, the ability to sample a larger number of segregating loci and alleles, and estimation of allele effects across diverse genetic backgrounds. Here, we investigate the genetic architecture of resistance to crown rot disease caused by Phytophthora cactorum in strawberry (Fragaria × ananassa), using connected full-sib families from a breeding population. Clonal replicates of > 1100 seedlings from 139 full-sib families arising from 61 parents were control-inoculated during two consecutive seasons. Subgenome-specific single nucleotide polymorphism (SNP) loci were mapped in allo-octoploid strawberry (2n = 8 × = 56), and FlexQTL software was utilized to perform a Bayesian, pedigree-based QTL analysis. A major locus on linkage group (LG) 7D, which we name FaRPc2, accounts for most of the genetic variation for resistance. Four predominant SNP haplotypes were detected in the FaRPc2 region, two of which are strongly associated with two different levels of resistance, suggesting the presence of multiple resistance alleles. The phenotypic effects of FaRPc2 alleles across trials and across numerous genetic backgrounds make this locus a highly desirable target for genetic improvement of resistance in cultivated strawberry.

Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Background

The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S₁ mapping population of the cultivar ‘Reikou’ with an IStraw90 Axiom® SNP array and previously published SSR markers.

Results

The ‘Reikou’ linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes.

Conclusions

Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3762-y) contains supplementary material, which is available to authorized users.

Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree-based QTL analysis

The cultivated strawberry (Fragaria×ananassa) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis. In this study, breeder-specified traits were evaluated in the Eastern (Michigan) and Western (Oregon) United States for a common set of breeding populations during 2 years. Several QTLs were validated for soluble solids content (SSC), fruit weight (FWT), pH and titratable acidity (TA) using a pedigree-based QTL analysis approach. For fruit quality, a QTL for SSC on linkage group (LG) 6A, a QTL for FWT on LG 2BII, a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were detected. In addition, a large-effect QTL for flowering was detected at the distal end of LG 4A, coinciding with the FaPFRU locus. Marker haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal flowering. SNP probes in the FaPFRU region may help facilitate marker-assisted selection for this trait.

DNA-informed breeding of rosaceous crops: promises, progress and prospects

Crops of the Rosaceae family provide valuable contributions to rural economies and human health and enjoyment. Sustained solutions to production challenges and market demands can be met with genetically improved new cultivars. Traditional rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and accuracy. Use of DNA information is becoming conventional in rosaceous crop breeding, contributing to many decisions and operations, but only after past decades of solved challenges and generation of sufficient resources. Successes in deployment of DNA-based knowledge and tools have arisen when the 'chasm' between genomics discoveries and practical application is bridged systematically. Key steps are establishing breeder desire for use of DNA information, adapting tools to local breeding utility, identifying efficient application schemes, accessing effective services in DNA-based diagnostics and gaining experience in integrating DNA information into breeding operations and decisions. DNA-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics research. DNA-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering programs. DNA-based diagnostics is now expanding from specific loci to genome-wide considerations. Realizing the full potential of this expansion will require improved accuracy of predictions, multi-trait DNA profiling capabilities, streamlined breeding information management systems, strategies that overcome plant-based features that limit breeding progress and widespread training of current and future breeding personnel and allied scientists.

Sensory sacrifices when we mass-produce mass produce

Plant breeders have been extremely successful at driving genetic improvements in crops. However, 'improvements' are truly a question of perspective. Over the last one-hundred years most plant genetic innovations have been driven by industry demand. Larger fruits, heavier yields, uniformity, increased resistance to disease and better shipping quality are just a few of the traits that have ensured profits on the farm and affordable food for consumers. However, these milestones have come at the expense of sensory qualities, which have been sacrificed in exchange for practical production objectives. With a base of industry-sufficient genetics, today's breeders can now turn to the consumer for guidance in defining critical desires. New approaches to plant breeding start with the analysis of consumer preferences, and then merge them with modern genomics and analytical chemistry tools. The result is the next generation of crops that meet supply chain demands while presenting improvements in flavor, nutrition, color, aroma and texture. This review analyzes the approach of consumer-assisted selection as it has been applied to tomato and strawberry, two complementary annual crops that have been intensively bred to meet industry expectations. Current breeding efforts start with the consumer, with the objective of reclaiming lost sensory qualities.

The genetic aspects of berries: from field to health

Berries are a relevant source of micronutrients and nonessential phytochemicals, such as polyphenol compounds, that play a synergistic and cumulative role in human health promotion. Several systematic analyses showed that berry phenolics are able to detoxify reactive oxygen and nitrogen species, blocking their production, to intervene in the cell cycle, participating in the transduction and expression of genes involved in apoptosis, and to repair oxidative DNA damage. As a consequence, the improvement of the nutritional quality of berries has become a new quality target of breeding and biotechnological strategies, to control or to increase the content of specific health-related compounds in fruits. This work reviews, on the basis of the in vitro and in vivo evidence, the main berries' phytochemical compounds and their possible mechanisms of action on pathways involved in several type of diseases, with particular attention to cancer, inflammation, neurodegeneration, diabetes and cardiovascular diseases.

Sugars in peach fruit: a breeding perspective

The last decade has been characterized by a decrease in peach (Prunus persica) fruit consumption in many countries, foremost due to unsatisfactory quality. The sugar content is one of the most important quality traits perceived by consumers, and the development of novel peach cultivars with sugar-enhanced content is a primary objective of breeding programs to revert the market inertia. Nevertheless, the progress reachable through classical phenotypic selection is limited by the narrow genetic bases of peach breeding material and by the complex quantitative nature of the trait, which is deeply affected by environmental conditions and agronomical management. The development of molecular markers applicable in MAS or MAB has become an essential strategy to boost the selection efficiency. Despite the enormous advances in 'omics' sciences, providing powerful tools for plant genotyping, the identification of the genetic bases of sugar-related traits is hindered by the lack of adequate phenotyping methods that are able to address strong within-plant variability. This review provides an overview of the current knowledge of the metabolic pathways and physiological mechanisms regulating sugar accumulation in peach fruit, the main advances in phenotyping approaches and genetic background, and finally addressing new research priorities and prospective for breeders.

Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals

Petal color is one of the key characteristics determining the attractiveness and therefore the commercial value of an ornamental crop. Here, we present the first genome-wide association study for the important ornamental crop rose, focusing on the anthocyanin and carotenoid contents in petals of 96 diverse tetraploid garden rose genotypes. Cultivated roses display a vast phenotypic and genetic diversity and are therefore ideal targets for association genetics. For marker analysis, we used a recently designed Axiom SNP chip comprising 68,000 SNPs with additionally 281 SSRs, 400 AFLPs and 246 markers from candidate genes. An analysis of the structure of the rose population revealed three subpopulations with most of the genetic variation between individual genotypes rather than between clusters and with a high average proportion of heterozygous loci. The mapping of markers significantly associated with anthocyanin and carotenoid content to the related Fragaria and Prunus genomes revealed clusters of associated markers indicating five genomic regions associated with the total anthocyanin content and two large clusters associated with the carotenoid content. Among the marker clusters associated with the phenotypes, we found several candidate genes with known functions in either the anthocyanin or the carotenoid biosynthesis pathways. Among others, we identified a glutathione-S-transferase, 4CL, an auxin response factor and F3'H as candidate genes affecting anthocyanin concentration, and CCD4 and Zeaxanthine epoxidase as candidates affecting the concentration of carotenoids. These markers are starting points for future validation experiments in independent populations as well as for functional genomic studies to identify the causal factors for the observed color phenotypes. Furthermore, validated markers may be interesting tools for marker-assisted selection in commercial breeding programmes in that they provide the tools to identify superior parental combinations that combine several associated markers in higher dosages.

Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa)

Cultivated strawberry (Fragaria × ananassa) is a genetically complex allo-octoploid crop with 28 pairs of chromosomes (2n = 8x = 56) for which a genome sequence is not yet available. The diploid Fragaria vesca is considered the donor species of one of the octoploid sub-genomes and its available genome sequence can be used as a reference for genomic studies. A wide number of strawberry cultivars are stored in ex situ germplasm collections world-wide but a number of previous studies have addressed the genetic diversity present within a limited number of these collections. Here, we report the development and application of two platforms based on the implementation of Diversity Array Technology (DArT) markers for high-throughput genotyping in strawberry. The first DArT microarray was used to evaluate the genetic diversity of 62 strawberry cultivars that represent a wide range of variation based on phenotype, geographical and temporal origin and pedigrees. A total of 603 DArT markers were used to evaluate the diversity and structure of the population and their cluster analyses revealed that these markers were highly efficient in classifying the accessions in groups based on historical, geographical and pedigree-based cues. The second DArTseq platform took benefit of the complexity reduction method optimized for strawberry and the development of next generation sequencing technologies. The strawberry DArTseq was used to generate a total of 9,386 SNP markers in the previously developed ‘232’ × ‘1392’ mapping population, of which, 4,242 high quality markers were further selected to saturate this map after several filtering steps. The high-throughput platforms here developed for genotyping strawberry will facilitate genome-wide characterizations of large accessions sets and complement other available options.

Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site

Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5' LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria × ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a "unique" insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars.

Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses

BACKGROUND

Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and strawberry. Early studies on lactone biosynthesis suggest that several enzymatic pathways could be responsible for the diversity of lactones, but detailed information on them remained elusive. In this study, we have integrated genetic mapping and genome-wide transcriptome analysis to investigate the molecular basis of natural variation in γ-decalactone content in strawberry fruit.

RESULTS

As a result, the fatty acid desaturase FaFAD1 was identified as the gene underlying the locus at LGIII-2 that controls γ-decalactone production in ripening fruit. The FaFAD1 gene is specifically expressed in ripe fruits and its expression fully correlates with the presence of γ-decalactone in all 95 individuals of the mapping population. In addition, we show that the level of expression of FaFAH1, with similarity to cytochrome p450 hydroxylases, significantly correlates with the content of γ-decalactone in the mapping population. The analysis of expression quantitative trait loci (eQTL) suggests that the product of this gene also has a regulatory role in the biosynthetic pathway of lactones.

CONCLUSIONS

Altogether, this study provides mechanistic information of how the production of γ-decalactone is naturally controlled in strawberry, and proposes enzymatic activities necessary for the formation of this VOC in plants.

Genomic resources in fruit plants: an assessment of current status

The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

BACKGROUND

Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation.

RESULTS

The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes.

CONCLUSION

The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps.

Molecular genetics and genomics of the Rosoideae: state of the art and future perspectives

The Rosoideae is a subfamily of the Rosaceae that contains a number of species of economic importance, including the soft fruit species strawberry (Fragaria ×ananassa), red (Rubus idaeus) and black (Rubus occidentalis) raspberries, blackberries (Rubus spp.) and one of the most economically important cut flower genera, the roses (Rosa spp.). Molecular genetics and genomics resources for the Rosoideae have developed rapidly over the past two decades, beginning with the development and application of a number of molecular marker types including restriction fragment length polymorphisms, amplified fragment length polymorphisms and microsatellites, and culminating in the recent publication of the genome sequence of the woodland strawberry, Fragaria vesca, and the development of high throughput single nucleotide polymorphism (SNP)-genotyping resources for Fragaria, Rosa and Rubus. These tools have been used to identify genes and other functional elements that control traits of economic importance, to study the evolution of plant genome structure within the subfamily, and are beginning to facilitate genomic-assisted breeding through the development and deployment of markers linked to traits such as aspects of fruit quality, disease resistance and the timing of flowering. In this review, we report on the developments that have been made over the last 20 years in the field of molecular genetics and structural genomics within the Rosoideae, comment on how the knowledge gained will improve the efficiency of cultivar development and discuss how these advances will enhance our understanding of the biological processes determining agronomically important traits in all Rosoideae species.

Deep sequencing discovery of novel and conserved microRNAs in wild type and a white-flesh mutant strawberry

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base pairing to mRNA target sequences, and play crucial roles in plant development and stress responses. The knowledge on post-transcriptional regulation by miRNAs in strawberry is rather limited so far. In order to understand the role of miRNA in the molecular control during strawberry fruit development, small RNA libraries were constructed from fruits at the turning stage of strawberry cultivar 'Sachinoka' and its white-flesh mutant by using the Solexa platform. One hundred and twenty conserved miRNAs belonging to 27 miRNA families and 33 putative novel strawberry miRNAs were identified in both libraries. Their target genes were predicted using the Fragaria vesca genome. Nine of all miRNAs showed significant expression differences between two types of samples. Four miRNAs were up-regulated and five were down-regulated in white-flesh mutant. The sequencing results were partially validated by quantitative RT-PCR. Among them, the expression of miR399a shows the biggest change between the two samples. The prediction of its target gene showed that miR399 may play an important role in phosphate homeostasis of strawberry fruits. Furthermore, we deduce that the expression of miR399 has negative correlation with the content of sugars.

Metabolic engineering of aroma components in fruits

Plants have the ability to produce a diversity of volatile metabolites, which attract pollinators and seed dispersers and strengthen plant defense responses. Selection by plant breeders of traits such as rapid growth and yield leads, in many cases, to the loss of flavor and aroma quality in crops. How the aroma can be improved without affecting other fruit attributes is a major unsolved issue. Significant advances in metabolic engineering directed at improving the set of volatiles that the fruits emit has been aided by the characterization of enzymes involved in the biosynthesis of flavor and aroma compounds in some fruits. However, before this technology can be successfully applied to modulate the production of volatiles in different crops, further basic research is needed on the mechanisms that lead to the production of these compounds in plants. Here we review the biosynthesis and function of volatile compounds in plants, and the attempts that have been made to manipulate fruit aroma biosynthesis by metabolic engineering. In addition, we discuss the possibilities that molecular breeding offers for aroma enhancement and the implications of the latest advances in biotechnological modification of fruit flavor and aroma.

Metabolic interaction between anthocyanin and lignin biosynthesis is associated with peroxidase FaPRX27 in strawberry fruit

Plant phenolics have drawn increasing attention due to their potential nutritional benefits. Although the basic reactions of the phenolics biosynthetic pathways in plants have been intensively analyzed, the regulation of their accumulation and flux through the pathway is not that well established. The aim of this study was to use a strawberry (Fragaria × ananassa) microarray to investigate gene expression patterns associated with the accumulation of phenylpropanoids, flavonoids, and anthocyanins in strawberry fruit. An examination of the transcriptome, coupled with metabolite profiling data from different commercial varieties, was undertaken to identify genes whose expression correlated with altered phenolics composition. Seventeen comparative microarray analyses revealed 15 genes that were differentially (more than 200-fold) expressed in phenolics-rich versus phenolics-poor varieties. The results were validated by heterologous expression of the peroxidase FaPRX27 gene, which showed the highest altered expression level (more than 900-fold). The encoded protein was functionally characterized and is assumed to be involved in lignin formation during strawberry fruit ripening. Quantitative trait locus analysis indicated that the genomic region of FaPRX27 is associated with the fruit color trait. Down-regulation of the CHALCONE SYNTHASE gene and concomitant induction of FaPRX27 expression diverted the flux from anthocyanins to lignin. The results highlight the competition of the different phenolics pathways for their common precursors. The list of the 15 candidates provides new genes that are likely to impact polyphenol accumulation in strawberry fruit and could be used to develop molecular markers to select phenolics-rich germplasm.

Regulation of ripening and opportunities for control in tomato and other fruits

Fruits are an important part of a healthy diet. They provide essential vitamins and minerals, and their consumption is associated with a reduced risk of heart disease and certain cancers. These important plant products can, however, be expensive to purchase, may be of disappointing quality and often have a short shelf life. A major challenge for crop improvement in fleshy fruit species is the enhancement of their health-promoting attributes while improving quality and reducing postharvest waste. To achieve these aims, a sound mechanistic understanding of the processes involved in fruit development and ripening is needed. In recent years, substantial insights have been made into the mechanistic basis of ethylene biosynthesis, perception and signalling and the identity of master regulators of ripening that operate upstream of, or in concert with a regulatory pathway mediated by this plant hormone. The role of other plant hormones in the ripening process has, however, remained elusive, and the links between regulators and downstream processes are still poorly understood. In this review, we focus on tomato as a model for fleshy fruit and provide an overview of the molecular circuits known to be involved in ripening, especially those controlling pigment accumulation and texture changes. We then discuss how this information can be used to understand ripening in other fleshy fruit-bearing species. Recent developments in comparative genomics and systems biology approaches are discussed. The potential role of epigenetic changes in generating useful variation is highlighted along with opportunities for enhancing the level of metabolites that have a beneficial effect on human health.

Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability

The cultivated strawberry (Fragaria× ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA′A′BBB′B′ model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. × ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. × ananassa EST-derived SSR markers) from F. × ananassa ESTs, and 125 markers (F. × ananassa transcriptome-derived SSR markers) from F. × ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. × ananassa and the genome of F. vesca. Variety distinction on 129 F. × ananassa lines was demonstrated using 45 selected SSR markers.