An association mapping approach to identify favourable alleles for tomato fruit quality breeding

The art of tartness: the genetics of organic acid content in fresh fruits

Organic acids are major determinants of fruit flavor and a primary focus of fruit crop breeding. The accumulation of organic acids is determined by their synthesis, degradation, and transport, all of which are manipulated by sophisticated genetic mechanisms. Constant exploration of the genetic basis of organic acid accumulation, especially through linkage analysis, association analysis, and evolutionary analysis, have identified numerous loci in recent decades. In this review, the genetic loci and genes responsible for malate and citrate contents in fruits are discussed from the genetic perspective. Technologies such as gene transformation and genome editing as well as efficient breeding using marker-assisted selection (MAS) and genomic selection (GS) are expected to break the bottleneck of traditional fruit crop breeding and promote fruit quality improvement.

Characterization of Lithuanian Tomato Varieties and Hybrids Using Phenotypic Traits and Molecular Markers

The aim of this study was to evaluate phenotypic traits and genetic diversity of the 13 tomato (Solanum lycopersicum L.) varieties and 6 hybrids developed at the Institute of Horticulture Lithuanian Research Centre for Agriculture and Forestry (LRCAF IH). For the molecular characterisation, seven previously published microsatellite markers (SSR) were used. A24 and 26 alleles were detected in tomato varieties and hybrids, respectively. Based on the polymorphism information content (PIC) value, the most informative SSR primers for varieties were TMS52, TGS0007, LEMDDNa and Tom236-237, and the most informative SSR primers for hybrids were SSR248 and TMS52. In UPGMA cluster analysis, tomato varieties are grouped in some cases due to genetic relationships, as the same cluster cultivars 'Viltis' (the parent of cv. 'Laukiai') and 'Aušriai' (the progeny of cv. 'Jurgiai') are present. The grouping of all hybrids in the dendrogram is related to the parental forms, and it shows the usefulness of molecular markers for tomato breeding, as they can be used to trace the origin of hybrids and, eventually, varieties accurately. The knowledge about the genetic background of Lithuanian tomato cultivars will help plan targeted crosses in tomato breeding programs.

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

Mapping phenotypic performance and novel SNPs for cold tolerance in tomato (Solanum lycopersicum) genotypes through GWAS and population genetics

The cold stress susceptibility of tomato (Solanum lycopersicum) curtails its cultivation, with significant impact in temperate regions and on cropping seasons. To unravel genomic regions responsible for cold stress resilience, a diverse set of fifty genotypes encompassing cultivated, wild species, and landraces were genotyped using genotyping-by-sequencing. Over two years and six trials employing both early and late sowing, these lines were evaluated. Illumina-based next-generation sequencing produced up to 3 million reads per sample from individually sequenced library pools. The Tassel pipeline yielded 10,802 variants, subsequently filtered to 3,854 SNPs for genome-wide association analysis (GWAS). Employing clustering methods (population structure) via TASSEL, SNPhylo, and Kinship matrix, the fifty genotypes clustered into four distinct gene pools. The GWAS for cold tolerance in tomato integrated key traits including yield. Using six independent phenotypic datasets representing various environments, the study identified 4,517 significant marker-trait associations for cold tolerance traits. Notably, pivotal variations (> 10%) in cold stress tolerance, particularly proline content, were linked to marker-trait associations. Additionally, 5,727 significant marker-trait associations for yield and yield-related traits were unveiled, shedding light on fruit yield and directly associated attributes. The investigation pinpointed 685 candidate genes across all examined traits, including 60 genes associated with biological processes within these genomic regions. Remarkably, 7 out of the 60 genes were directly linked to abiotic stress tolerance, functioning as stress-responsive genes either directly or indirectly. The identified genes, particularly those associated with stress response, could hold the key to enhancing cold tolerance and overall crop productivity in tomato cultivation.

Diversity and genetic architecture of agro-morphological traits in a core collection of European traditional tomato

European traditional tomato varieties have been selected by farmers given their consistent performance and adaptation to local growing conditions. Here we developed a multipurpose core collection, comprising 226 accessions representative of the genotypic, phenotypic, and geographical diversity present in European traditional tomatoes, to investigate the basis of their phenotypic variation, gene×environment interactions, and stability for 33 agro-morphological traits. Comparison of the traditional varieties with a modern reference panel revealed that some traditional varieties displayed excellent agronomic performance and high trait stability, as good as or better than that of their modern counterparts. We conducted genome-wide association and genome-wide environment interaction studies and detected 141 quantitative trait loci (QTLs). Out of those, 47 QTLs were associated with the phenotype mean (meanQTLs), 41 with stability (stbQTLs), and 53 QTL-by-environment interactions (QTIs). Most QTLs displayed additive gene actions, with the exception of stbQTLs, which were mostly recessive and overdominant QTLs. Both common and specific loci controlled the phenotype mean and stability variation in traditional tomato; however, a larger proportion of specific QTLs was observed, indicating that the stability gene regulatory model is the predominant one. Developmental genes tended to map close to meanQTLs, while genes involved in stress response, hormone metabolism, and signalling were found within regions affecting stability. A total of 137 marker-trait associations for phenotypic means and stability were novel, and therefore our study enhances the understanding of the genetic basis of valuable agronomic traits and opens up a new avenue for an exploitation of the allelic diversity available within European traditional tomato germplasm.

The dissection of tomato flavor: biochemistry, genetics, and omics

Flavor and quality are the major drivers of fruit consumption in the US. However, the poor flavor of modern commercial tomato varieties is a major cause of consumer dissatisfaction. Studies in flavor research have informed the role of volatile organic compounds in improving overall liking and sweetness of tomatoes. These studies have utilized and applied the tools of molecular biology, genetics, biochemistry, omics, machine learning, and gene editing to elucidate the compounds and biochemical pathways essential for good tasting fruit. Here, we discuss the progress in identifying the biosynthetic pathways and chemical modifications of important tomato volatile compounds. We also summarize the advances in developing highly flavorful tomato varieties and future steps toward developing a "perfect tomato".

Limitations and advantages of using metabolite-based genome-wide association studies: focus on fruit quality traits

In the last decades, linkage mapping has help in the location of metabolite quantitative trait loci (QTL) in many species; however, this approach shows some limitations. Recently, thanks to the most recent advanced in high-throughput genotyping technologies like next-generation sequencing, metabolite genome-wide association study (mGWAS) has been proposed a powerful tool to identify the genetic variants in polygenic agrinomic traits. Fruit flavor is a complex interaction of aroma volatiles and taste being sugar and acid ratio key parameter for flavor acceptance. Here, we review recent progress of mGWAS in pinpoint gene polymorphisms related to flavor-related metabolites in fruits. Despite clear successes in discovering novel genes or regions associated with metabolite accumulation affecting sensory attributes in fruits, GWAS incurs in several limitations summarized in this review. In addition, in our own work, we performed mGWAS on 194 Citrus grandis accessions to investigate the genetic control of individual primary and lipid metabolites in ripe fruit. We have identified a total of 667 associations for 14 primary metabolites including amino acids, sugars, and organic acids, and 768 associations corresponding to 47 lipids. Furthermore, candidate genes related to important metabolites related to fruit quality such as sugars, organic acids and lipids were discovered.

Genome-wide association study for the extractable phenolic profile and coat color of common bean seeds (Phaseolus vulgaris L.)

BACKGROUND

A large variation in seed coat colors and seed phenolic metabolites is present in common bean (Phaseolus vulgaris L.). The study of the relationships between seed coat color phenotype and the phenolic profile is an important step in the elucidation of the gene network involved in the phenylpropanoid biosynthetic pathway. However, this relationship is still poorly understood in this species.

RESULTS

A genome-wide association study (GWAS) was used to investigate the genomic regions associated with the synthesis of 10 flavonoids (5 anthocyanins and 5 flavonols) and with 10 seed coat color traits using a set of 308 common bean lines of the Spanish Diversity Panel (SDP) which have been genotyped with 11,763 SNP markers.. A total of 31 significant SNP-trait associations (QTNs) were identified, grouped in 20 chromosome regions: 6 for phenolic metabolites on chromosomes Pv01, Pv02, Pv04, Pv08, and Pv09, 13 for seed coat color on chromosomes Pv01, Pv02, Pv06, Pv07, and Pv10, and 1 including both types of traits located on chromosome Pv08. In all, 58 candidate genes underlying these regions have been proposed, 31 of them previously described in the phenylpropanoid pathway in common bean, and 27 of them newly proposed in this work based on the association study and their homology with Arabidopsis anthocyanin genes.

CONCLUSIONS

Chromosome Pv08 was identified as the main chromosome involved in the phenylpropanoid pathway and in consequence in the common bean seed pigmentation, with three independent chromosome regions identified, Phe/C_Pv08(2.7) (expanding from 2.71 to 4.04 Mbp), C_Pv08(5.8) (5.89-6.59 Mbp), and Phe_Pv08(62.5) (62.58 to 63.28 Mbp). Candidate genes previously proposed by other authors for the color genes V and P were validated in this GWAS. Candidate genes have been tentatively proposed from this study for color genes B and Rk on Pv02, Asp on Pv07, and complex C on Pv08. These results help to clarify the complex network of genes involved in the genetic control of phenolic compounds and seed color in common bean and provide the opportunity for future validation studies.

Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.

Genetic control of tomato fruit quality: from QTL mapping to Genome Wide Association studies and breeding

Consumers began to complain about the taste of tomato varieties in the late 1990's. Although tomato taste is influenced by environmental and post-harvest conditions, varieties show a large diversity for fruit quality traits. We herein review our past and present research work intended to improve tomato fruit quality. First, results from sensory analysis allowed identifying important traits for consumer preferences. Then, we dissected the genetic control of flavor related traits by mapping several QTL in the last 20 years, and identified the genes corresponding to a few major QTL. Since the availability of the tomato genome sequence, genome-wide association studies were performed on several panels of tomato accessions. We discovered a large number of associations for fruit composition and identified relevant allele combinations for breeding. We then performed a meta-analysis combining the results of several studies. We also checked the inheritance of quality traits at the hybrid level and assessed how genomic prediction could help selecting better tomato varieties.

Phenotypic and molecular analyses in diploid and tetraploid genotypes of Solanum tuberosum L. reveal promising genotypes and candidate genes associated with phenolic compounds, ascorbic acid contents, and antioxidant activity

Potato tubers contain biochemical compounds with antioxidant properties that benefit human health. However, the genomic basis of the production of antioxidant compounds in potatoes has largely remained unexplored. Therefore, we report the first genome-wide association study (GWAS) based on 4488 single nucleotide polymorphism (SNP) markers and the phenotypic evaluation of Total Phenols Content (TPC), Ascorbic Acid Content (AAC), and Antioxidant Activity (AA) traits in 404 diverse potato genotypes (84 diploids and 320 tetraploids) conserved at the Colombian germplasm bank that administers AGROSAVIA. The concentration of antioxidant compounds correlated to the skin tuber color and ploidy level. Especially, purple-blackish tetraploid tubers had the highest TPC (2062.41 ± 547.37 mg GAE), while diploid pink-red tubers presented the highest AA (DDPH: 14967.1 ± 4687.79 μmol TE; FRAP: 2208.63 ± 797.35 mg AAE) and AAC (4.52 mg ± 0.68 AA). The index selection allowed us to choose 20 promising genotypes with the highest values for the antioxidant compounds. Genome Association mapping identified 58 SNP-Trait Associations (STAs) with single-locus models and 28 Quantitative Trait Nucleotide (QTNs) with multi-locus models associated with the evaluated traits. Among models, eight STAs/QTNs related to TPC, AAC, and AA were detected in common, flanking seven candidate genes, from which four were pleiotropic. The combination in one population of diploid and tetraploid genotypes enabled the identification of more genetic associations. However, the GWAS analysis implemented independently in populations detected some regions in common between diploids and tetraploids not detected in the mixed population. Candidate genes have molecular functions involved in phenolic compounds, ascorbic acid biosynthesis, and antioxidant responses concerning plant abiotic stress. All candidate genes identified in this study can be used for further expression analysis validation and future implementation in marker-assisted selection pre-breeding platforms targeting fortified materials. Our study further revealed the importance of potato germplasm conserved in national genebanks, such as AGROSAVIA's, as a valuable genetic resource to improve existing potato varieties.

Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms)

Seed size is an important yield and quality-determining trait in higher plants and is also crucial to their evolutionary fitness. In African yam bean (AYB), seed size varies widely among different accessions. However, the genetic basis of such variation has not been adequately documented. A genome-wide marker-trait association study was conducted to identify genomic regions associated with four seed size traits (seed length, seed width, seed thickness, and 100-seed weight) in a panel of 195 AYB accessions. A total of 5416 SNP markers were generated from the diversity array technology sequence (DArTseq) genotype-by-sequencing (GBS)- approach, in which 2491 SNPs were retained after SNP quality control and used for marker-trait association analysis. Significant phenotypic variation was observed for the traits. Broad-sense heritability ranged from 50.0% (seed width) to 66.4% (seed length). The relationships among the traits were positive and significant. Genome-wide association study (GWAS) using the general linear model (GLM) and the mixed linear model (MLM) approaches identified 12 SNP markers significantly associated with seed size traits across the six test environments. The 12 makers explained 6.5-10.8% of the phenotypic variation. Two markers (29420334|F|0-52:C>G-52:C>G and 29420736|F|0-57:G>T-57:G>T) with pleiotropic effects associated with seed width and seed thickness were found. A candidate gene search identified five significant markers (100026424|F|0-37:C>T-37:C>T, 100041049|F|0-42:G>C-42:G>C, 100034480|F|0-31:C>A-31:C>A, 29420365|F|0-55:C>G-55:C>G, and 29420736|F|0-57:G>T-57:G>T) located close to 43 putative genes whose encoding protein products are known to regulate seed size traits. This study revealed significant makers not previously reported for seed size in AYB and could provide useful information for genomic-assisted breeding in AYB.

Germplasm Screening Using DNA Markers and Genome-Wide Association Study for the Identification of Powdery Mildew Resistance Loci in Tomato

Powdery mildew (PM), caused by Oidium spp. in tomato, is a global concern that leads to diminished yield. We aimed to evaluate previously reported DNA markers linked to powdery mildew resistance (PMR) and identify novel quantitative trait loci (QTLs) for PMR through a genome-wide association study in tomato. Sequencing analysis of the internal transcribed spacer (ITS) of a PM strain (PNU_PM) isolated from Miryang, Gyeongnam, led to its identification as Oidium neolycopersici. Thereafter, a PM bioassay was conducted for a total of 295 tomato accessions, among which 24 accessions (4 S. lycopersicum accessions and 20 accessions of seven wild species) showed high levels of resistance to PNU_PM. Subsequently, we genotyped 11 markers previously linked to PMR in 56 accessions. PMR-specific banding patterns were detected in 15/22 PMR accessions, while no such bands were observed in the powdery mildew-susceptible accessions. The genome-wide association study was performed using TASSEL and GAPIT, based on the phenotypic data of 290 accessions and 11,912 single nucleotide polymorphisms (SNPs) obtained from the Axiom® Tomato SNP Chip Array. Nine significant SNPs in chromosomes 1, 4, 6, 8, and 12, were selected and five novel QTL regions distinct from previously known PMR-QTL regions were identified. Of these QTL regions, three putative candidate genes for PMR were selected from chromosomes 4 and 8, including two nucleotide binding site-leucine rich repeat class genes and a receptor-like kinase gene, all of which have been identified previously as causative genes for PMR in several crop species. The SNPs discovered in these genes provide useful information for understanding the molecular basis of PMR and developing DNA markers for marker-assisted selection of PMR in tomato.

Next generation sequencing technologies to explore the diversity of germplasm resources: achievements and trends in tomato

Tomato is one of the major vegetable crops grown worldwide and a model species for genetic and biological research. Progress in genomic technologies made possible the development of forefront methods for high-scale sequencing, providing comprehensive insight into the genetic architecture of germplasm resources. This review revisits next-generation sequencing strategies and applications to investigate the diversity of tomato, describing the common platforms used for SNP genotyping of large collections, de novo sequencing, and whole genome resequencing. Significant findings in evolutionary history are outlined, thus discussing how genomics has provided new hints about the processes behind domestication. Finally, achievement and perspectives on pan-genome construction and graphical pan-genome development toward precise mining of the natural variation to be exploited for breeding purposes are presented.

Phenotypic and Genotypic Diversity of the Tomato Germplasm From the Lazio Region in Central Italy, With a Focus on Landrace Distinctiveness

Italy is a recognized secondary center of diversification for cultivated tomato (Solanum lycopersicum L.). The study of phenotypic and genetic diversity in landrace collections is important for germplasm conservation and valorization. Here, we set up to study the tomato germplasm collected in the region of Lazio in Central Italy, with a focus on the distinctiveness among landraces and the attribution of membership to unnamed accessions. Our regional collection included 32 accessions belonging to eight different locally recognized landraces and 19 unnamed accessions. All accessions were gathered from local farmers and are preserved in the collection held at the Regional Agency for the Development and the Innovation of Lazio Agriculture (ARSIAL) and at the University of Tuscia. We included 13 control genotypes comprising nine landraces from neighbor regions and four reference cultivars. The collection showed wide phenotypic variability for several qualitative and quantitative traits, such as leaf border and shape, inflorescence type, fruit shape, green shoulder, fruit weight (range 14-277 g), locule number (2-12), shape index (0.54-2.65), yield (0.24-3.08 kg/plant), and soluble solids (3.4-7.5°B). A few landraces showed uncommon phenotypes, such as potato leaf, colorless fruit epidermis, or delayed ripening. Multivariate analysis of 25 cardinal phenotypic variables separated the accessions into two distinct groups; accessions showing a flattened-ribbed fruit were distinguished from those with round to elongate fruits with smooth structure. Genotyping analysis of 7,720 SNPs was performed using the tomato array platform SolCAP, to point out the genetic relationship among the studied accessions. A neighbor-joining tree analysis allowed to confirm or deny phenotypic data and to assign some of the unnamed accessions to recognized groups. Allelic status at marker loci linked to resistance genes commonly used in breeding identified accessions putatively derived from modern material or commercial hybrids, thus not classifiable as landraces. Overall, this study provided the information useful to preserve, valorize, and juridically protect tomato local landraces from the Lazio region and will in addition be helpful to their improvement by breeding.

Effect of Elevated Temperature on Tomato Post-Harvest Properties

The fleshy fruit of tomato (Solanum lycopersicum) is a commodity used worldwide as a fresh or processed product. Like many crops, tomato plants and harvested fruits are susceptible to the onset of climate change. Temperature plays a key role in tomato fruit production and ripening, including softening, development of fruit colour, flavour and aroma. The combination of climate change and the drive to reduce carbon emission and energy consumption is likely to affect tomato post-harvest storage conditions. In this study, we investigated the effect of an elevated storage temperature on tomato shelf life and fungal susceptibility. A collection of 41 genotypes with low and high field performance at elevated temperature, including different growth, fruit and market types, was used to assess post-harvest performances. A temperature increase from 18–20 °C to 26 °C reduced average shelf life of fruit by 4 days ± 1 day and increased fungal susceptibility by 11% ± 5% across all genotypes. We identified tomato varieties that exhibit both favourable post-harvest fruit quality and high field performance at elevated temperature. This work contributes to efforts to enhance crop resilience by selecting for thermotolerance combined with traits suitable to maintain and improve fruit quality, shelf life and pathogen susceptibility under changing climate conditions.

Postharvest Quality Evolution in Long Shelf-Life “Vesuviano” Tomato Landrace

“Vesuviano” or “piennolo” tomato is among the most famous Italian small tomato landraces and is cultivated on the slopes of Vesuvio volcano (Southern Italy). The “piennolo” tomato is an interesting case with regard to its potential sustainability, as it is traditionally grown in water-deficit conditions with a low fertilizer input. Fruits with a high firmness and a thick skin can be stored for 3–4 months at room temperature (“long shelf-life” or LSL tomato) without postharvest fungicide applications. The aim of this research was to study the retention, changes in quality, and nutritional traits of “Vesuviano” tomatoes over 120 days of “natural” storage. The dry matter, soluble sugar, organic acids, volatile compounds, and carotenoid contents were evaluated at harvesting and in fruits stored for 40, 80, and 120 days. Slight decreases in dry matter content, soluble sugars, and sweetness index were found, while the organic acids levels remained relatively stable. Moreover, interesting increases in the concentrations of certain flavor volatiles, alcohols, aldehydes, and terpenes were detected. Regarding carotenoids, the total lycopene levels exhibited a 1.5-fold increase from harvest to 120 days. The unchanged lycopene cis-isomer levels and the β-carotene/total lycopene ratio is characteristic of relatively stable isomerization activity and indicated an optimal ripening pattern up until the end of the “natural” storage period. These results, which demonstrate good overall quality retention of this LSL tomato, represent a well-grounded reason to enhance the cultivation and marketing of this genetic resource, the fruits of which can be appreciated by consumers during the winter–early spring, when high-quality fresh tomatoes are not available on the markets.

Genome wide association mapping for agronomic, fruit quality, and root architectural traits in tomato under organic farming conditions

BACKGROUND

Opportunity and challenges of the agriculture scenario of the next decades will face increasing demand for secure food through approaches able to minimize the input to cultivations. Large panels of tomato varieties represent a valuable resource of traits of interest under sustainable cultivation systems and for genome-wide association studies (GWAS). For mapping loci controlling the variation of agronomic, fruit quality, and root architecture traits, we used a heterogeneous set of 244 traditional and improved tomato accessions grown under organic field trials. Here we report comprehensive phenotyping and GWAS using over 37,300 SNPs obtained through double digest restriction-site associated DNA (dd-RADseq).

RESULTS

A wide range of phenotypic diversity was observed in the studied collection, with highly significant differences encountered for most traits. A variable level of heritability was observed with values up to 69% for morphological traits while, among agronomic ones, fruit weight showed values above 80%. Genotype by environment analysis highlighted the strongest genotypic effect for aboveground traits compared to root architecture, suggesting that the hypogeal part of tomato plants has been a minor objective for breeding activities. GWAS was performed by a compressed mixed linear model leading to 59 significantly associated loci, allowing the identification of novel genes related to flower and fruit characteristics. Most genomic associations fell into the region surrounding SUN, OVATE, and MYB gene families. Six flower and fruit traits were associated with a single member of the SUN family (SLSUN31) on chromosome 11, in a region involved in the increase of fruit weight, locules number, and fruit fasciation. Furthermore, additional candidate genes for soluble solids content, fruit colour and shape were found near previously reported chromosomal regions, indicating the presence of synergic and multiple linked genes underlying the variation of these traits.

CONCLUSIONS

Results of this study give new hints on the genetic basis of traits in underexplored germplasm grown under organic conditions, providing a framework for the development of markers linked to candidate genes of interest to be used in genomics-assisted breeding in tomato, in particular under low-input and organic cultivation conditions.

Accelerating the Development of Heat Tolerant Tomato Hybrids through a Multi-Traits Evaluation of Parental Lines Combining Phenotypic and Genotypic Analysis

The constitution of heat tolerant F₁ hybrids is a challenge to ensure high yield and good fruit quality in the global climate. In the present work, we evaluated 15 genotypes for yield-related traits highly affected by high temperatures (HT). This phenotypic analysis allowed to identify four parental genotypes showing promising yield performances under HT conditions. Two of these genotypes also exhibited good fruit quality traits. A molecular marker analysis was carried out for six resistance genes to pathogens mostly affecting tomatoes. This analysis evidenced the presence of a maximum of three resistant alleles in parental genotypes. Exploring single nucleotide polymorphisms (SNPs) revealed by two high-throughput genotyping platforms allowed identifying additional 12 genes potentially involved in resistance to biotic stress, to be further investigated. Following these considerations, 13 F₁ hybrids were constituted combining the parental genotypes and then evaluated for multiple traits under HT conditions. By estimating a hybrid index based on yield performances, desirable quality and resistance gene, we identified seven hybrids showing the best performances. The promising results obtained in the present work should be confirmed by evaluating the best hybrids selected for additional years and environments before proposing them as novel commercial hybrids that could maintain high performances under HT conditions.

Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicum L.)

Genome-wide association study (GWAS) is effective in identifying favorable alleles for traits of interest with high mapping resolution in crop species. In this study, we conducted GWAS to explore quantitative trait loci (QTL) for eight fruit traits using 162 tomato accessions with diverse genetic backgrounds. The eight traits included fruit weight, fruit width, fruit height, fruit shape index, pericarp thickness, locule number, fruit firmness, and brix. Phenotypic variations of these traits in the tomato collection were evaluated with three replicates in field trials over three years. We filtered 34,550 confident SNPs from the 51 K Axiom^® tomato array based on < 10% of missing data and > 5% of minor allele frequency for association analysis. The 162 tomato accessions were divided into seven clusters and their membership coefficients were used to account for population structure along with a kinship matrix. To identify marker-trait associations (MTAs), four phenotypic data sets representing each of three years and combined were independently analyzed in the multilocus mixed model (MLMM). A total of 30 significant MTAs was detected over data sets for eight fruit traits at P < 0.0005. The number of MTA per trait ranged from one (brix) to seven (fruit weight and fruit width). Two SNP markers on chromosomes 1 and 2 were significantly associated with multiple traits, suggesting pleiotropic effects of QTL. Furthermore, 16 of 30 MTAs suggest potential novel QTL for eight fruit traits. These results facilitate genetic dissection of tomato fruit traits and provide a useful resource to develop molecular tools for improving fruit traits via marker-assisted selection and genomic selection in tomato breeding programs.

Evaluation of the basic saccharides content in tomatoes

Saccharides are the basic dry matter components of all fruits and vegetables. The dominant tomatoes saccharides are fructose and glucose, minor ones are sucrose but also arabinose, xylose, and galactose. The objective of this paper is to analyze carbohydrates such as glucose, fructose and sucrose in the selected tomatoes varieties intended for the direct consumption and industrial processing. We used 14 varieties and 3 newly selected tomatoes varieties. The glucose content in the studied varieties was in the range of 4.87 – 15.9 g.kg-1, the fructose content was 11.1 – 22.27 g.kg-1 and sucrose content was 0.07 – 1.73 g.kg-1. The highest fructose and sucrose content was detected in the Tomanova variety, the highest sucrose content was found out in the Bovita variety. When comparing the glucose content it was found out that the higher content on average was achieved in the varieties intended for the industrial processing (10.10 g.kg-1) than in the varieties for the direct consumption (7.96 g.kg-1). The varieties intended for industrial processing were generally characterized by higher glucose and fructose content than the varieties intended for the direct consumption. When comparing the fructose content, we found a higher average content in the varieties intended for industrial processing (15.70 g.kg-1) than in the varieties for the direct consumption (14.40 g.kg-1). In most of the studied varieties sucrose was present in low content (<1.0 g.kg-1), only in the Tomanova variety sucrose content represented more than 1 g.kg-1.

Genomic and Phenotypic Diversity of Cultivated and Wild Tomatoes with Varying Levels of Heat Tolerance

Assessment of genetic variability in heat-tolerant tomato germplasm is a pre-requisite to improve yield and fruit quality under heat stress. We assessed the population structure and diversity in a panel of three Solanum pimpinellifolium (wild tomatoes) and 42 S. lycopersicum (cultivated tomatoes) lines and accessions with varying heat tolerance levels. The DArTseq marker was used for the sequencing and 5270 informative single nucleotide polymorphism (SNP) markers were retained for the genomic analysis. The germplasm was evaluated under two heat stress environments for five yield and flower related traits. The phenotypic evaluation revealed moderate broad-sense heritabilities for fruit weight per plant and high broad-sense heritabilities for fruit weight, number of inflorescences per plant, and number of flowers per inflorescence. The hierarchical clustering based on identity by state dissimilarity matrix and UPGMA grouped the germplasm into three clusters. The cluster analysis based on heat-tolerance traits separated the germplasm collection into five clusters. The correlation between the phenotypic and genomic-based distance matrices was low (r = 0.2, p < 0.05). The joint phenotypic and genomic-based clustering grouped the germplasm collection into five clusters well defined for their response to heat stress ranging from highly sensitive to highly tolerant groups. The heat-sensitive and heat-tolerant clusters of S. lycopersicum lines were differentiated by a specific pattern of minor allele frequency distribution on chromosome 11. The joint phenotypic and genomic analysis revealed important diversity within the germplasm collection. This study provides the basis for efficient selection of parental lines to breed heat-tolerant varieties.

The Genetic Basis of Tomato Aroma

Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as "sweet", "smoky", or "fruity" aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceived tomato aroma. These VOCs can be grouped in five clusters, according to their biosynthetic origins. In the last decades, a vast array of scientific studies has investigated the genetic component of tomato aroma in modern tomato cultivars and their relatives. In this paper we aim to collect, compare, integrate and summarize the available literature on flavour-related QTLs in tomato. Three hundred and 5ifty nine (359) QTLs associated with tomato fruit VOCs were physically mapped on the genome and investigated for the presence of potential candidate genes. This review makes it possible to (i) pinpoint potential donors described in literature for specific traits, (ii) highlight important QTL regions by combining information from different populations, and (iii) pinpoint potential candidate genes. This overview aims to be a valuable resource for researchers aiming to elucidate the genetics underlying tomato flavour and for breeders who aim to improve tomato aroma.

GWAS Based on RNA-Seq SNPs and High-Throughput Phenotyping Combined with Climatic Data Highlights the Reservoir of Valuable Genetic Diversity in Regional Tomato Landraces

Tomato (Solanum lycopersicum L.) is a widely used model plant species for dissecting out the genomic bases of complex traits to thus provide an optimal platform for modern "-omics" studies and genome-guided breeding. Genome-wide association studies (GWAS) have become a preferred approach for screening large diverse populations and many traits. Here, we present GWAS analysis of a collection of 115 landraces and 11 vintage and modern cultivars. A total of 26 conventional descriptors, 40 traits obtained by digital phenotyping, the fruit content of six carotenoids recorded at the early ripening (breaker) and red-ripe stages and 21 climate-related variables were analyzed in the context of genetic diversity monitored in the 126 accessions. The data obtained from thorough phenotyping and the SNP diversity revealed by sequencing of ripe fruit transcripts of 120 of the tomato accessions were jointly analyzed to determine which genomic regions are implicated in the expressed phenotypic variation. This study reveals that the use of fruit RNA-Seq SNP diversity is effective not only for identification of genomic regions that underlie variation in fruit traits, but also of variation related to additional plant traits and adaptive responses to climate variation. These results allowed validation of our approach because different marker-trait associations mapped on chromosomal regions where other candidate genes for the same traits were previously reported. In addition, previously uncharacterized chromosomal regions were targeted as potentially involved in the expression of variable phenotypes, thus demonstrating that our tomato collection is a precious reservoir of diversity and an excellent tool for gene discovery.

Exploring wild alleles from Solanum pimpinellifolium with the potential to improve tomato flavor compounds

Most consumers complain about the flavor of current tomato cultivars and many pay a premium for alternatives such as heirloom varieties. Breeding for fruit flavor is difficult because it is a quantitatively inherited trait influenced by taste, aroma and environmental factors. A lack of genetic diversity in modern tomato cultivars also necessitates exploration of new sources for flavor alleles. Wild tomato S. pimpinellifolium and inbred backcross lines were assessed for individual sugars and organic acids which are two of the main components of tomato flavor. S. pimpinellifolium was found to harbor alleles that could be used to increase glucose and fructose content and adjust acidity by altering malic and citric acid levels. Single nucleotide polymorphism markers were used to detect 14 quantitative trait loci (QTLs) for sugars and 71 for organic acids. Confirmation was provided by comparing map locations with previously identified loci. Thus, seven (50 %) of the sugar QTLs and 22 (31 %) of the organic acids loci were supported by analyses in other tomato populations. Examination of the genomic sequence containing the QTLs allowed identification of potential candidate genes for several flavor components.

Physiological Basis of Salt Stress Tolerance in a Landrace and a Commercial Variety of Sweet Pepper (Capsicum annuum L.)

Salt stress is one of the most impactful abiotic stresses that plants must cope with. Plants’ ability to tolerate salt stress relies on multiple mechanisms, which are associated with biomass and yield reductions. Sweet pepper is a salt-sensitive crop that in Mediterranean regions can be exposed to salt build-up in the root zone due to irrigation. Understanding the physiological mechanisms that plants activate to adapt to soil salinization is essential to develop breeding programs and agricultural practices that counteract this phenomenon and ultimately minimize yield reductions. With this aim, the physiological and productive performances of Quadrato D’Asti, a common commercial sweet pepper cultivar in Italy, and Cazzone Giallo, a landrace of the Campania region (Italy), were compared under different salt stress treatments. Quadrato D’Asti had higher tolerance to salt stress when compared to Cazzone Giallo in terms of yield, which was associated with higher leaf biomass vs. fruit ratio in the former. Ion accumulation and profiling between the two genoptypes revealed that Quadrato D’Asti was more efficient at excluding chloride from green tissues, allowing the maintenance of photosystem functionality under stress. In contrast, Cazzone Giallo seemed to compartmentalize most sodium in the stem. While sodium accumulation in the stems has been shown to protect shoots from sodium toxicity, in pepper and/or in the specific experimental conditions imposed, this strategy was less efficient than chloride exclusion for salt stress tolerance.

High-Throughput Genotyping of Resilient Tomato Landraces to Detect Candidate Genes Involved in the Response to High Temperatures

The selection of tolerant varieties is a powerful strategy to ensure highly stable yield under elevated temperatures. In this paper, we report the phenotypic and genotypic characterization of 10 tomato landraces to identify the best performing under high temperatures. The phenotyping of five yield-related traits allowed us to select one genotype that exhibits highly stable yield performances in different environmental conditions. Moreover, a Genotyping-by-Sequencing approach allowed us to explore the genetic variability of the tested genotypes. The high and stable yielding landrace E42 was the most polymorphic one, with ~49% and ~47% private SNPs and InDels, respectively. The effect of 26,113 mutations on proteins’ structure was investigated and it was discovered that 37 had a high impact on the structure of 34 proteins of which some are putatively involved in responses to high temperatures. Additionally, 129 polymorphic sequences aligned against tomato wild species genomes revealed the presence in the genotype E42 of several introgressed regions deriving from S. pimpinellifolium. The position on the tomato map of genes affected by moderate and high impact mutations was also compared with that of known markers/QTLs (Quantitative Trait Loci) associated with reproductive and yield-related traits. The candidate genes/QTLs regulating heat tolerance in the selected landrace E42 could be further investigated to better understand the genetic mechanisms controlling traits for high and stable yield trait under high temperatures.

Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies

High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identification of single-nucleotide polymorphisms (SNPs) associated with economically important traits. Choosing a cost-effective genotyping method for crop GWAS requires careful examination of several aspects, namely, the purpose and the scale of the study, crop-specific genomic features, and technical and economic matters associated with each genotyping option. Once genotypic data have been obtained, quality control (QC) procedures must be applied to avoid bias and false signals in genotype–phenotype association tests. QC for human GWAS has been extensively reviewed; however, QC for crop GWAS may require different actions, depending on the GWAS population type. Here, we review most popular genotyping methods based on next-generation sequencing (NGS) and array hybridization, and report observations that should guide the investigator in the choice of the genotyping method for crop GWAS. We provide recommendations to perform QC in crop species, and deliver an overview of bioinformatics tools that can be used to accomplish all needed tasks. Overall, this work aims to provide guidelines to harmonize those procedures leading to SNP datasets ready for crop GWAS.

Improving the Health Benefits of Snap Bean: Genome-Wide Association Studies of Total Phenolic Content

Snap beans are a significant source of micronutrients in the human diet. Among the micronutrients present in snap beans are phenolic compounds with known beneficial effects on human health, potentially via their metabolism by the gut-associated microbiome. The genetic pathways leading to the production of phenolics in snap bean pods remain uncertain. In this study, we quantified the level of total phenolic content (TPC) in the Bean Coordinated Agriculture Program (CAP) snap bean diversity panel of 149 accessions. The panel was characterized spectrophotometrically for phenolic content with a Folin-Ciocalteu colorimetric assay. Flower, seed and pod color were also quantified, as red, purple, yellow and brown colors are associated with anthocyanins and flavonols in common bean. Genotyping was performed through an Illumina Infinium Genechip BARCBEAN6K_3 single nucleotide polymorphism (SNP) array. Genome-Wide Association Studies (GWAS) analysis identified 11 quantitative trait nucleotides (QTN) associated with TPC. An SNP was identified for TPC on Pv07 located near the P gene, which is a major switch in the flavonoid biosynthetic pathway. Candidate genes were identified for seven of the 11 TPC QTN. Five regulatory genes were identified and represent novel sources of variation for exploitation in developing snap beans with higher phenolic levels for greater health benefits to the consumer.

Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis

BACKGROUND

The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although an integrated analysis of these collections in a global diversity perspective has not been possible. In this study, a sample of Indian collections together with a selection of world-wide cultivars to analyze the genetic diversity structure based on Genotype by Sequence data.

RESULTS

A set of 6158 informative Single Nucleotide Polymorphism (SNP) in 175 melon accessions was generated. Melon germplasm could be classified into six major groups, in concordance with horticultural groups. Indian group was in the center of the diversity plot, with the highest genetic diversity. No strict genetic differentiation between wild and cultivated accessions was appreciated in this group. Genomic regions likely involved in the process of diversification were also found. Interestingly, some SNPs differentiating inodorus and cantalupensis groups are linked to Quantitiative Trait Loci involved in ripening behavior (a major characteristic that differentiate those groups). Linkage disequilibrium was found to be low (17 kb), with more rapid decay in euchromatic (8 kb) than heterochromatic (30 kb) regions, demonstrating that recombination events do occur within heterochromatn, although at lower frequency than in euchromatin. Concomitantly, haplotype blocks were relatively small (59 kb). Some of those haplotype blocks were found fixed in different melon groups, being therefore candidate regions that are involved in the diversification of melon cultivars.

CONCLUSIONS

The results support the hypothesis that India is the primary center of diversity of melon, Occidental and Far-East cultivars have been developed by divergent selection. Indian germplasm is genetically distinct from African germplasm, supporting independent domestication events. The current set of traditional Indian accessions may be considered as a population rather than a standard collection of fixed landraces with high intercrossing between cultivated and wild melons.

New insights in the control of antioxidants accumulation in tomato by transcriptomic analyses of genotypes exhibiting contrasting levels of fruit metabolites

Background

Tomato is an economically important crop with fruits that are a significant source of bioactive compounds such as ascorbic acid and phenolics. Nowadays, the majority of the enzymes of the biosynthetic pathways and of the structural genes controlling the production and the accumulation of antioxidants in plants are known; however, the mechanisms that regulate the expression of these genes are yet to be investigated. Here, we analyzed the transcriptomic changes occurring during ripening in the fruits of two tomato cultivars (E1 and E115), characterized by a different accumulation of antioxidants, in order to identify candidate genes potentially involved in the biosynthesis of ascorbic acid and phenylpropanoids.

Results

RNA sequencing analyses allowed identifying several structural and regulator genes putatively involved in ascorbate and phenylpropanoids biosynthesis in tomato fruits. Furthermore, transcription factors that may control antioxidants biosynthesis were identified through a weighted gene co-expression network analysis (WGCNA). Results obtained by RNA-seq and WGCNA analyses were further confirmed by RT-qPCR carried out at different ripening stages on ten cultivated tomato genotypes that accumulate different amount of bioactive compounds in the fruit. These analyses allowed us to identify one pectin methylesterase, which may affect the release of pectin-derived D-Galacturonic acid as metabolic precursor of ascorbate biosynthesis. Results reported in the present work allowed also identifying one L-ascorbate oxidase, which may favor the accumulation of reduced ascorbate in tomato fruits. Finally, the pivotal role of the enzymes chalcone synthases (CHS) in controlling the accumulation of phenolic compounds in cultivated tomato genotypes and the transcriptional control of the CHS genes exerted by Myb12 were confirmed.

Conclusions

By using transcriptomic analyses, candidate genes encoding transcription factors and structural genes were identified that may be involved in the accumulation of ascorbic acid and phenylpropanoids in tomato fruits of cultivated genotypes. These analyses provided novel insights into the molecular mechanisms controlling antioxidants accumulation in ripening tomato fruits. The structural genes and regulators here identified could also be used as efficient genetic markers for selecting high antioxidants tomato cultivars.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5428-4) contains supplementary material, which is available to authorized users.

Exploiting Genetic and Genomic Resources to Enhance Heat-Tolerance in Tomatoes

High temperature is one of the most detrimental abiotic stresses in tomatoes. Many studies highlighted that even small increases in temperature can alter the plant reproductive system, causing a significant reduction in tomato yield. The aim of this study was to exploit the phenotypic and genomic variations of a tomato landrace collection grown at high temperatures. Fifteen genotypes were selected as the best performing in two experimental fields. The selection was based on six yield-related traits, including flower earliness, number of flowers per inflorescence, fruit set, number of fruit per plant, fruit weight and yield per plant. In order to identify markers targeting traits that could be highly influenced by adverse climate conditions, such as flowering and fruit setting, an association mapping approach was undertaken exploiting a tomato high-throughput genomic array. The phenotypic variability observed allowed us to identify a total of 15 common markers associated with the studied traits. In particular, the most relevant associations co-localized with genes involved in the floral structure development, such as the style2.1 gene, or with genes directly involved in the response to abiotic stresses. These promising candidate genes will be functionally validated and transferred to a cultivated tomato to improve its performance under high temperatures.

Trait discovery and editing in tomato

Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.

Association mapping unveils favorable alleles for grain iron and zinc concentrations in lentil (Lens culinaris subsp. culinaris)

Lentil is a major cool-season grain legume grown in South Asia, West Asia, and North Africa. Populations in developing countries of these regions have micronutrient deficiencies; therefore, breeding programs should focus more on improving the micronutrient content of food. In the present study, a set of 96 diverse germplasm lines were evaluated at three different locations in India to examine the variation in iron (Fe) and zinc (Zn) concentration and identify simple sequence repeat (SSR) markers that associate with the genetic variation. The genetic variation among genotypes of the association mapping (AM) panel was characterized using a genetic distance-based and a general model-based clustering method. The model-based analysis identified six subpopulations, which satisfactorily explained the genetic structure of the AM panel. AM analysis identified three SSRs (PBALC 13, PBALC 206, and GLLC 563) associated with grain Fe concentration explaining 9% to 11% of phenotypic variation and four SSRs (PBALC 353, SSR 317-1, PLC 62, and PBALC 217) were associated with grain Zn concentration explaining 14%, to 21% of phenotypic variation. These identified SSRs exhibited consistent performance across locations. These candidate SSRs can be used in marker-assisted genetic improvement for developing Fe and Zn fortified lentil varieties. Favorable alleles and promising genotypes identified in this study can be utilized for lentil biofortification.

Genetic dissection of adventitious shoot regeneration in roses by employing genome-wide association studies

We analysed the capacity to regenerate adventitious shoots in 96 rose genotypes and found 88 SNP markers associated with QTLs, some of which are derived from candidate genes for shoot regeneration. In an association panel of 96 rose genotypes previously analysed for petal colour, we conducted a genome-wide association study on the capacity of leaf petioles for direct shoot regeneration. Shoot regeneration rate and shoot ratio (number of shoots/total number of explants) were used as phenotypic descriptors for regeneration capacity. Two independent experiments were carried out with six replicates of ten explants each. We found significant variation between the genotypes ranging from 0.88 to 88.33% for the regeneration rate and from 0.008 to 1.2 for the shoot ratio, which exceeded the rates reported so far. Furthermore, we found 88 SNP markers associated with either the shoot regeneration rate or the shoot ratio. In this association analysis, we found 12 SNP markers from ESTs (expressed sequence tags) matching known candidate genes that are involved in shoot morphogenesis. The best markers explained more than 51% of the variance in the shoot regeneration rate and more than 0.65 of the variance in the shoot regeneration ratio between the homozygote marker classes. The genes underlying some of the best markers such as a GT-transcription factor or an LRR receptor-like protein kinase are novel candidate genes putatively involved in the observed phenotypic differences. The associated markers were mapped to the closely related genome of Fragaria vesca and revealed many distinct clusters, which also comprised the known candidate genes that functioned in the organogenesis of plant shoots. However, the validation of candidate genes and their functional relationship to shoot regeneration require further analysis in independent rose populations and functional analyses.

Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato

Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F₂ population derived from a cross between two commercial F₁ cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F₁ cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F₂ plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers

Tomato (Solanum lycopersicum) fruit weight (FW), soluble solid content (SSC), fruit shape and fruit color are crucial for yield, quality and consumer acceptability. In this study, a 192 accessions tomato association panel comprising a mixture of wild species, cherry tomato, landraces, and modern varieties collected worldwide was genotyped with 547 InDel markers evenly distributed on 12 chromosomes and scored for FW, SSC, fruit shape index (FSI), and color parameters over 2 years with three replications each year. The association panel was sorted into two subpopulations. Linkage disequilibrium ranged from 3.0 to 47.2 Mb across 12 chromosomes. A set of 102 markers significantly (p < 1.19-1.30 × 10-4) associated with SSC, FW, fruit shape, and fruit color was identified on 11 of the 12 chromosomes using a mixed linear model. The associations were compared with the known gene/QTLs for the same traits. Genetic analysis using F2 populations detected 14 and 4 markers significantly (p < 0.05) associated with SSC and FW, respectively. Some loci were commonly detected by both association and linkage analysis. Particularly, one novel locus for FW on chromosome 4 detected by association analysis was also identified in F2 populations. The results demonstrated that association mapping using limited number of InDel markers and a relatively small population could not only complement and enhance previous QTL information, but also identify novel loci for marker-assisted selection of fruit traits in tomato.

Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway

Tomato (Solanum lycopersicum L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent's SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene, cis- and trans-lycopene. We targeted 230 kb of genomic regions including all exons and regulatory regions and observed ~40% of on-target capture. We found ample genetic variation among all the genotypes under study and generated an extensive catalog of SNPs/InDels located in both genic and regulatory regions. SNPs/InDels were also classified based on genomic location and putative biological effect. With our work we contributed to the identification of allelic variations possibly underpinning a key agronomic trait in tomato. Results from this study can be exploited for the promotion of novel studies on tomato bio-fortification as well as of breeding programs related to carotenoid accumulation in fruits.

Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape

Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards. Furthermore, progress has largely been limited to simple agronomic traits easy-to-observe, whereas the vast majority of quality attributes, specifically those relating to flavor and nutrition, are complex and have mostly been neglected. Fortunately, wild germplasm, which is used for resistance against/tolerance of environmental stresses (including pathogens), is still available and harbors significant genetic variation for taste and health-promoting traits. Similarly, heirloom/traditional varieties could be used to identify which genes contribute to flavor and health quality and, at the same time, serve as a good source of the best alleles for organoleptic quality improvement. Grape (Vitis vinifera L.) and tomato (Solanum lycopersicum L.) produce fleshy, berry-type fruits, among the most consumed in the world. Both have undergone important domestication and selection processes, that have dramatically reduced their genetic variability, and strongly standardized fruit traits. Moreover, more and more consumers are asking for sustainable production, incompatible with the wide range of chemical inputs. In the present paper, we review the genetic resources available to tomato/grape breeders, and the recent technological progresses that facilitate the identification of genes/alleles of interest within the natural or generated variability gene pool. These technologies include omics, high-throughput phenotyping/phenomics, and biotech approaches. Our review also covers a range of technologies used to transfer to tomato and grape those alleles considered of interest for fruit quality. These include traditional breeding, TILLING (Targeting Induced Local Lesions in Genomes), genetic engineering, or NPBT (New Plant Breeding Technologies). Altogether, the combined exploitation of genetic variability and innovative biotechnological tools may facilitate breeders to improve fruit quality tacking more into account the consumer standards and the needs to move forward into more sustainable farming practices.

Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP

The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of targeted genomic regions. Here, we present SUPER-CAP, a bioinformatics web tool aimed at handling Sequence Capture data, fine calculating the allele frequency of variations and building genotype-specific sequence of captured genes. The dataset used to develop this in silico strategy consists of 378 loci and related regulative regions in a collection of 44 tomato landraces. About 14,000 high-quality variants were identified. The high depth (>40×) of coverage and adopting the correct filtering criteria allowed identification of about 4,000 rare variants and 10 genes with a different copy number variation. We also show that the tool is capable to reconstruct genotype-specific sequences for each genotype by using the detected variants. This allows evaluating the combined effect of multiple variants in the same protein. The architecture and functionality of SUPER-CAP makes the software appropriate for a broad set of analyses including SNP discovery and mining. Its functionality, together with the capability to process large data sets and efficient detection of sequence variation, makes SUPER-CAP a valuable bioinformatics tool for genomics and breeding purposes.

New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype

Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies. These strategies are complementary in most instances, and indeed, one is often used to confirm the results of the other. Despite significant advances, an emerging trend is that the outcome and efficiency of the different approaches depend greatly on the genetic architecture of the trait in the genetic material under study.

Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers

The potato (Solanum tuberosum L.) is the fourth most important crop food in the world and Colombia has one of the most important collections of potato germplasm in the world (the Colombian Central Collection-CCC). Little is known about its potential as a source of genetic diversity for molecular breeding programs. In this study, we analyzed 809 Andigenum group accessions from the CCC using 5968 SNPs to determine: 1) the genetic diversity and population structure of the Andigenum germplasm and 2) the usefulness of this collection to map qualitative traits across the potato genome. The genetic structure analysis based on principal components, cluster analyses, and Bayesian inference revealed that the CCC can be subdivided into two main groups associated with their ploidy level: Phureja (diploid) and Andigena (tetraploid). The Andigena population was more genetically diverse but less genetically substructured than the Phureja population (three vs. five subpopulations, respectively). The association mapping analysis of qualitative morphological data using 4666 SNPs showed 23 markers significantly associated with nine morphological traits. The present study showed that the CCC is a highly diverse germplasm collection genetically and phenotypically, useful to implement association mapping in order to identify genes related to traits of interest and to assist future potato genetic breeding programs.

Carotenoids in fresh and processed tomato (Solanum lycopersicum) fruits protect cells from oxidative stress injury

BACKGROUND

Lipophilic antioxidants in tomato (Solanum lycopersicum) fruits exert important functions in reducing the risk of human diseases. Here the effect of thermal processing on the antioxidant activity of lipophilic extracts from the commercial tomato hybrid 'Zebrino' was analysed. Carotenoid content and lipophilic antioxidant activity were determined and the ability of tomato extracts in rescuing cells from oxidative stress was assessed.

RESULTS

Lipophilic antioxidant activity was completely retained after heat treatment and extracts were able to mitigate the detrimental effect induced by oxidative stress on different cell lines. Lycopene alone was able to rescue cells from oxidative stress, even if to a lower extent compared with tomato extracts. These results were probably due to the synergistic effect of tomato compounds in protecting cells from oxidative stress injury.

CONCLUSION

The current study provides valuable insights into the health effect of the dietary carotenoids present in fresh and processed tomato fruits. © 2016 Society of Chemical Industry.

Genetic Transformation and Genomic Resources for Next-Generation Precise Genome Engineering in Vegetable Crops

In the frame of modern agriculture facing the predicted increase of population and general environmental changes, the securement of high quality food remains a major challenge to deal with. Vegetable crops include a large number of species, characterized by multiple geographical origins, large genetic variability and diverse reproductive features. Due to their nutritional value, they have an important place in human diet. In recent years, many crop genomes have been sequenced permitting the identification of genes and superior alleles associated with desirable traits. Furthermore, innovative biotechnological approaches allow to take a step forward towards the development of new improved cultivars harboring precise genome modifications. Sequence-based knowledge coupled with advanced biotechnologies is supporting the widespread application of new plant breeding techniques to enhance the success in modification and transfer of useful alleles into target varieties. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system, zinc-finger nucleases, and transcription activator-like effector nucleases represent the main methods available for plant genome engineering through targeted modifications. Such technologies, however, require efficient transformation protocols as well as extensive genomic resources and accurate knowledge before they can be efficiently exploited in practical breeding programs. In this review, we revise the state of the art in relation to availability of such scientific and technological resources in various groups of vegetables, describe genome editing results obtained so far and discuss the implications for future applications.

Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools

BACKGROUND

Melon (Cucumis melo L.) is one of the most important horticultural species, which includes several taxonomic groups. With the advent of next-generation sequencing, single nucleotide polymorphism (SNP) markers are widely used in the study of genetic diversity and genomics.

RESULTS

We report the first successful application of genotyping-by-sequencing (GBS) technology in melon. We detected 25,422 SNPs by the analysis of 72 accessions collected in Apulia, a secondary centre of diversity in Southern Italy. Analyses of genetic structure, principal components, and hierarchical clustering support the identification of three distinct subpopulations. One of them includes accessions known with the folk name of 'carosello', referable to the chate taxonomic group. This is one of the oldest domesticated forms of C. melo, once widespread in Europe and now exposed to the risk of genetic erosion. The second subpopulation contains landraces of 'barattiere', a regional vegetable production that was never characterized at the DNA level and we show was erroneously considered another form of chate melon. The third subpopulation includes genotypes of winter melon (C. melo var. inodorus). Genetic analysis within each subpopulation revealed patterns of diversity associated with fruit phenotype and geographical origin. We used SNP data to describe, for each subpopulation, the average linkage disequilibrium (LD) decay, and to highlight genomic regions possibly resulting from directional selection and associated with phenotypic variation.

CONCLUSIONS

We used GBS to characterize patterns of genetic diversity and genomic features within C. melo. We provide useful information to preserve endangered gene pools and to guide the use of germplasm in breeding. Finally, our findings lay a foundation for molecular breeding approaches and the identification of genes underlying phenotypic traits.

Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice

Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs. Therefore, combined use of QTL and association mapping strategies can provide advantages associated with both these methods. In the current study, we utilized meta-analysis approach to identify metaQTLs associated with grain size/weight in diverse Indian indica and aromatic rice accessions. Subsequently, attempt has been made to narrow-down identified grain size/weight metaQTLs through individual SNP- as well as haplotype-based regional association analysis. The study identified six different metaQTL regions, three of which were successfully revalidated, and substantially scaled-down along with GS3 QTL interval (positive control) by regional association analysis. Consequently, two potential candidate genes within two reduced metaQTLs were identified based on their differential expression profiles in different tissues/stages of rice accessions during seed development. The developed strategy has broader practical utility for rapid delineation of candidate genes and natural alleles underlying QTLs associated with complex agronomic traits in rice as well as major crop plants enriched with useful genetic and genomic information.

The historical role of species from the Solanaceae plant family in genetic research

This article evaluates the main contributions of tomato, tobacco, petunia, potato, pepper and eggplant to classical and molecular plant genetics and genomics since the beginning of the twentieth century. Species from the Solanaceae family form integral parts of human civilizations as food sources and drugs since thousands of years, and, more recently, as ornamentals. Some Solanaceous species were subjects of classical and molecular genetic research over the last 100 years. The tomato was one of the principal models in twentieth century classical genetics and a pacemaker of genome analysis in plants including molecular linkage maps, positional cloning of disease resistance genes and quantitative trait loci (QTL). Besides that, tomato is the model for the genetics of fruit development and composition. Tobacco was the major model used to establish the principals and methods of plant somatic cell genetics including in vitro propagation of cells and tissues, totipotency of somatic cells, doubled haploid production and genetic transformation. Petunia was a model for elucidating the biochemical and genetic basis of flower color and development. The cultivated potato is the economically most important Solanaceous plant and ranks third after wheat and rice as one of the world's great food crops. Potato is the model for studying the genetic basis of tuber development. Molecular genetics and genomics of potato, in particular association genetics, made valuable contributions to the genetic dissection of complex agronomic traits and the development of diagnostic markers for breeding applications. Pepper and eggplant are horticultural crops of worldwide relevance. Genetic and genomic research in pepper and eggplant mostly followed the tomato model. Comparative genome analysis of tomato, potato, pepper and eggplant contributed to the understanding of plant genome evolution.

Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.

Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity

Domestication of tomato has resulted in large diversity in fruit phenotypes. An intensive phenotyping of 127 tomato accessions from 20 countries revealed extensive morphological diversity in fruit traits. The diversity in fruit traits clustered the accessions into nine classes and identified certain promising lines having desirable traits pertaining to total soluble salts (TSS), carotenoids, ripening index, weight and shape. Factor analysis of the morphometric data from Tomato Analyzer showed that the fruit shape is a complex trait shared by several factors. The 100% variance between round and flat fruit shapes was explained by one discriminant function having a canonical correlation of 0.874 by stepwise discriminant analysis. A set of 10 genes (ACS2, COP1, CYC-B, RIN, MSH2, NAC-NOR, PHOT1, PHYA, PHYB and PSY1) involved in various plant developmental processes were screened for SNP polymorphism by EcoTILLING. The genetic diversity in these genes revealed a total of 36 non-synonymous and 18 synonymous changes leading to the identification of 28 haplotypes. The average frequency of polymorphism across the genes was 0.038/Kb. Significant negative Tajima’D statistic in two of the genes, ACS2 and PHOT1 indicated the presence of rare alleles in low frequency. Our study indicates that while there is low polymorphic diversity in the genes regulating plant development, the population shows wider phenotype diversity. Nonetheless, morphological and genetic diversity of the present collection can be further exploited as potential resources in future.