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

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.

In Vitro Cultivation and Ginsenosides Accumulation in Panax ginseng: A Review

The use of in vitro tissue culture for herbal medicines has been recognized as a valuable source of botanical secondary metabolites. The tissue culture of ginseng species is used in the production of bioactive compounds such as phenolics, polysaccharides, and especially ginsenosides, which are utilized in the food, cosmetics, and pharmaceutical industries. This review paper focuses on the in vitro culture of Panax ginseng and accumulation of ginsenosides. In vitro culture has been applied to study organogenesis and biomass culture, and is involved in direct organogenesis for rooting and shooting from explants and in indirect morphogenesis for somatic embryogenesis via the callus, which is a mass of disorganized cells. Biomass production was conducted with different types of tissue cultures, such as adventitious roots, cell suspension, and hairy roots, and subsequently on a large scale in a bioreactor. This review provides the cumulative knowledge of biotechnological methods to increase the ginsenoside resources of P. ginseng. In addition, ginsenosides are summarized at enhanced levels of activity and content with elicitor treatment, together with perspectives of new breeding tools which can be developed in P. ginseng in the future.

QTL Mapping and Genome-Wide Association Study Reveal Genetic Loci and Candidate Genes Related to Soluble Solids Content in Melon

Melon (Cucumis melo L.) is an economically important Cucurbitaceae crop grown around the globe. The sweetness of melon is a significant factor in fruit quality and consumer appeal, and the soluble solids content (SSC) is a key index of melon sweetness. In this study, 146 recombinant inbred lines (RILs) derived from two oriental melon materials with different levels of sweetness containing 1427 bin markers, and 213 melon accessions containing 1,681,775 single nucleotide polymorphism (SNP) markers were used to identify genomic regions influencing SSC. Linkage mapping detected 10 quantitative trait loci (QTLs) distributed on six chromosomes, seven of which were overlapped with the reported QTLs. A total of 211 significant SNPs were identified by genome-wide association study (GWAS), 138 of which overlapped with the reported QTLs. Two new stable, co-localized regions on chromosome 3 were identified by QTL mapping and GWAS across multiple environments, which explained large phenotypic variance. Five candidate genes related to SSC were identified by QTL mapping, GWAS, and qRT-PCR, two of which were involved in hydrolysis of raffinose and sucrose located in the new stable loci. The other three candidate genes were involved in raffinose synthesis, sugar transport, and production of substrate for sugar synthesis. The genomic regions and candidate genes will be helpful for molecular breeding programs and elucidating the mechanisms of sugar accumulation.

Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum

BACKGROUND

Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs.

METHODS

In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species, Geodorum eulophioides (endemic and endangered in Southwest China), and a widespread species, G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level.

RESULTS

The results showed that the nucleotide diversity and heterozygosity of G. eulophioides were significantly higher than those of G. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a few G. eulophioides individuals were detected with genetic components from G. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat of G. eulophioides invasion by G. densiflorum under anthropogenic disturbance may be the main factor causing interspecific hybridization.

CONCLUSIONS

Therefore, reducing or avoiding habitat disturbance is a key measure to protect the G. eulophioides populations. This study provides valuable information for future conservation programs for narrowly distributed species.

Genetic diversity analysis and variety identification using SSR and SNP markers in melon

Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R² = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of 'Jingyu' and 'Jingmi' series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon.

Spanish Melon Landraces: Revealing Useful Diversity by Genomic, Morphological, and Metabolomic Analysis

Spain is a secondary centre of the diversification of the melon (Cucumis melo L.), with high diversity represented in highly appreciated landraces belonging to the Flexuosus and Ibericus groups. A collection of 47 accessions of Flexuosus, Chate, Piel de Sapo, Tendral, Amarillo, Blanco, and Rochet was analysed using a genotyping-by-sequencing (GBS) approach. A total of 66,971 quality SNPs were identified. Genetic analysis differentiated Ibericus accessions and exotic materials (Ameri, Momordica, Kachri, and Agrestis), while Flexuous accessions shared ancestry between them. Within the Ibericus group, no clear genomic distinction could be identified for the different landraces evaluated, with accessions of different landraces showing high genetic similarity. The morphological characterization confirmed that the external colour and fruit shape had been used as recognition patterns for Spanish melon landraces, but variability within a landrace exists. Differences were found in the sugars and acid and volatile profiles of the materials. Flexuosus and Chate melons at the immature commercial stage accumulated malic acid and low levels of hexoses, while Ibericus melons accumulated high contents of sucrose and citric acid. Specific trends could be identified in the Ibericus landraces. Tendral accumulated low levels of sugars and citric acid and high of malic acid, maintaining higher firmness, Rochet reached higher levels of sugars, and Amarillo tended to lower malic acid contents. Interestingly, high variability was found within landraces for the acidic profile, offering possibilities to alter taste tinges. The main volatile organic compounds (VOCs) in Flexuosus and Chate were aldehydes and alcohols, with clear differences between both groups. In the Ibericus landraces, general trends for VOC accumulation could be identified, but, again, a high level of variation exists. This situation highlights the necessity to develop depuration programs to promote on-farm in situ conservation and, at the same time, offers opportunities to establish new breeding program targets and to take advantage of these sources of variation.

Recent status of Genotyping by Sequencing (GBS) Technology in cucumber (Cucumis sativus L.): a review

Current and advanced breeding tools are being used to improve economically important horticultural crops to meet the consumers' needs and preferences. Genotyping-by-sequencing (GBS) is an extremely useful tool in the investigation and analysis of the genetic diversity of different cultivars. Based on a broad range of genetic backgrounds like single nucleotide polymorphism (SNPs), GBS is known as a novel technique to facilitate the detection of quantitative trait loci (QTL) regions robustly linked with interested traits compared to genome-wide association study (GWAS) and QTL. GBS has gained popularity among breeders in recent years and it is also employed in cucumber breeding programs. Cucumbers (C. sativus L.) are monoecious, gynoecious and some of them are parthenocarpic species. Cucumber is one of the most economical and essential crops in the Cucurbitaceae family. For time immemorial, cucumber has been produced and consumed all over the world like other cucurbits. To a large extent, cultivated cucurbits are beneficial to human health for providing necessary minerals and fibers.Therefore, this review portrays the current status of advances made by using GBS and its combination with other tools in various studies of cucumber such as the use of GBS and single nucleotide polymorphism (SNP) markers, GBS and GWAS, also with QTL and marker-assisted selection (MAS) are applied to display and detect explicit genetic architecture complex traits in crops and chromosome rearrangements.Cucumber breeding programs have undoubtedly benefited from genotyping-by-sequencing. Using the GBS method, research discovered lots of new candidate genes that control various traits including spine color, fruit stalk-end color, and disease resistance in cucumber lines.

Nutraceutical Profile of "Carosello" (Cucumis melo L.) Grown in an Out-of-Season Cycle under LEDs

The world population is projected to increase to 9.9 billion by 2050 and, to ensure food security and quality, agriculture must sustainably multiply production, increase the nutritional value of fruit and vegetables, and preserve genetic variability. In this work, an Apulian landrace of Cucumis melo L. called "Carosello leccese" was grown in a greenhouse with a soilless technique under light-emitting diodes (LEDs) used as supplementary light system. The obtained results showed that "Carosello leccese" contains up to 71.0 mg·g-1 dried weight (DW) of potassium and several bioactive compounds important for human health such as methyl gallate (35.58 µg·g-1 DW), α-tocopherol (10.12 µg·g-1 DW), and β-carotene (up to 9.29 µg·g-1 DW under LEDs). In fact, methyl gallate has antioxidative and antiviral effects in vitro and in vivo, tocopherols are well recognized for their effective inhibition of lipid oxidation in foods and biological systems and carotenoids are known to be very efficient physical and chemical quenchers of singlet oxygen. Finally, it was demonstrated that the LEDs' supplementary light did not negatively influence the biochemical profile of the peponids, confirming that it can be considered a valid technique to enhance horticultural production without reducing the content of the bioactive compounds of the fruits.

Genome-wide diversity analysis to infer population structure and linkage disequilibrium among Colombian coconut germplasm

Genetic diversity and relatedness of accessions for coconut growing in Colombia was unknown until this study. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) with the goal of analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diverse coconut panel consisting of 112 coconut accessions from the Atlantic and Pacific coasts of Colombia. A comprehensive catalog of approximately 40,000 SNPs with a minor allele frequency (MAF) of > 0.05 is presented. A total of 40,614 SNPs were found but only 19,414 anchored to chromosomes. Of these, 10,338 and 4606 were exclusive to the Atlantic and Pacific gene pools, respectively, and 3432 SNPs could differentiate both gene pools. A filtered subset of unlinked and anchored SNPs (1271) showed a population structure at K = 4, separating accessions from the Pacific and Atlantic coasts that can also be distinguished by palm height, as found in previous studies. The Pacific groups had a slow LD decay, low Fixation Index (Fst) and low nucleotide diversity (π), while the Atlantic group had slightly higher genetic diversity and faster LD decay. Genome-wide diversity analyses are of importance to promote germplasm conservation and breeding programs aimed at developing new cultivars better adapted to the region.

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history

Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections - a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding.

Enhancement of a Landrace of Carosello (Unripe Melon) through the Use of Light-Emitting Diodes (LED) and Nutritional Characterization of the Fruit Placenta

Landraces of ‘Carosello’ (Cucumis melo L.) are a typical expression of Apulia’s agro-biodiversity and are consumed in the same way as cucumbers. The aim of this research was to valorize the cultivation of a local variety of ‘Carosello’, extending the cultivation period and valorizing a part of the fruits that are generally wasted (endosperm). To accomplish this, a local variety called ‘Carosello leccese’ was grown in a greenhouse during the fall season under red + blue and red + blue + far red light-emitting diodes (LED) interlight. Yield, morphology, color and biochemical composition of the external and internal part of the fruit were evaluated. Although yield increased by 26% under supplemental light, the fruit quality was not influenced by LED application. However, the exocarp was greener (chlorophylls) and more yellow (carotenoids) than the mesocarp. Finally, the endosperm, which is the part of the fruit that is generally wasted, showed the highest polyphenols content, proving to be an important source of nutraceutical compounds. Therefore, it was demonstrated that the nutritional value of the endosperm is comparable or higher than the external part of the fruit, but further studies will be necessary to valorize it from a culinary perspective.

Extraseasonal Production in a Soilless System and Characterisation of Landraces of Carosello and Barattiere (Cucumis melo L.)

Barattiere and Carosello are typical melon (Cucumis melo L.) landraces of Puglia’s (Southern Italy) biodiversity. Their unripe fruits are locally consumed as an alternative to cucumbers (C. sativus L.) and are appreciated for their qualitative profile. Nevertheless, they are underutilized crops. For the high variability and confusing denominations, a morphological characterization is essential to discriminate and valorise landraces; additionally, it is fundamental to implement the agronomic technique to allow the cultivation outside the natural growth period (summer) by soilless cultivation. Two genotypes of Barattiere (‘Allungato’ and ‘Tondo’), two of Carosello (‘Scopatizzo’ and ‘Tomentoso’ (CAT)) and two of cucumber (‘Baby Star’ and ‘Modan’ hybrids) were vertically grown in the winter–spring period in a rockwool soilless system in a glasshouse with supplemental light. Landraces were characterized by morpho-physiological descriptors of melon; fruit biometrics and colour were analysed for all genotypes; productive parameters, leaf fluorescence, and chlorophyll content were measured. Genotypes varied in seeds, stem, leaf, fruit traits and they were andromonoecious; Carosello flowered earlier and produced more than Barattiere; CAT fruits were hairy and elongate, while other genotypes tended to rounder and glabrous fruits. Although landraces grew slower than cucumbers, both produced marketable fruits and the production of Carosello was comparable to cucumbers. In conclusion, Barattiere and Carosello have a productive potential and one vertically trained stem in a soilless system is appropriate for their extra-seasonal production.

Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing

Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r² = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.

QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps

BACKGROUND

Melon is a very important horticultural crop produced worldwide with high phenotypic diversity. Fruit size is among the most important domestication and differentiation traits in melon. The molecular mechanisms of fruit size in melon are largely unknown.

RESULTS

Two high-density genetic maps were constructed by whole-genome resequencing with two F₂ segregating populations (WAP and MAP) derived from two crosses (cultivated agrestis × wild agrestis and cultivated melo × cultivated agrestis). We obtained 1,871,671 and 1,976,589 high quality SNPs that show differences between parents in WAP and MAP. A total of 5138 and 5839 recombination events generated 954 bins in WAP and 1027 bins in MAP with the average size of 321.3 Kb and 301.4 Kb respectively. All bins were mapped onto 12 linkage groups in WAP and MAP. The total lengths of two linkage maps were 904.4 cM (WAP) and 874.5 cM (MAP), covering 86.6% and 87.4% of the melon genome. Two loci for fruit size were identified on chromosome 11 in WAP and chromosome 5 in MAP, respectively. An auxin response factor and a YABBY transcription factor were inferred to be the candidate genes for both loci.

CONCLUSION

The high-resolution genetic maps and QTLs analyses for fruit size described here will provide a better understanding the genetic basis of domestication and differentiation, and provide a valuable tool for map-based cloning and molecular marker assisted breeding.

Resequencing of 297 melon accessions reveals the genomic history of improvement and loci related to fruit traits in melon

Domestication and improvement are two important stages in crop evolution. Melon (Cucumis melo L.) is an important vegetable crop with wide phenotypic diversity in many horticultural traits, especially fruit size, flesh thickness and aroma, which are likely the results of long-term extensive selection during its evolution. However, selective signals in domestication and improvement stages for these remarkable variations remain unclear. We resequenced 297 wild, landrace and improved melon accessions and obtained 2 045 412 high-quality SNPs. Population structure and genetic diversity analyses revealed independent and two-step selections in two subspecies of melon: ssp. melo and ssp. agrestis during melon breeding. We detected 233 (~18.35 Mbp) and 159 (~17.71 Mbp) novel potential selective signals during the improvement stage in ssp. agrestis and spp. melo, respectively. Two alcohol acyltransferase genes (CmAATs) unique to the melon genome compared with other cucurbit crops may have undergone stronger selection in ssp. agrestis for the characteristic aroma as compared with other cucurbits. Genome-wide association analysis identified eight fruit size and seven flesh thickness signals overlapping with selective sweeps. Compared with thin-skinned ssp. agrestis, thick-skinned ssp. melo has undergone a stronger selection for thicker flesh. In most melon accessions, CmCLV3 has pleiotropic effects on carpel number and fruit shape. Findings from this study provide novel insights into melon crop evolution, and new tools to advance melon breeding.

Molecular confirmation of varietal status in bottle gourd (Lagenaria siceraria) using genotyping-by-sequencing

Bottle gourd (Lagenaria siceraria) is an important food, medicinal, and utilitarian crop with a large pan-tropical distribution. Two morphologically different types in the siceraria subspecies are sufficiently different to be considered as varieties, but they are assigned into different taxonomic ranks. Genotyping-by-sequencing (GBS) of 95 different accessions from the Nangui Abrogoua University collection was used to confirm the varietal status in bottle gourd. This analysis produced 22 575 single-nucleotide polymorphisms (SNPs). Cluster analyses conducted with 2250 (9.96%) SNPs distinctly separated hard-shelled from soft-shelled types. Analysis of 23 SNPs located in 11 genes coding for traits that differentiate the two types of gourds revealed that genes in the soft-shelled types had about 21% fewer SNPs than genes within hard-shelled gourds, but the latter had more non-synonymous SNPs. Cluster analyses conducted with the 23 SNPs fitted well with the structure defined by the 2250 SNPs, suggesting the implication of these SNPs in the varietal differentiation of bottle gourd. These nucleotide changes along with the genetic relationships between the accessions provide molecular proof supporting the status of two varieties. To prevent the confusion inherent in the use of synonyms and homonyms in bottle gourd, we suggest the terms hard-shelled and soft-shelled to designate, respectively, the varieties used as utensils and those grown for their edible seeds.

Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

Melon exhibits substantial natural variation especially in fruit ripening physiology, including both climacteric (ethylene-producing) and non-climacteric types. However, genomic mechanisms underlying such variation are not yet fully understood. Here, we report an Oxford Nanopore-based high-grade genome reference in the semi-climacteric cultivar Harukei-3 (378 Mb + 33,829 protein-coding genes), with an update of tissue-wide RNA-seq atlas in the Melonet-DB database. Comparison between Harukei-3 and DHL92, the first published melon genome, enabled identification of 24,758 one-to-one orthologue gene pairs, whereas others were candidates of copy number variation or presence/absence polymorphisms (PAPs). Further comparison based on 10 melon genome assemblies identified genome-wide PAPs of 415 retrotransposon Gag-like sequences. Of these, 160 showed fruit ripening-inducible expression, with 59.4% of the neighboring genes showing similar expression patterns (r > 0.8). Our results suggest that retrotransposons contributed to the modification of gene expression during diversification of melon genomes, and may affect fruit ripening-inducible gene expression.

Barattiere: An Italian Local Variety of Cucumis melo L. with Quality Traits between Melon and Cucumber

Barattiere, belonging to the Cucumis melo L. species, is a local variety of Puglia (Southern Italy), which is consumed as a vegetable at the immature stage, like cucumber. In this study, three Barattiere populations ('Monopoli', 'Carovigno' and 'Fasano') were evaluated for the main quality traits. All genotypes showed a very light green-yellow colour of flesh, without any difference regarding chlorophyll and carotenoid contents. Carovigno's Barattiere showed the highest values of dry weight (6.8 g 100 g^-1 fresh weight - FW), sugars (45 g kg^-1 FW), and sweetness index (7.3), while Monopoli's Barattiere showed the lowest total phenols content (21 mg kg^-1 FW). Fasano's Barattiere showed the highest content of Zn and Cu (2.3 and 0.3 mg kg^-1 FW, respectively), while 'Monopoli' showed the highest Ba content (0.3 mg kg^-1 FW) and the lowest Mg content (94 mg kg^-1 FW). No differences between populations were found concerning the content of Ca, K, Na, B, Mn, and Fe. In conclusion, the quality profile of Barattiere makes this local genotype interesting for its traits, and also suggests its consumption by people with specific dietary requirements.

Assessment of Genetic Diversity of the "Acquaviva Red Onion" (Allium cepa L.) Apulian Landrace

Onion (Allium cepa L.) is the second most important vegetable crop worldwide and is widely appreciated for its health benefits. Despite its significant economic importance and its value as functional food, onion has been poorly investigated with respect to its genetic diversity. Herein, we surveyed the genetic variation in the “Acquaviva red onion” (ARO), a landrace with a century-old history of cultivation in a small town in the province of Bari (Apulia, Southern of Italy). A set of 11 microsatellite markers were used to explore the genetic variation in a germplasm collection consisting of 13 ARO populations and three common commercial types. Analyses of genetic structure with parametric and non-parametric methods highlighted that the ARO represents a well-defined gene pool, clearly distinct from the Tropea and Montoro landraces with which it is often mistaken. In order to provide a description of bulbs, usually used for fresh consumption, soluble solid content and pungency were evaluated, showing higher sweetness in the ARO with respect to the two above mentioned landraces. Overall, the present study is useful for the future valorization of the ARO, which could be promoted through quality labels which could contribute to limit commercial frauds and improve the income of smallholders.

Genotyping by Sequencing of Cultivated Lentil (Lens culinaris Medik.) Highlights Population Structure in the Mediterranean Gene Pool Associated With Geographic Patterns and Phenotypic Variables

Cultivated lentil (Lens culinaris Medik.) is one of the oldest domesticated crops and one of the most important grain legumes worldwide. The Mediterranean Basin holds large part of lentil biodiversity; however, no genetic structure was defined within the Mediterranean gene pool. In this study, we used high-throughput genotyping by sequencing to resolve the genetic structure of the Mediterranean ex situ lentil collection held at the Italian National Research Council. Sequencing of a 188-plex genotyping-by-sequencing library and bioinformatics treatment of data yielded 6,693 single nucleotide polymorphisms. Analysis of nonredundant genotypes with nonparametric and parametric methods highlighted the occurrence of five highly differentiated genetic clusters. Clustering could be related to geographic patterns and phenotypic traits, indicating that post-domestication routes introducing cultivation in Mediterranean countries and selection were major forces shaping lentil population structure. The estimation of the fixation index F_ST at individual single nucleotide polymorphism loci allowed the identification of distinctive alleles across clusters, suggesting the possibility to set up molecular keys for the assignment of lentil germplasm to specific genetic groups. Finally, significant associations between markers and phenotypic data were identified. Overall, the results of this study are of major importance for lentil conservation genetics and breeding and provide insights on the lentil evolutionary history.

Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs

The olive is a fruit tree species with a century-old history of cultivation in theMediterranean basin. In Apulia (Southern Italy), the olive is of main social, cultural and economicimportance, and represents a hallmark of the rural landscape. However, olive cultivation in thisregion is threatened by the recent spread of the olive quick decline syndrome (OQDS) disease, thusthere is an urgent need to explore biodiversity and search for genetic sources of resistance. Herein,a genetic variation in Apulian olive germplasm was explored, as a first step to identify genotypeswith enhanced bio-agronomic traits, including resistance to OQDS. A preselected set of nuclearmicrosatellite markers allowed the acquisition of genotypic profiles, and to define geneticrelationships between Apulian germplasm and widespread cultivars. The analysis highlighted thebroad genetic variation in Apulian accessions and the presence of different unique genetic profiles.The results of this study lay a foundation for the organization of new breeding programs for olivegenetic improvement.

Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing

BACKGROUND

To efficiently protect and exploit germplasm resources for marker development and breeding purposes, we must accurately depict the features of the tea populations. This study focuses on the Camellia sinensis (C. sinensis) population and aims to (i) identify single nucleotide polymorphisms (SNPs) on the genome level, (ii) investigate the genetic diversity and population structure, and (iii) characterize the linkage disequilibrium (LD) pattern to facilitate next genome-wide association mapping and marker-assisted selection.

RESULTS

We collected 415 tea accessions from the Origin Center and analyzed the genetic diversity, population structure and LD pattern using the genotyping-by-sequencing (GBS) approach. A total of 79,016 high-quality SNPs were identified; the polymorphism information content (PIC) and genetic diversity (GD) based on these SNPs showed a higher level of genetic diversity in cultivated type than in wild type. The 415 accessions were clustered into three groups by STRUCTURE software and confirmed using principal component analyses (PCA)-wild type, cultivated type, and admixed wild type. However, unweighted pair group method with arithmetic mean (UPGMA) trees indicated the accessions should be grouped into more clusters. Further analyses identified four groups, the Pure Wild Type, Admixed Wild Type, ancient landraces and modern landraces using STRUCTURE, and the results were confirmed by PCA and UPGMA tree method. A higher level of genetic diversity was detected in ancient landraces and Admixed Wild Type than that in the Pure Wild Type and modern landraces. The highest differentiation was between the Pure Wild Type and modern landraces. A relatively fast LD decay with a short range (kb) was observed, and the LD decays of four inferred populations were different.

CONCLUSIONS

This study is, to our knowledge, the first population genetic analysis of tea germplasm from the Origin Center, Guizhou Plateau, using GBS. The LD pattern, population structure and genetic differentiation of the tea population revealed by our study will benefit further genetic studies, germplasm protection, and breeding.

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.

Microsatellite Markers Reveal Genetic Diversity and Relationships within a Melon Collection Mainly Comprising Asian Cultivated and Wild Germplasms

Melon, Cucumis melo L., is an important horticultural crop with abundant morphological variability, but the genetic diversity and relationships within wild and cultivated melons remain unclear to date. In this study, thick-skinned (TC) (cultivated subspecies melo), thin-skinned (TN) (cultivated subspecies agrestis), and wild accessions were analyzed for genetic diversity and relationships using 36 microsatellite markers. A total of 314 alleles were detected with a mean allelic number of 8.72 and polymorphism information content of 0.67. Cluster analysis of the accessions resulted in four distinct clusters (I, II, III, and IV) broadly matching with the TC, TN, and wild groups. Cluster I contained only two Indian wild accessions. Cluster II was consisted of 49 South Asian accessions, 34 wild accessions, and 15 TN accessions. Cluster III was a typical TC group including 51 multiorigin TC accessions and one wild accession. The remaining 88 accessions, including 75 TN accessions, 6 wild accessions, and 7 TC accessions, formed the cluster IV, and all the TN and wild accessions in this cluster were from China. These findings were also confirmed by Principal component analysis and STRUCTURE analysis. The South Asian subspecies agrestis accessions, wild and cultivated, had close genetic relationships with a distinctive genetic background. Chinese wild melons showed closeness to cultivated subspecies agrestis landraces and could be a return from the indigenous cultivated melons. The AMOVA and pairwise F statistics (F_ST) presented genetic differentiation among the three groups, with the strongest differentiation (F_ST = 0.380) between TC and TN melons. These results offer overall information on genetic diversity and affiliations within a variety of melon germplasms and favor efficient organization and utilization of these resources for the current breeding purpose.

QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map

BACKGROUND

Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools.

RESULTS

In order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: "Védrantais", from the cantalupensis group, and "Piel de Sapo", from the inodorus group. Both have desirable quality traits for the market, but their fruits differ in traits such as rind and flesh color, sugar content, ripening behavior, size and shape. We used a genotyping-by-sequencing strategy to construct a dense genetic map, which included around five thousand variants distributed in 824 bins. The RIL population was phenotyped for quality and morphology traits, and we mapped 33 stable QTLs involved in sugar and carotenoid content, fruit and seed morphology and major loci controlling external color of immature fruit and mottled rind. The median confidence interval of the QTLs was 942 kb, suggesting that the high density of the genetic map helped in increasing the mapping resolution. Some of these intervals contained less than a hundred annotated genes, and an integrative strategy combining gene expression and resequencing data enabled identification of candidate genes for some of these traits.

CONCLUSION

Several QTLs controlling fruit quality traits in melon were identified and delimited to narrow genomic intervals, using a RIL population and a GBS-based genetic map.

Biotechnological and Digital Revolution for Climate-Smart Plant Breeding

Climate change, associated with global warming, extreme weather events, and increasing incidence of weeds, pests and pathogens, is strongly influencing major cropping systems. In this challenging scenario, miscellaneous strategies are needed to expedite the rate of genetic gains with the purpose of developing novel varieties. Large plant breeding populations, efficient high-throughput technologies, big data management tools, and downstream biotechnology and molecular techniques are the pillars on which next generation breeding is based. In this review, we describe the toolbox the breeder has to face the challenges imposed by climate change, remark on the key role bioinformatics plays in the analysis and interpretation of big “omics” data, and acknowledge all the benefits that have been introduced into breeding strategies with the biotechnological and digital revolution.

GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars

Information on the distribution of genetic variation is essential to preserve olive germplasm from erosion and to recover alleles lost through selective breeding. In addition, knowledge on population structure and genotype-phenotype associations is crucial to support modern olive breeding programs that must respond to new environmental conditions imposed by climate change and novel biotic/abiotic stressors. To further our understanding of genetic variation in the olive, we performed genotype-by-sequencing on a panel of 94 Italian olive cultivars. A reference-based and a reference-independent SNP calling pipeline generated 22,088 and 8,088 high-quality SNPs, respectively. Both datasets were used to model population structure via parametric and non parametric clustering. Although the two pipelines yielded a 3-fold difference in the number of SNPs, both described wide genetic variability among our study panel and allowed individuals to be grouped based on fruit weight and the geographical area of cultivation. Multidimensional scaling analysis on identity-by-state allele-sharing values as well as inference of population mixtures from genome-wide allele frequency data corroborated the clustering pattern we observed. These findings allowed us to formulate hypotheses about geographical relationships of Italian olive cultivars and to confirm known and uncover novel cases of synonymy.

Genotyping-by-sequencing highlights patterns of genetic structure and domestication in artichoke and cardoon

Exploiting the biodiversity of crops and their wild relatives is fundamental for maintaining and increasing food security. The species Cynara cardunculus includes three taxa: the globe artichoke, one of the most important Mediterranean vegetables, the leafy cardoon, and the wild cardoon. In this study, genotyping by sequencing (GBS) was successfully applied to reveal thousands of polymorphisms in a C. cardunculus germplasm collection, including 65 globe artichoke, 9 leafy cardoon, and 21 wild cardoon samples. The collection showed a strong population structure at K = 2, separating the globe artichoke from the leafy and wild cardoon. At higher K values, further substructures were observed, in which the wild cardoon was separated from the leafy cardoon, and the latter included the Spanish wild cardoons, while the wild sample from Portugal was admixed. Moreover, subpopulations within the globe artichoke set were highlighted. Structure analysis restricted to the globe artichoke dataset pointed out genetic differentiation between the ˝Catanesi˝ typology and all the other samples (K = 2). At higher values of K, the separation of the ˝Catanesi˝ group still held true, and green headed landraces from Apulia region, Italy (˝Green Apulian˝) formed a distinct subpopulation. ˝Romaneschi˝ artichoke types fell in a variable group with admixed samples, indicating that they should not be considered as a genetically uniform typology. The results of principal component analysis and Neighbor-Joining hierarchical clustering were consistent with structure results, and in addition provided a measure of genetic relationships among individual genotypes. Both analyses attributed the wild material from Spain and Portugal to the cultivated cardoon group, supporting the idea that this might be indeed a feral form of the leafy cardoon. Different reproductive habit and possibly selective pressure led to a slower LD decay in artichoke compared to cardoon. Genotyping by sequencing has proven a reliable methodology to obtain valuable SNPs and assess population genetics in C. cardunculus.

Characterizing Palestinian snake melon (Cucumis melo var. flexuosus) germplasm diversity and structure using SNP and DArTseq markers

BACKGROUND

Crop landraces embody a source of beneficial genes potentially providing endurance to environmental stress and other agronomic qualities including yield. Our study included 88 snake melon accessions (Cucumis melo var. flexuosus) collected from 9 districts in the Palestinian West-Bank. These accessions represent four landraces of Palestinian snake melon: Green, and White Baladi, and Green, and White Sahouri.

RESULTS

This is the first report on successful application of genotyping by sequencing in snake melon. Nine thousand seven hundred fifty single-nucleotide polymorphism (SNP) and 7400 DArTseq genetic markers were employed to evaluate genetic biodiversity and population structure of Palestinian snake melon germplasm collection. Clustering based on neighbor-joining-analysis, principle coordinate and Bayesian model implemented in Structure showed that patterns of genetic diversity of snake melon landraces depends on their geographical source and unraveled the presence of two major local landraces (Sahouri, and Baladi) with accessions from each group clustering together. A significant correlation was observed between both types of markers in Mantel correlation test. A significant association between genetic and geographic matrices (P < 0.0001) was also detected. AMOVA indicated that majority of variation (90%) was due to the difference within accessions.

CONCLUSION

The Palestinian landraces seem to have unique genes that may allow the enhancement of the global snake melon gene pool and developments of the plant production worldwide. Our subsequent objective is to detect genotypes with promising qualities and to conduct association mapping studies concentrating on Fusarium-wilt resistance, yield, and environmental stresses.

1H-NMR-based metabolomic profiles of different sweet melon (Cucumis melo L.) Salento varieties: Analysis and comparison

Melon (Cucumis melo L.) is a significant source of substances able to provide human health benefits. From the 18th century in the Salento area (Apulia region), the cultivation of melon varieties (C. melo L.) has always been intense. Over the years, the production of this fruit has involved a large number of selected and preserved varieties in the different local districts. Unfortunately, most of the characteristics of locally grown vegetable varieties do not match the food industry requirements. Moreover, the agricultural land abandon leads these varieties to quickly disappear, thus affecting the intraspecific biodiversity. In order to characterize the inter-variety diversity of sweet melon (C. melo L. ssp. melo group inodorus) and the potential differences in the nutritional quality of fruits, a first investigation on the juice of five sweet melon varieties (locally known as "allungato", "scurzune", "egiziano", "minna de monaca", "pinto"), cultivated exclusively in the Salento area, was performed by ¹H-NMR spectroscopy and Multivariate Analysis (MVA). The analysis grouped the samples into clusters according to the different variety. Interestingly, a different sugar (mono and disaccharides) content was observed among the grouped varieties, being sweetness the main characteristic of sweet melon quality and taste. A relative higher accumulation of monosaccharides (α-d and β-d glucose and α/β-d fructose) was found, in particular for the "minna de monaca" with respect to "allungato", "egiziano" and "pinto" varieties. Moreover, a marked high content of polyphenols and aromatic aminoacids as phenylalanine and tyrosine characterize the "allungato", "minna de monaca" and "pinto" varieties. An NMR-based metabolomic approach was used for the first time to describe these local landraces. This method may integrate other actions in order to achieving a reduction in the current rate of erosion of the biodiversity of Apulian horticultural species.

QTL Analyses in Multiple Populations Employed for the Fine Mapping and Identification of Candidate Genes at a Locus Affecting Sugar Accumulation in Melon (Cucumis melo L.)

Sugar content is the major determinant of both fruit quality and consumer acceptance in melon (Cucumis melo L), and is a primary target for crop improvement. Near-isogenic lines (NILs) derived from the intraspecific cross between a "Piel de Sapo" (PS) type and the exotic cultivar "Songwhan Charmi" (SC), and several populations generated from the cross of PS × Ames 24294 ("Trigonus"), a wild melon, were used to identify QTL related to sugar and organic acid composition. Seventy-eight QTL were detected across several locations and different years, with three important clusters related to sugar content located on chromosomes 4, 5, and 7. Two PS × SC NILs (SC5-1 and SC5-2) sharing a common genomic interval of 1.7 Mb at the top of chromosome 5 contained QTL reducing soluble solids content (SSC) and sucrose content by an average of 29 and 68%, respectively. This cluster collocated with QTL affecting sugar content identified in other studies in lines developed from the PS × SC cross and supported the presence of a stable consensus locus involved in sugar accumulation that we named SUCQSC5.1. QTL reducing soluble solids and sucrose content identified in the "Trigonus" mapping populations, as well as QTL identified in previous studies from other ssp. agrestis sources, collocated with SUCQSC5.1, suggesting that they may be allelic and implying a role in domestication. In subNILs derived from the PS × SC5-1 cross, SUCQSC5.1 reduced SSC and sucrose content by an average of 18 and 34%, respectively, and was fine-mapped to a 56.1 kb interval containing four genes. Expression analysis of the candidate genes in mature fruit showed differences between the subNILs with PS alleles that were "high" sugar and SC alleles of "low" sugar phenotypes for MELO3C014519, encoding a putative BEL1-like homeodomain protein. Sequence differences in the gene predicted to affect protein function were restricted to SC and other ssp. agrestis cultivar groups. These results provide the basis for further investigation of genes affecting sugar accumulation in melon.

NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops

Demographic trends and changes to climate require a more efficient use of plant genetic resources in breeding programs. Indeed, the release of high-yielding varieties has resulted in crop genetic erosion and loss of diversity. This has produced an increased susceptibility to severe stresses and a reduction of several food quality parameters. Next generation sequencing (NGS) technologies are being increasingly used to explore “gene space” and to provide high-resolution profiling of nucleotide variation within germplasm collections. On the other hand, advances in high-throughput phenotyping are bridging the genotype-to-phenotype gap in crop selection. The combination of allelic and phenotypic data points via genome-wide association studies is facilitating the discovery of genetic loci that are associated with key agronomic traits. In this review, we provide a brief overview on the latest NGS-based and phenotyping technologies and on their role to unlocking the genetic potential of vegetable crops; then, we discuss the paradigm shift that is underway in horticultural crop breeding.

Genome-Wide Linkage-Disequilibrium Mapping to the Candidate Gene Level in Melon (Cucumis melo)

Cucumis melo is highly diverse for fruit traits providing wide breeding and genetic research opportunities, including genome-wide association (GWA) analysis. We used a collection of 177 accessions representing the two C. melo subspecies and 11 horticultural groups for detailed characterization of fruit traits variation and evaluation of the potential of GWA for trait mapping in melon. Through genotyping-by-sequencing, 23,931 informative SNPs were selected for genome-wide analyses. We found that linkage-disequilibrium decays at ~100 Kb in this collection and that population structure effect on association results varies between traits. We mapped several monogenic traits to narrow intervals overlapping with known causative genes, demonstrating the potential of diverse collections and GWA for mapping Mendelian traits to a candidate-gene level in melon. We further report on mapping of fruit shape quantitative trait loci (QTLs) and comparison with multiple previous QTL studies. Expansion of sample size and a more balanced representation of taxonomic groups might improve efficiency for simple traits dissection. But, as in other plant species, integrated linkage-association multi-allelic approaches are likely to produce better combination of statistical power, diversity capture and mapping resolution in melon. Our data can be utilized for selection of the most appropriate accessions for such approaches.

Residue analysis of picoxystrobin in oriental melon using gas chromatography coupled with electron capture detection and mass spectrometric confirmation: application to dissipation kinetics and risk assessment

This study was carried out to determine the residual amounts of picoxystrobin in oriental melon (Cucumis melo L.) grown under plastic house conditions at two different sites. Samples collected over 10 days were extracted using acetonitrile and salting out (using solid sodium chloride) and purified using Florisil SPE cartridges. The analyte was determined using GC-ECD and field-incurred residues were verified using GC-MS. The calibration curve was linear over the range 0.02-2.0 mg/L with a R 2  = 0.9998. The LOD and LOQ were 0.003 and 0.01 mg/kg, respectively. Recoveries, tested at three spiking levels, were satisfactory with rates in the range 87.7-101.5% and relative standard deviations ≤9.6. The dissipation half-lives were 3.4 and 3.7 days for sites 1 and 2, respectively. Hazard estimates obtained using hazard quotients revealed no health risk from the suggested pesticide application dosage when considering an adult's body weight, oriental melon consumption, and the acceptable daily intake of picoxystrobin.