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Characterization of local germplasm is an effective way to identify elite breeding material and develop improved varieties. This study was aimed to assess 52 tomato accessions comprised of local varieties (28), landraces (8), breeding lines (14), and wild relatives (2), and their characterization for 30 morphological/agronomic, four fruit quality, and tomato mosaic virus (ToMV) resistance traits. Morphological, quality, and ToMV traits were evaluated using phenotyping, biochemical assays, and molecular markers, respectively. Fruit shape and size showed appreciable variation, with fruits varying from rounded to heart shaped and small to big size. Significant variation was observed for fruit weight (1.6–564.8 g), fruits per plant (6.0–174.7), productivity (130.5–5146.5 g), soluble solids (4.1%–8.4%), vitamin C (9.5–46.4 mg·100 g−1), antioxidant activity (2.5–9.6 μmol Fe2+·g−1 fresh weight), and total polyphenols (23.9–124.2 GAE·100 g−1 fresh weight). All accessions were phenotypically screened for the virus resistance in the growth chamber, and CAPS molecular markers were used to identify accessions with ToMV Tm-22 resistant alleles, and accessions LYC-13, LYC-15, LYC-17, LYC-26, and LYC-52 were identified as resistant. Multivariate analysis of morphological and quality traits showed that 35 principal components contributed to the total variation and the first two and 12 principal components explained 47.2% and 90% of the variation, respectively. The evaluated tomato collection appears to have breeding potential, and around 20% of the accessions in the collection (LYC-6, LYC-17, LYC-18, LYC-26 to LYC-31, and LYC 33) are promising genetic resources for variety development that are enriched with enhanced fruit quality and high yield.

Selection of high-performance lines with respect to traits of interest is a key step in plant breeding. Genomic prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers, e.g. single-nucleotide polymorphisms (SNPs), and machine learning approaches, which can therefore shorten breeding cycles, referring to genomic selection (GS). Here, we applied GS approaches in two populations of Solanaceous crops, i.e. tomato and pepper, to predict morphometric and colorimetric traits. The traits were measured by using scoring-based conventional descriptors (CDs) as well as by Tomato Analyzer (TA) tool using the longitudinally and latitudinally cut fruit images. The GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits, respectively. The results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous fruits. The highest predictability of 0.89 was achieved for fruit width in pepper, with an average predictability of 0.69 over all traits. The multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in pepper. While model validation performs poorly on wild tomato accessions, the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits (e.g. fruit shape for which predictability in unseen scenario increased from zero to 0.6). Overall, GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding.

Significance This study provides a deep population genomic analysis of 10,000 Capsicum accessions held in genebanks and representing a frame of the global diversity of the genus. By combining single nucleotide polymorphisms (SNPs) based data and passport information, we investigated the genomic diversity and population structure of wild and domesticated peppers, tracing back to routes of evolution and providing a model of Capsicum annuum distribution, which reflects human trade and historical/cultural influences. Our results highlight west–east routes of expansion, shedding light on the links between South and Mesoamerica, Africa, and East/South Asia, the latter two constituting important diversification centers of pepper diversity. Finally, we outline a roadmap for genebank management and future direction for better exploitation of germplasm resources., Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper (Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.

Region-specific local landraces represent a germplasm diversity adapted and acclimatized to local conditions, and are ideal to breed for targeted market niches while maintaining the variability of heirloom traits. A collection of 180 pepper accessions, collected from 62 diverse locations across six Balkan countries, were characterized and evaluated for phenotypic and biochemical variation during a multi-year environment. An assortment of 32 agro-morphological, fruit quality, and virus resistance traits were evaluated, and the top 10% accessions were identified. A wide range of trait variation concerning plant architecture, inflorescence and fruit traits, yield and fruit quality was observed, and appreciable variation was noticed. According to hierarchical clustering, six distinct clusters were established based on pre-defined varietal groups. Divergence among accessions for phenotypic and fruit compositional variability was analyzed, and eight principal components were identified that contributed ~71% of the variation, with fruit shape, width, wall thickness, weight, and fruit quality traits being the most discriminant. Evaluation of the response to tobacco mosaic virus (TMV) and pepper mild mottle mosaic virus (PMMoV) showed that 24 and 1 accession were resistant, respectively while no tomato spotted wilt virus (TSWV) resistance was found. Considerable diversity for agro-bio-morphological traits indicates the Balkan pepper collection as good gene sources for pre-breeding and cultivar development that are locally adapted.

Common bean (Phaseolus vulgaris) is a traditional vegetable in Bulgaria. The area grown in for 2013 was estimated to be 344 ha which increased gradually to reach 708 ha in 2016. During the summer of 2013, leaf samples (n=76) with …

Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are among the biggest threats for snap bean production in Bulgaria due to their seed, aphid and mechanical transmission. Old valuable Bulgarian snap bean varieties are being neglected, because of the high percentage of virus-infected seeds. Breeding resistant cultivars is the best way to solve the problem. The genetic control towards both viruses is assured by one dominant I gene and a number of recessive (bc-u, bc-1, bc-12, bc-2, bc-22 and bc-3) genes. Our aim was to identify resistance gene combinations in advanced F8 breeding lines, derived from two crosses (A-8-40-7-2-1 × IVT 7214) and (Zaria × RH 26D), by the application of conventional and molecular approaches. Four methods were applied for the characterization of their resistance gene makeup: (i) leaf-abscission infection test designed to identify I gene by direct inoculation with NL3 strain of BCMNV; (ii) intact-plant infection test with strain NY15 of BCMV to separate immune genotypes, possessing bc-ubc-12, bc-ubc-22,bc-ubc-2bc-3, I, Ibc-12, Ibc-22 or Ibc-3; (iii) PCR analysis with the following markers: SCAR – SW13 (for I gene), SBD5 (for bc-12), ROC11 (for bc-3) and CAPS – eIFE4 (for bc-3); and 4) high-temperature (more than 30°C) infection test with NL3 of BCMNV to provoke systemic necrosis in I, Ibc-1, Ibc-12, Ibc-12bc-22 or Ibc-3. The four methods applied worked properly and complemented each other. Valuable gene combination (Ibc-3) was established in seven breeding lines with immune reaction to BCMNV. They will be included in the snap bean breeding programme for virus resistance.

Virus-like chlorotic symptoms were observed on tomato plants, cv. Velocity, grown in a greenhouse, region of Plovdiv. Samples collected from the leaves with interveinal yellowing and with initial interveinal chlorosis were tested for virus presence. Only the samples collected from the upper leaves with slight interveinal chlorosis were positive for Tomato infectious chlorosis virus (TICV) in indirect ELISA. Further, RT-PCR analysis with specific primers for Tomato chlorosis virus (ToCV) heat shock protein 70, for TICV heat shock protein 70 and for TICV minor capsid protein was positive for TICV in all tested samples. No signals were obtained with primers for ToCV. Phylogenetic analysis showed that the Bulgarian sequence of Hsp70 and a sequence of Greek isolate clustered together having the highest resampling score. Regarding CPm, the Bulgarian isolate was more relevant to the French isolate. The obtained results from phylogenetic analysis supported the idea of a close relationship between the Bulgarian and Greek isolates.

Potyviruses are a common threat for snap bean production in Bulgaria. During virus surveys of bean plots in the south central region, we identified an isolate of Clover yellow vein virus (ClYVV), designated ClYVV 11B, by indirect ELISA and RT-PCR causing severe mosaic symptoms and systemic necrosis. Indirect and direct ELISA using ClYVV antisera differentiated the ClYVV isolate from Bean yellow mosaic virus (BYMV), but serological analysis could not distinguish the Bulgarian isolate ClYVV 11B from an Italian ClYVV isolate used as a reference (ClYVV 505/7). RT-PCR analyses with specific primers revealed that both isolates were ClYVV. Sequence analysis of an 800 bp fragment corresponding to the coat protein coding region showed 94% identity at the nucleotide level between the two isolates. Phylogenetic analyses of aligned nucleotide sequences available in the database confirmed the existence of two groups of isolates, but ClYVV 11B and ClYVV505/7 belonged to the same group. We compared the virulence of both isolates on a set of differential cultivars and 19 bean breeding lines resistant to Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV): Bulgarian isolate ClYVV 11B was able to infect systemically all tested bean differential cultivars and breeding lines including those with genotypes Ibc3 and Ibc22; Italian isolate ClYVV 505/7 was not able to infect systemically some differentials with genotypes bc-ubc1, bc-ubc22, bc-ubc2bc3, Ibc12, Ibc22, Ibc3. The role of bc3 gene as a source of resistance to potyviruses is discussed.

Tomato spotted wilt virus (TSWV) is one of the most destruc-tive pathogens worldwide. In Bulgaria the virus was found toseverely damage a number of solanaceous vegetables andca.25 ornamentals (Hristova et al.2001 ). In spring 2014, about30% of lisianthus plants (ca. 1000 plants) grown in a privatefarm nearby Plovdiv, Bulgaria showed yellowing and/or lightbrown necrosis on leaves and petals followed by subsequentwilting. To identify the causal agent of this infection,Chenopodium quinoa,Nicotiana glutinosa,andPetuniahybridaplants were sap inoculated with material from 10symptomatic individuals.