Jaime Prohens

Application of genomic tools in plant breeding.

Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, ‘breeding by design’, or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the ‘superdomestication’ of crops and the genetic dissection and breeding for complex traits.

Effects of Organic and Conventional Cultivation Methods on Composition of Eggplant Fruits

Organic food is associated by the general public with improved nutritional properties, and this has led to increasing demand for organic vegetables. The effects of organic and conventional cultivation methods on dry matter, protein, minerals, and total phenolic content has been studied for two successive years in two landraces and one commercial hybrid of eggplant. In the first year, organically produced eggplants had higher mean contents (expressed on a fresh weight basis) of K (196 vs 171 mg 100 g(-1)), Ca (11.1 vs 8.7 mg 100 g(-1)), Mg (6.0 vs 4.6 mg 100 g(-1)), and total phenolics (49.8 vs 38.2 mg 100 g(-1)) than conventionally grown eggplants. In the second year, in which matched plots having a history of organic management were cultivated following organic or conventional fertilization practices, organically produced eggplants still had higher contents of K (272 vs 249 mg 100 g(-1)) and Mg (8.8 vs 7.6), as well as of Cu (0.079 vs 0.065 mg 100 g(-1)), than conventionally fertilized eggplants. Conventionally cultivated eggplants had a higher polyphenol oxidase activity than organically cultivated ones (3.19 vs 2.17 enzyme activity units), although no differences in browning were observed. Important differences in mineral concentrations between years were detected, which resulted in many correlations among mineral contents being significant. The first component of the principal component analysis separates the eggplants according to year, whereas the second component separates them according to the cultivation method (organic or conventional). Overall, the results show that organic management and fertilization have a positive effect on the accumulation of certain beneficial minerals and phenolic compounds in eggplant and that organically and conventionally produced eggplants might be distinguished according to their composition profiles.

Breeding and Domesticating Crops Adapted to Drought and Salinity: A New Paradigm for Increasing Food Production

World population is expected to reach 9.2 × 109 people by 2050. Feeding them will require a boost in crop productivity using innovative approaches. Current agricultural production is very dependent on large amounts of inputs and water availability is a major limiting factor. In addition, the loss of genetic diversity and the threat of climate change make a change of paradigm in plant breeding and agricultural practices necessary. Average yields in all major crops are only a small fraction of record yields, and drought and soil salinity are the main factors responsible for yield reduction. Therefore there is the need to enhance crop productivity by improving crop adaptation. Here we review the present situation and propose the development of crops tolerant to drought and salt stress for addressing the challenge of dramatically increasing food production in the near future. The success in the development of crops adapted to drought and salt depends on the efficient and combined use of genetic engineering and traditional breeding tools. Moreover, we propose the domestication of new halophilic crops to create a ‘saline agriculture’ which will not compete in terms of resources with conventional agriculture.

Wild Relatives of the Eggplant (Solanum melongena L.: Solanaceae): New Understanding of Species Names in a Complex Group

Background The common or brinjal eggplant (Solanum melongena L.) belongs to the Leptostemonum Clade (the “spiny” solanums) of the species-rich genus Solanum (Solanaceae). Unlike most of the genus, the eggplant and its relatives are from the Old World; most eggplant wild relatives are from Africa. An informal system for naming eggplant wild relatives largely based on crossing and other biosystematics data has been in use for approximately a decade. This system recognises several forms of two broadly conceived species, S. incanum L. and S. melongena. Recent morphological and molecular work has shown that species-level differences exist between these entities, and a new species-level nomenclature has been identified as necessary for plant breeders and for the maintenance of accurately named germplasm. Methodology/Principal Findings We examined herbarium specimens from throughout the wild species ranges as part of a larger revision of the spiny solanums of Africa. Based on these morphological and molecular studies, we delimited species in the group to which the common eggplant belongs and constructed identification keys for the group. We also examined the monophyly of the group considered as the eggplant relatives by previous authors. Conclusions/Significance We recognise ten species in this group: S. aureitomentosum Bitter, S. campylacanthum A.Rich., S. cerasiferum Dunal, S. incanum L., S. insanum L., S. lichtensteinii Willd., S. linnaeanum Hepper & P.-M.L.Jaeger, S. melongena L., S. rigidum Lam. and S. umtuma Voronts. & S.Knapp. We review the history of naming and provide keys and character lists for all species. Ploidy level differences have not been investigated in the eggplant wild relatives; we identify this as a priority for improvement of crop wild relative use in breeding. The application of species-level names to these entities will help focus new collecting efforts for brinjal eggplant improvement and help facilitate information exchange.

α-Solasonine and α-solamargine contents of gboma (Solanum macrocarpon L.) and scarlet (Solanum aethiopicum L.) eggplants.

The gboma (Solanum macrocarpon L.) and scarlet eggplants (Solanum aethiopicum L.), which form part of the traditional sub-Saharan African culture, are two of the many neglected crops with potential for increased cultivation or as a genetic resource for improving agronomic traits of the common eggplant. This work is focused on the analysis of glycoalkaloid levels in S. macrocarpon and S. aethiopicum to assess their safety. Liquid chromatography-mass spectrometry was used to quantify glycoalkaloids in S. macrocarpon and S. aethiopicum compared to Solanum melongena L. Fruits of S. aethiopicum and S. melongena contained 0.58-4.56 mg/100 g of alpha-solamargine and 0.17-1 mg/100 g of alpha-solasonine, on a wet basis. S. macrocarpon fruits had much higher values of alpha-solamargine (124-197 mg/100 g) and alpha-solasonine (16-23 mg/100 g). However, the proportions of alpha-solamargine and alpha-solasonine of S. melongena and S. macrocarpon were similar (76-89% of alpha-solamargine), whereas in S. aethiopicum fruit composition was more variable (48-89% of alpha-solamargine). According to these results, the glycoalkaloid levels of S. macrocarpon fruits are 5-10 times higher than the value considered to be safe in foods and might not be considered suitable for human consumption; however, the glycoalkaloid levels of S. aethiopicum were similar to those of S. melongena (about 14% of values considered as toxic) and could be considered as safe for consumption. The incorporation of the cultivated African S. aethiopicum into eggplant breeding programs to develop improved varieties of the common eggplant may represent an alternative to crossing with wild species.

Diversity and Relationships of Eggplants from Three Geographically Distant Secondary Centers of Diversity

Eggplant (Solanum melongena L.) was domesticated in the Indo-Birmanian region, which is also the primary center of diversity for this crop. From there eggplant spread to other regions, and diversity accumulated in several secondary centers of diversity. We have assessed the diversity and relationships of 52 accessions of eggplant from three geographically distant secondary centers of diversity (China, Spain, and Sri Lanka) using 28 morphological descriptors and 12 highly polymorphic genomic SSRs. A wide variation was found for most morphological traits, and significant differences among the three centers of diversity were detected for 22 of these traits. The PCA analysis showed that eggplants from the three origins were morphologically differentiated, and accessions from each of the three secondary centers of diversity presented a typical combination of morphological characteristics. In this respect, discriminant analysis showed that accessions could be correctly classified to their origin using only six traits. The SSR characterization identified 110 alleles and allowed obtaining a unique genetic fingerprint for each accession. Many alleles were found to be private to each origin, but no universal alleles were found for any of the origins. The PCA analysis showed that the genetic differentiation among origins was less clear than for morphological traits, although the analysis of the population structure shows that accessions mostly group according to the origin, but also provides evidence of migration among the three secondary centers of diversity. The genetic diversity (HT) within each origin was high, ranging between HT = 0.5400 (Sri Lanka) and HT = 0.4943 (China), while the standardized genetic differentiation (G’ST) among origins was moderate (G’ST = 0.2657). The correlation between morphological and SSR distances was non-significant (r = 0.044), indicating that both data are complementary for the conservation of germplasm and breeding of eggplant. These results are relevant for the management of genetic resources, breeding programmes, and evolutionary studies of eggplant.

The pepino (Solanum muricatum, Solanaceae): a "new" crop with a history

Pepino,Solanum muricatum, is an herbaceous subshrub that has long been grown in its native Andean South America. Pepino is usually cultivated for its edible fruits, but also has other economic uses. In spite of being a prominent crop in prehispanic times in the Andes, interest in pepino was cast into oblivion from some decades after the Spanish arrival to the present. Pepino etymology, prehispanic distribution, and postcolumbian dispersal are presented, with emphasis on outstanding historical aspects. Speculations on why the pepino has been neglected are also given. These include some features of pepino itself together with misconceptions. However, the pepino is today a species of increasing economic interest, and has a considerable potential for future exploitation.ResumenEl pepino dulce (Solanum muricatum),es una planta herbácea que ha sido cultivada durante mucho tiempo en los Andes, su zona de origen. El pepino dulce normalmente se cultiva por sus frutos comestibles, aunque también tiene otros usos de importancia económica. A pesar de ser un cultivo importante en la zona andina durante la época precolombina, desde unas décadas después de la llegada de los españoles en adelante, el interés por el pepino dulce cayé en el olvido. En este artículo se presentan la etimología, distribución en la época precolombina y su difusión postcolombina, haciendo particular énfasis en los aspectos históricos más destacados. También se dan algunas razones que podrían haber tenido influencia para marginar al pepino dulce. Entre éstas se incluyen algunas carícterísticas propias del pepino dulce junto con falsas creencias. Sin embargo, en la actualidad, el pepino dulce es una planta con un interés económico creciente y con un potencial considerable para su explotación en el futuro.

Diversity and relationships in key traits for functional and apparent quality in a collection of eggplant: fruit phenolics content, antioxidant activity, polyphenol oxidase activity, and browning.

Eggplant (Solanum melongena) varieties with increased levels of phenolics in the fruit present enhanced functional quality, but may display greater fruit flesh browning. We evaluated 18 eggplant accessions for fruit total phenolics content, chlorogenic acid content, DPPH scavenging activity, polyphenol oxidase (PPO) activity, liquid extract browning, and fruit flesh browning. For all the traits we found a high diversity, with differences among accessions of up to 3.36-fold for fruit flesh browning. Variation in total content in phenolics and in chlorogenic acid content accounted only for 18.9% and 6.0% in the variation in fruit flesh browning, and PPO activity was not significantly correlated with fruit flesh browning. Liquid extract browning was highly correlated with chlorogenic acid content (r = 0.852). Principal components analysis (PCA) identified four groups of accessions with different profiles for the traits studied. Results suggest that it is possible to develop new eggplant varieties with improved functional and apparent quality.

AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): implications for evolution and domestication

The pepino (Solanum muricatum) is a vegetatively propagated, domesticated native of the Andes, where it grows with wild relatives. We used AFLPs and a 1-kb sequence of the 3-methylcrotonyl-CoA carboxylase gene to study variation of 27 accessions of S. muricatum and 35 collections of 10 species of wild relatives (Solanum section Basarthrum). A total of 298 AFLP fragments and 29 DNA sequence haplotypes were detected. Cluster and principal coordinate analyses and other genetic parameters estimated from both types of markers, show that S. muricatum is closely related to the species from one of the series (Caripensia) of section Basarthrum and that >90% of the variation of the cultigen is also represented in that series. Pepino is highly diverse, either because it is not monophyletic or it has been subjected to regular introgression with wild species, or both. Although a continuous distribution of the genetic variation occurred within the cultivated species, three genetic clusters were recognized. Cluster 1 is mostly centered in Ecuador, cluster 2 in Ecuador and Peru, and cluster 3 in Colombia and Ecuador. Cluster 3 also includes all modern cultivars studied. These results and other evidence suggest that northern Ecuador/southern Colombia is the main center of pepino diversity and the center of origin. The high genetic variation of this cultigen indicates that domestication does not always produce a genetic bottleneck.

“Heirloom” varieties as sources of variation for the improvement of fruit quality in greenhouse-grown tomatoes

Summary Greenhouse-grown tomatoes (Lycopersicon esculentum) often have poor internal organoleptic and nutritional qualities. “Heirloom” (traditional) varieties of tomato possess unique or superior fruit quality characteristics and may be useful for the development of new greenhouse tomato cultivars with improved internal quality. A collection of 55 North American “heirloom” varieties was evaluated for fruit colour, shape, weight, firmness (external quality traits) and total soluble solids (TSS) content, titratable acidity (TA), TSS:TA ratio, flavour intensity (FI; TSS TA) and ascorbic acid (AA) concentration (internal quality traits). The F1 hybrid ‘Daniela’ and pure line ‘NE-1’ were used as controls. A wide diversity was found among “heirlooms” for all traits studied, and several sources of variation (e.g., varieties ‘Moira’, ‘Paragon’, ‘White Queen’, ‘Black Prince’ and ‘Green Zebra’) useful for the improvement of fruit quality were identified. Brightness (L*), hue angle and chroma parameters facilitated the classification of varieties into colour groups (white, yellow, orange, red or black) and the identification of the varieties with better colour characteristics within each colour group. Although all “heirloom” varieties had lower firmness than the delayed ripening cv. ‘Daniela’, some of them (e.g., ‘Moira’ and ‘Paragon’) were very firm. Values obtained for TSS, TA, FI and AA demonstrated that many “heirloom” varieties had better organoleptic and nutritional qualities than modern varieties. As considerable variation was found for most traits, some of the materials studied represent sources of variation of great interest for tomato breeding.