Phenolics content, fruit flesh colour and browning in cultivated eggplant, wild relatives and interspecific hybrids and implications for fruit quality breeding

[EN] Increasing the content in bioactive phenolics in the eggplant (Satanum melongena) fruit is of interest, but may result in enhanced browning. We evaluated six varieties of S. melongena, 22 accessions of wild related species and 42 interspecific hybrids between cultivated eggplant and wild relatives for phenolics content, fruit flesh colour, polyphenol oxidase (PPO) activity, and fruit flesh browning. Wild relatives generally had a higher content in phenolics and a broader range of variation than cultivated eggplant. Chlorogenic acid was the predominant ( > 65.0%) phenolic acid in cultivated eggplant and its primary genepool wild ancestor S. insanum, while for the other wild species on average represented < 50% of the chromatogram peak area. Fruit flesh colour was lighter in S. melongena than in the wild species, while PPO activity and browning was much higher in wild species of the secondary and tertiary genepools. Interspecific hybrids between S. melongena and S. insanum were intermediate in their characteristics, while those with secondary and tertiary genepool species were more similar to the wild species. No significant correlations were found between total phenolics or chlorogenic acid contents and fruit flesh browning, but PPO activity was correlated to both the degree of browning (r = 0.404) and colour difference (r = 0.458). The results indicate that wild species can contribute to improving the bioactive properties of eggplant without affecting negatively fruit flesh colour and browning.This work has been funded in part by the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway (GS13044 and GS17011). This project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website: http://www.cwrdiversity.org/. Funding has also been received from the European Union's Horizon 2020 - Research and Innovation Framework Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and from Spanish Ministerio de Economia y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER). Prashant Kaushik is grateful to ICAR for a pre-doctoral grant. Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract.Kaushik, P.; Gramazio, P.; Vilanova Navarro, S.; Raigón Jiménez, MD.; Prohens Tomás, J.; Plazas Ávila, MDLO. (2017). Phenolics content, fruit flesh colour and browning in cultivated eggplant, wild relatives and interspecific hybrids and implications for fruit quality breeding. Food Research International. 102:392-401. https://doi.org/10.1016/j.foodres.2017.09.028S39240110

Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background

[EN] Advanced backcrosses (ABs) and introgression lines (ILs) of eggplant (Solanum melongena) can speed up genetics and genomics studies and breeding in this crop. We have developed the first full set of ABs and ILs in eggplant using Solanum incanum, a wild eggplant that has a relatively high tolerance to drought, as a donor parent. The development of these ABs and IL eggplant populations had a low efficiency in the early stages, because of the lack of molecular markers and genomic tools. However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. A set of 73 selected ABs covered 99% of the S. incanum genome, while 25 fixed immortal ILs, each carrying a single introgressed fragment in homozygosis, altogether spanned 61.7% of the S. incanum genome. The introgressed size fragment in the ILs contained between 0.1 and 10.9% of the S. incanum genome, with a mean value of 4.3%. Sixty-eight candidate genes involved in drought tolerance were identified in the set of ILs. This first set of ABs and ILs of eggplant will be extremely useful for the genetic dissection of traits of interest for eggplant, and represents an elite material for introduction into the breeding pipelines for developing new eggplant cultivars adapted to the challenges posed by the climate-change scenario.This work has been funded in part by the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives," which is supported by the Government of Norway. This project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website: http://www.cwrdiversity.org/. Funding has also been received from the European Union's Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and from Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL201564755-R from MINECO/ FEDER). PG is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract. MP is grateful to Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Juan de la Cierva programme (FCJI-2015-24835). GM is grateful to Conselleria d'Educacio, Investigacio, Cultura i Esport de la Generalitat Valenciana for a pre-doctoral grant within the Santiago Grisolia programme (GRISOLIAP/2016/012). Authors also thank the Italian Eggplant Genome Sequencing Consortium for providing access to an improved version of the eggplant genome.Gramazio, P.; Prohens Tomás, J.; Plazas Ávila, MDLO.; Mangino, G.; Herraiz García, FJ.; Vilanova Navarro, S. (2017). Development and Genetic Characterization of Advanced Backcross Materials and An Introgression Line Population of Solanum incanum in a S. melongena Background. Frontiers in Plant Science. 8. https://doi.org/10.3389/fpls.2017.01477S1477

The Gene Pool Concept Applied to Crop Wild Relatives: An Evolutionary Perspective

Crop wild relatives (CWR) can provide important resources for the genetic improvement of cultivated species. Because crops are often related to many wild species and because exploration of CWR for useful traits can take many years and substantial resources, the categorization of CWR based on a comprehensive assessment of their potential for use is an important knowledge foundation for breeding programs. The initial approach for categorizing CWR was based on crossing studies to empirically establish which species were interfertile with the crop. The foundational concept of distinct gene pools published almost 50 years ago was developed from these observations. However, the task of experimentally assessing all potential CWR proved too vast; therefore, proxies based on phylogenetic and other advanced scientific information have been explored. A current major approach to categorize CWR aims to comprehensively synthesize experimental data, taxonomic information, and phylogenetic studies. This approach very often ends up relying not only on the synthesis of data but also intuition and expert opinion and is therefore difficult to apply widely in a reproducible manner. Here, we explore the potential for a stronger standardization of the categorization method, with focus on evolutionary relationships among species combined with information on patterns of interfertility between species. Evolutionary relationships can be revealed with increasing resolution via next-generation sequencing, through the application of the multispecies coalescent model and using focused analyses on species discovery and delimitation that bridge population genetics and phylogenetics fields. Evolutionary studies of reproductive isolation can inform the understanding of patterns of interfertility in plants. For CWR, prezygotic postpollination reproductive barriers and intrinsic postzygotic barriers are the most important factors and determine the probability of producing viable and fertile offspring. To further the assessment of CWR for use in plant breeding, we present observed and predicted gene pool indices. The observed index quantifies patterns of interfertility based on fertilization success, seed production, offspring viability, and hybrid fertility. The predicted gene pool index requires further development of the understanding of quantitative and qualitative relationships between reproductive barriers, measures of genetic relatedness, and other relevant characteristics for crops and their wild relatives

AusTraits, a curated plant trait database for the Australian flora

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge

Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics

Abstract Background Heterogeneous rates of molecular evolution are universal across the tree of life, posing challenges for phylogenetic inference. The temperate woody bamboos (tribe Arundinarieae, Poaceae) are noted for their extremely slow molecular evolutionary rates, supposedly caused by their mysterious monocarpic reproduction. However, the correlation between substitution rates and flowering cycles has not been formally tested. Results Here we present 15 newly sequenced plastid genomes of temperate woody bamboos, including the first genomes ever sequenced from Madagascar representatives. A data matrix of 46 plastid genomes representing all 12 lineages of Arundinarieae was assembled for phylogenetic and molecular evolutionary analyses. We conducted phylogenetic analyses using different sequences (e.g., coding and noncoding) combined with different data partitioning schemes, revealing conflicting relationships involving internodes among several lineages. A great difference in branch lengths were observed among the major lineages, and topological inconsistency could be attributed to long-branch attraction (LBA). Using clock model-fitting by maximum likelihood and Bayesian approaches, we furthermore demonstrated extensive rate variation among these major lineages. Rate accelerations mainly occurred for the isolated lineages with limited species diversification, totaling 11 rate shifts during the tribe’s evolution. Using linear regression analysis, we found a negative correlation between rates of molecular evolution and flowering cycles for Arundinarieae, notwithstanding that the correlation maybe insignificant when taking the phylogenetic structure into account. Conclusions Using the temperate woody bamboos as an example, we found further evidence that rate heterogeneity is universal in plants, suggesting that this will pose a challenge for phylogenetic reconstruction of bamboos. The bamboos with longer flowering cycles tend to evolve more slowly than those with shorter flowering cycles, in accordance with a putative generation time effect

ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa-Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae)

The Bambusa-Dendrocalamus-Gigantochloa complex (BDG complex) is the most diversified and phylogenetically recalcitrant group of the paleotropical woody bamboos. Species of this complex occur in tropical and subtropical Asia and most of them are of great economic, cultural and ecological value. The lack of resolution achieved through the analyses of previous molecular datasets has long confounded its phylogenetic estimation and generic delimitation. Here, we adopted a ddRAD-seq strategy to investigate phylogenetic relationships of the four main genera (Bambusa, Dendrocalamus, Gigantochloa, and Melocalamus) in the BDG complex. A total of 102 species were sampled, and SNP data were generated. Both MP and ML analyses of the ddRAD-seq data resulted in a well-resolved topology with Gigantochloa and Melocalamus confirmed as monophyletic, and Melocalamus resolved as sister to the rest of the complex. Bambusa and Dendrocalamus were both resolved as paraphyletic. The phylogenetic relationships were mostly supported by morphological evidence including characters of the branch complement, rachilla, lodicules, filaments and stigma. We also generated and assembled complete plastid genomes of 48 representative species. There were conflicts between the plastome and the ddRAD topologies. Our study demonstrated that RAD-seq can be used to reconstruct evolutionary history of lineages such as the bamboos where ancient hybridization and polyploidy play a significant role. The four genera of the BDG complex have a complex evolutionary history which is likely a product of ancient introgression events

Additional file 11: of Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics

Sequence length and model selected for the three data sets used in the study. (DOC 29 kb

Additional file 10: of Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics

Relative plastid rate of molecular evolution among the lineages of Arundinarieae from Bayesian analysis under the lognormal uncorrelated relaxed clock (LURC) model. Branch thickness is proportional to the inferred median rate for the branch with detail numbers. (PDF 372 kb

Additional file 8: of Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics

Phylogenetic relationships among major lineages of Arundinarieae based on plastid noncoding sequences in partitioned maximum likelihood (ML) (A) and Bayesian analysis (B). The partitioned scheme was determined by the software PartitionFinder. Values associated with the nodes indicate the ML or Bayesian support values and the unlabeled nodes receive 100% ML bootstrap support or 1.0 Bayesian posterior probability. (PDF 400 kb