Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.

Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration-diversification routes

Eggplant (Solanum melongena) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena, similar to what was described for other fruit-bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving 'local' phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P-SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetable.

Conventional and new genetic resources for an eggplant breeding revolution

Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. It is closely related to over 500 species of Solanum subgenus Leptostemonum that belong to its primary, secondary, and tertiary genepools and exhibit a wide range of characteristics useful for eggplant breeding, including traits adaptive to climate change. Germplasm banks worldwide hold more than 19 000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and for adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in its relatives can greatly contribute to eggplant breeding. The recent creation of new genetic resources such as mutant libraries, core collections, recombinant inbred lines, and sets of introgression lines will be another crucial element and will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change.

Genomic Analysis Highlights Putative Defective Susceptibility Genes in Tomato Germplasm

Tomato (Solanum lycopersicum L.) is one of the most widely grown vegetables in the world and is impacted by many diseases which cause yield reduction or even crop failure. Breeding for disease resistance is thus a key objective in tomato improvement. Since disease arises from a compatible interaction between a plant and a pathogen, a mutation which alters a plant susceptibility (S) gene facilitating compatibility may induce broad-spectrum and durable plant resistance. Here, we report on a genome-wide analysis of a set of 360 tomato genotypes, with the goal of identifying defective S-gene alleles as a potential source for the breeding of resistance. A set of 125 gene homologs of 10 S-genes (PMR 4, PMR5, PMR6, MLO, BIK1, DMR1, DMR6, DND1, CPR5, and SR1) were analyzed. Their genomic sequences were examined and SNPs/indels were annotated using the SNPeff pipeline. A total of 54,000 SNPs/indels were identified, among which 1300 were estimated to have a moderate impact (non-synonymous variants), while 120 were estimated to have a high impact (e.g., missense/nonsense/frameshift variants). The latter were then analyzed for their effect on gene functionality. A total of 103 genotypes showed one high-impact mutation in at least one of the scouted genes, while in 10 genotypes, more than 4 high-impact mutations in as many genes were detected. A set of 10 SNPs were validated through Sanger sequencing. Three genotypes carrying high-impact homozygous SNPs in S-genes were infected with Oidium neolycopersici, and two highlighted a significantly reduced susceptibility to the fungus. The existing mutations fall within the scope of a history of safe use and can be useful to guide risk assessment in evaluating the effect of new genomic techniques.

Diversity analyses in two ornamental and large-genome Ranunculaceae species based on a low-cost Klenow NGS-based protocol

Persian buttercup (Ranunculus asiaticus L.) and poppy anemone (Anemone coronaria L.) are ornamental, outcrossing, perennial species belonging to the Ranunculaceae family, characterized by large and highly repetitive genomes. We applied K-seq protocol in both species to generate high-throughput sequencing data and produce a large number of genetic polymorphisms. The technique entails the application of Klenow polymerase-based PCR using short primers designed by analyzing k-mer sets in the genome sequence. To date the genome sequence of both species has not been released, thus we designed primer sets based on the reference the genome sequence of the related species Aquilegia oxysepala var. kansuensis (Brühl). A whole of 11,542 SNPs were selected for assessing genetic diversity of eighteen commercial varieties of R. asiaticus, while 1,752 SNPs for assessing genetic diversity in six cultivars of A. coronaria. UPGMA dendrograms were constructed and in R. asiaticus integrated in with PCA analysis. This study reports the first molecular fingerprinting within Persian buttercup, while the results obtained in poppy anemone were compared with a previously published SSR-based fingerprinting, proving K-seq to be an efficient protocol for the genotyping of complex genetic backgrounds.

A Compendium for Novel Marker-Based Breeding Strategies in Eggplant

The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.

First genetic maps development and QTL mining in Ranunculus asiaticus L. through ddRADseq

Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating, which are propagated through rhizomes or micro-propagated in vitro. In order to escalate selection efficiency and respond to market requests, more knowledge of buttercup genetics would facilitate the identification of markers associated with loci and genes controlling key ornamental traits, opening the way for molecular assisted breeding programs. Reduced-representation sequencing (RRS) represents a powerful tool for plant genotyping, especially in case of large genomes such as the one of buttercup, and have been applied for the development of high-density genetic maps in several species. We report on the development of the first molecular-genetic maps in R. asiaticus based on of a two-way pseudo-testcross strategy. A double digest restriction-site associated DNA (ddRAD) approach was applied for genotyping two F₁ mapping populations, whose female parents were a genotype of a so called 'ponpon' and of a 'double flower' varieties, while the common male parental ('Cipro') was a genotype producing a simple flower. The ddRAD generated a total of ~2Gb demultiplexed reads, resulting in an average of 8,3M reads per line. The sstacks pipeline was applied for the construction of a mock reference genome based on sequencing data, and SNP markers segregating in only one of the parents were retained for map construction by treating the F₁ population as a backcross. The four parental maps (two of the female parents and two of the common male parent) were aligned with 106 common markers and 8 linkage groups were identified, corresponding to the haploid chromosome number of the species. An average of 586 markers were associated with each parental map, with a marker density ranging from 1 marker/cM to 4.4 markers/cM. The developed maps were used for QTL analysis for flower color, leading to the identification of major QTLs for purple pigmentation. These results contribute to dissect on the genetics of Persian buttercup, enabling the development of new approaches for future varietal development.

Genome-wide association study of individual sugar content in fruit of Japanese pear (Pyrus spp.)

BACKGROUND

Understanding mechanisms of sugar accumulation and composition is essential to determining fruit quality and maintaining a desirable balance of sugars in plant storage organs. The major sugars in mature Rosaceae fruits are sucrose, fructose, glucose, and sorbitol. Among these, sucrose and fructose have high sweetness, whereas glucose and sorbitol have low sweetness. Japanese pear has extensive variation in individual sugar contents in mature fruit. Increasing total sugar content and that of individual high-sweetness sugars is a major target of breeding programs. The objective of this study was to identify quantitative trait loci (QTLs) associated with fruit traits including individual sugar accumulation, to infer the candidate genes underlying the QTLs, and to assess the potential of genomic selection for breeding pear fruit traits.

RESULTS

We evaluated 10 fruit traits and conducted genome-wide association studies (GWAS) for 106 cultivars and 17 breeding populations (1112 F1 individuals) using 3484 tag single-nucleotide polymorphisms (SNPs). By implementing a mixed linear model and a Bayesian multiple-QTL model in GWAS, 56 SNPs associated with fruit traits were identified. In particular, a SNP located close to acid invertase gene PPAIV3 on chromosome 7 and a newly identified SNP on chromosome 11 had quite large effects on accumulation of sucrose and glucose, respectively. We used 'Golden Delicious' doubled haploid 13 (GDDH13), an apple reference genome, to infer the candidate genes for the identified SNPs. In the region flanking the SNP on chromosome 11, there is a tandem repeat of early responsive to dehydration (ERD6)-like sugar transporter genes that might play a role in the phenotypes observed.

CONCLUSIONS

SNPs associated with individual sugar accumulation were newly identified at several loci, and candidate genes underlying QTLs were inferred using advanced apple genome information. The candidate genes for the QTLs are conserved across Pyrinae genomes, which will be useful for further fruit quality studies in Rosaceae. The accuracies of genomic selection for sucrose, fructose, and glucose with genomic best linear unbiased prediction (GBLUP) were relatively high (0.67-0.75), suggesting that it would be possible to select individuals having high-sweetness fruit with high sucrose and fructose contents and low glucose content.

Exploring the genetic diversity and population structure of scarlet eggplant germplasm from Rwanda through iPBS-retrotransposon markers

BACKGROUND

Scarlet eggplant (Solanum aethiopicum gr. gilo) is a part of African indigenous vegetables and acknowledged as a source of variations in the breeding of Brinjal. Since its genetic diversity is still largely unexplored, therefore genetic diversity and population structure of this plant were investigated in this study.

METHODS AND RESULTS

Scarlet eggplant germplasm made of fifty-two accessions originated from two districts of Rwanda was assessed by employing the iPBS-retrotransposon markers system. Twelve most polymorphic primers were employed for molecular characterization and they yielded 329 total bands whereupon 85.03% were polymorphic. The recorded mean polymorphism information content was 0.363 and other diversity indices such as; mean the effective number of alleles, mean Shannon's information index and gene diversity with the following values; 1.298, 0.300 and 0.187 respectively. A superior level of diversity was noticed among accessions from Musanze district. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) gathered scarlet germplasm in a divergence manner to their collection district. Analysis of molecular variance (AMOVA) displayed that the utmost variations (81%) in scarlet eggplant germplasm are resulting in differences within populations.

CONCLUSIONS

The extensive diversity of scarlet eggplant in Rwanda might be used to form the base and genetic resource of an exhaustive breeding program of this economically important African indigenous vegetable. For instance, accessions MZE53 and GKE11 might be proposed as parent candidates due to their high relative genetic distance (0.6781).

Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding

Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant '67/3' reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.

Genetics and breeding for climate change in Orphan crops

Climate change is rapidly changing how we live, what we eat and produce, the crops we breed and the target traits. Previously underutilized orphan crops that are climate resilient are receiving much attention from the crops research community, as they are often the only crops left in the field after periods of extreme weather conditions. There are several orphan crops with incredible resilience to biotic and abiotic stresses. Some are nutritious, while others provide good sources of biofuel, medicine and other industrial raw materials. Despite these benefits, orphan crops are still lacking in important genetic and genomic resources that could be used to fast track their improvement and make their production profitable. Progress has been made in generating draft genomes of at least 28 orphan crops over the last decade, thanks to the reducing cost of sequencing. The implementation of a structured breeding program that takes advantage of additional modern crop improvement tools such as genomic selection, speed breeding, genome editing, high throughput phenotyping and breeding digitization would make rapid improvement of these orphan crops possible, but would require coordinated research investment. Other production challenges such as lack of adequate germplasm conservation, poor/non-existent seed systems and agricultural extension services, as well as poor marketing channels will also need to be improved if orphan crops were to be profitable. We review the importance of breeding orphan crops under the increasing effects of climate change, highlight existing gaps that need to be addressed and share some lessons to be learned from major crops.

The Genetic Basis of Tomato Aroma

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

A Deep Learning-Based System (Microscan) for the Identification of Pollen Development Stages and Its Application to Obtaining Doubled Haploid Lines in Eggplant

The development of double haploids (DHs) is a straightforward path for obtaining pure lines but has multiple bottlenecks. Among them is the determination of the optimal stage of pollen induction for androgenesis. In this work, we developed Microscan, a deep learning-based system for the detection and recognition of the stages of pollen development. In a first experiment, the algorithm was developed adapting the RetinaNet predictive model using microspores of different eggplant accessions as samples. A mean average precision of 86.30% was obtained. In a second experiment, the anther range to be cultivated in vitro was determined in three eggplant genotypes by applying the Microscan system. Subsequently, they were cultivated following two different androgenesis protocols (Cb and E6). The response was only observed in the anther size range predicted by Microscan, obtaining the best results with the E6 protocol. The plants obtained were characterized by flow cytometry and with the Single Primer Enrichment Technology high-throughput genotyping platform, obtaining a high rate of confirmed haploid and double haploid plants. Microscan has been revealed as a tool for the high-throughput efficient analysis of microspore samples, as it has been exemplified in eggplant by providing an increase in the yield of DHs production.

Development of High-Density Genetic Linkage Maps and Identification of Loci for Chestnut Gall Wasp Resistance in Castanea spp

Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.

A New Intra-Specific and High-Resolution Genetic Map of Eggplant Based on a RIL Population, and Location of QTLs Related to Plant Anthocyanin Pigmentation and Seed Vigour

Eggplant is the second most important solanaceous berry-producing crop after tomato. Despite mapping studies based on bi-parental progenies and GWAS approaches having been performed, an eggplant intraspecific high-resolution map is still lacking. We developed a RIL population from the intraspecific cross ‘305E40’, (androgenetic introgressed line carrying the locus Rfo-Sa1 conferring Fusarium resistance) x ‘67/3’ (breeding line whose genome sequence was recently released). One hundred and sixty-three RILs were genotyped by a genotype-by-sequencing (GBS) approach, which allowed us to identify 10,361 polymorphic sites. Overall, 267 Gb of sequencing data were generated and ~773 M Illumina paired end (PE) reads were mapped against the reference sequence. A new linkage map was developed, including 7249 SNPs assigned to the 12 chromosomes and spanning 2169.23 cM, with iaci@liberoan average distance of 0.4 cM between adjacent markers. This was used to elucidate the genetic bases of seven traits related to anthocyanin content in different organs recorded in three locations as well as seed vigor. Overall, from 7 to 17 QTLs (at least one major QTL) were identified for each trait. These results demonstrate that our newly developed map supplies valuable information for QTL fine mapping, candidate gene identification, and the development of molecular markers for marker assisted selection (MAS) of favorable alleles.

A highly efficient organogenesis protocol based on zeatin riboside for in vitro regeneration of eggplant

BACKGROUND

Efficient organogenesis induction in eggplant (Solanum melongena L.) is required for multiple in vitro culture applications. In this work, we aimed at developing a universal protocol for efficient in vitro regeneration of eggplant mainly based on the use of zeatin riboside (ZR). We evaluated the effect of seven combinations of ZR with indoleacetic acid (IAA) for organogenic regeneration in five genetically diverse S. melongena and one S. insanum L. accessions using two photoperiod conditions. In addition, the effect of six different concentrations of indolebutyric acid (IBA) in order to promote rooting was assessed to facilitate subsequent acclimatization of plants. The ploidy level of regenerated plants was studied.

RESULTS

In a first experiment with accessions MEL1 and MEL3, significant (p < 0.05) differences were observed for the four factors evaluated for organogenesis from cotyledon, hypocotyl and leaf explants, with the best results obtained (9 and 11 shoots for MEL1 and MEL3, respectively) using cotyledon tissue, 16 h light / 8 h dark photoperiod conditions, and medium E6 (2 mg/L of ZR and 0 mg/L of IAA). The best combination of conditions was tested in the other four accessions and confirmed its high regeneration efficiency per explant when using both cotyledon and hypocotyl tissues. The best rooting media was R2 (1 mg/L IBA). The analysis of ploidy level revealed that between 25 and 50% of the regenerated plantlets were tetraploid.

CONCLUSIONS

An efficient protocol for organogenesis of both cultivated and wild accessions of eggplant, based on the use of ZR, is proposed. The universal protocol developed may be useful for fostering in vitro culture applications in eggplant requiring regeneration of plants and, in addition, allows developing tetraploid plants without the need of antimitotic chemicals.

Comparative analysis of the responses to water stress in eggplant (Solanum melongena) cultivars

Little information is available on the physiological and biochemical responses to water stress in eggplant (Solanum melongena). We evaluated four genetically diverse eggplant varieties (MEL3-MEL6) under control and water stress conditions. Measurements were taken for plant growth, tissue water content, levels of chlorophylls a and b, carotenoids, proline, malondialdehyde, total phenolics, total flavonoids, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR) activities. For most traits, the water stress treatment had a greater contribution than the variety effect to the total sums of squares in an ANOVA analysis, except for total flavonoids, SOD, APX, and GR. The water stress treatment had a strong effect on plant growth and tissue water content. In general, water stress reduced the three photosynthetic pigments, increased proline, malondialdehyde, total phenolics, and total flavonoids, although some varietal differences were observed. Different patterns were also detected in the activities of the four enzymes evaluated, but few differences were observed for individual varieties between the control and water stress treatments. Many significant phenotypic correlations were observed among the traits studied, but only eight environmental correlations were detected. A PCA analysis distinctly separated individuals according to the treatment, and revealed a clearer separation of varieties under water stress than under control conditions, pointing to varietal differences in the responses to stress. Our results suggest that proline could be used as a marker for drought stress tolerance in this species. The information obtained provides new insight on the physiological and biochemical responses of eggplant to drought stress.

Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm

Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies panel design, and allows higher levels of multiplexing than PCR-based genotyping. Thanks to the sequencing of the regions surrounding the target SNP, SPET allows the discovery of thousands of closely linked, novel SNPs. In order to assess the potential of SPET for high-throughput genotyping in plants, a panel comprising 5k target SNPs, designed both on coding regions and introns/UTRs, was developed for tomato and eggplant. Genotyping of two panels composed of 400 tomato and 422 eggplant accessions, comprising both domesticated material and wild relatives, generated a total of 12,002 and 30,731 high confidence SNPs, respectively, which comprised both target and novel SNPs in an approximate ratio of 1:1.6, and 1:5.5 in tomato and eggplant, respectively. The vast majority of the markers was transferrable to related species that diverged up to 3.4 million years ago (Solanum pennellii for tomato and S. macrocarpon for eggplant). Maximum Likelihood phylogenetic trees and PCA outputs obtained from the whole dataset highlighted genetic relationships among accessions and species which were congruent with what was previously reported in literature. Better discrimination among domesticated accessions was achieved by using the target SNPs, while better discrimination among wild species was achieved using the whole SNP dataset. Our results reveal that SPET genotyping is a robust, high-throughput technology for genetic fingerprinting, with a high degree of cross-transferability between crops and their cultivated and wild relatives, and allows identification of duplicates and mislabeled accessions in genebanks.

Genetic Analysis for Fruit Phenolics Content, Flesh Color, and Browning Related Traits in Eggplant (Solanum melongena)

Eggplant varieties rich in bioactive chlorogenic acid along with less browning are preferred by consumers. Therefore, genetics of fruit phenolics, fruit flesh colour, and browning related traits were studied in the genotypes of eggplant, comprising of nine cultivated varieties and one accession of eggplant‘s primary genepool wild relative Solanum insanum (INS2). These accessions were genotyped based on the 7335 polymorphic single-nucleotide polymorphisms (SNP) markers. After that, genotypes were crossed in half diallel fashion to produce 45 hybrids. The INS2 displayed the highest values for the total phenolics and chlorogenic acid content (CGA). For all of the biochemical traits studied, significant values of general and specific combining ability (GCA and SCA) effects were determined. The baker ratio estimates were high (>0.75) for all of the traits. Highly significant and positive heterosis (%) was determined for the dry matter, total phenolics, CGA, and area (%) of CGA content. The phenolics content of the fruit (total phenolics and CGA) was not significantly correlated with flesh colour and browning related traits. However, when the path coefficient analysis was performed considering the CGA as a dependent variable, it was determined that the flesh colour related traits most considerably affected the CGA. The genetic distance showed a diminutive correlation with the hybrid means, heterosis, and SCA values. Overall, this study provides important information regarding the underlying genetics of important biochemical traits of eggplant fruit.

Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement

Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8× and comparing to the high-quality reference genome "67/3" over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding.

Shedding new light on the origin and spread of the brinjal eggplant (Solanum melongena L.) and its wild relatives

PREMISE OF THE STUDY

While brinjal eggplant (Solanum melongena L.) is the second most important solanaceous fruit crop, we lack firm knowledge of its evolutionary relationships. This in turn limits efficient use of crop wild relatives in eggplant improvement. Here, we examine the hypothesis of linear step-wise expansion of the eggplant group from Africa to Asia.

METHODS

We use museum collections to generate nuclear and full-plastome data for all species of the Eggplant clade. We combine a phylogenomic approach with distribution data to infer a biogeographic scenario for the clade.

KEY RESULTS

The Eggplant clade has Pleistocene origins in northern Africa. Dispersals to tropical Asia gave rise to Solanum insanum, the wild progenitor of the eggplant, and to African distinct lineages of widespread and southern African species. Results suggest that spread of the species to southern Africa has been recent and likely facilitated by large mammalian herbivores, such as the African elephant and impala feeding on Solanum fruit.

CONCLUSIONS

Rather than a linear 'Out Of Africa' sequence, our results are more consistent with an initial dispersal event into Asia, and subsequent wide dispersal and differentiation across Africa driven by large mammalian herbivores. Our evolutionary results will affect future work on eggplant domestication and affect the use of wild relatives in breeding of this increasingly important solanaceous crop.

Diallel genetic analysis for multiple traits in eggplant and assessment of genetic distances for predicting hybrids performance

Evaluation and prediction of the performance of hybrids is important in eggplant (Solanum melongena) breeding. A set of 10 morphologically highly diverse eggplant parents, including nine inbred S. melongena and one weedy S. insanum accessions, were intercrossed according to a half-diallel mating design without reciprocals to obtain 45 hybrids. Parents and hybrids were evaluated for 14 morphological and agronomic conventional descriptors and 14 fruit morphometric traits using Tomato Analyzer. Genetic distances among parents were estimated with 7,335 polymorphic SNP markers. Wide ranges of variation and significant differences were observed in the set of 55 genotypes for all traits, although the hybrids group had significantly higher vigour and yield than parents. General and specific combining abilities (GCA and SCA) were significant for most (GCA) or all (SCA) traits, although a wide variation was obtained for GCA/SCA ratios. Many relevant traits associated to vigour and yield had low GCA/SCA ratios and narrow-sense heritability (h2) values, while the reverse occurred for most fruit shape descriptors. Broad-sense heritability (H2) values were generally high, irrespective of GCA/SCA ratios. Significant correlations were found between traits related to size of leaf, flower and fruit, as well as among many fruit morphometric traits. Genetic distances (GD) among parents were coherent with their phylogenetic relationships, but few significant and generally low correlations were found between GD and hybrid means, heterosis or SCA. The results provide relevant information for developing appropriate strategies for parent selection and hybrid development in eggplant and suggest that GD among parents have limited value to predict hybrid performance in this crop.

Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource

We have characterized the simple sequence repeat (SSR) markers of the eggplant (Solanum melongena) using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were complex, with two stretches of repeats separated by an intervening block of <100 nt. Di- and trinucleotide SSRs accounted, respectively, for 43 and 37% of the total. The SSRs were classified according to their number of repeats and overall length, and were assigned to their linkage group. We found 2,449 of the perfect SSRs in 2,086 genes, with an overall density of 18.5 SSRs/Mbp across the gene space; 3,524 imperfect SSRs were present in 2,924 genes at a density of 26.7 SSRs/Mbp. Putative functions were assigned via ontology to genes containing at least one SSR. Using this data we developed an "Eggplant Microsatellite DataBase" (EgMiDB) which permits identification of SSR markers in terms of their location on the genome, type of repeat (perfect vs. imperfect), motif type, sequence, repeat number and genomic/gene context. It also suggests forward and reverse primers. We employed an in silico PCR analysis to validate these SSR markers, using as templates two CDS sets and three assembled transcriptomes obtained from diverse eggplant accessions.