Production of interspecific hybrids between commercial cultivars of the eggplant (Solanum melongena L.) and its wild relative S. torvum

Genetic mapping and quantitative trait loci analysis for pistillate flowers per node and multi-pistillate flower traits in the F2 cucumber population

This study focused on cucumbers' multi-pistillate flower (MPF) trait, which is essential for high yields. A genetic linkage map was constructed using a population of 219 F2 plants to analyze quantitative trait loci (QTL) associated with MPF traits. Crossbreeding of EWSCU-809 (MPF) with EWSCU-989 (single pistillate flower: SPF) generated an F1 hybrid that self-pollinated to form an F2 population. Based on 244 single nucleotide polymorphic markers across seven cucumber chromosomes, a linkage map facilitated QTL analysis considering average pistillate flowers (PFs) per node and nodes with MPF traits. The results indicated a 9:6:1 epistatic ratio in the F2 populations, revealing recessive allele control of the MPF trait in gynoecious plants. Three QTLs (qMP2.1, qMP3, qMP7) on chromosomes 2, 3, and 7 were associated with average PFs per node, explaining 5.6 to 10.3% of phenotypic variation. Four QTLs (qMP2.2, qMP3, qMP4, qMP7) on chromosomes 2, 3, 4, and 7 were linked to the presence of nodes with MPF traits, explaining 5.8 to 10.6% of phenotypic variance. Notably, QTL regions overlapped between the two datasets, suggesting pleiotropic effects, particularly on chromosomes 3 and 7. These reliable QTLs have the potential to improve breeding programs, enhance PF development, and increase cucumber yields.

Characteristics, Comparative Analysis, and Phylogenetic Relationships of Chloroplast Genomes of Cultivars and Wild Relatives of Eggplant (Solanum melongena)

The eggplant (Solanum melongena) is a popular vegetable around the world. However, the origin and evolution of eggplant has long been considered complex and unclear, which has become the barrier to improvements in eggplant breeding. Sequencing and comparative analyses of 13 complete chloroplast (cp) genomes of seven Solanum species were performed. Genome sizes were between 154,942 and 156,004 bp, the smallest genome was from S. torvum and the largest from S. macrocapon. Thirteen cp genomes showed highly conserved sequences and GC contents, particularly at the subgenus level. All genes in the 13 genomes were annotated. The cp genomes in this study comprised 130 genes (i.e., 80 protein-coding genes, 8 rRNA genes, and 42 tRNA genes), apart from S. sisymbriifolium, which had 129 (79 protein-coding genes, 8 rRNA genes, and 42 tRNA genes.). The rps16 was absent from the cp genome of S. sisymbriifolium, resulting in a nonsense mutation. Twelve hotspot regions of the cp genome were identified, which showed a series of sequence variations and differed significantly in the inverted repeat/single-copy boundary regions. Furthermore, phylogenetic analysis was conducted using 46 cp genomic sequences to determine interspecific genetic and phylogenetic relationships in Solanum species. All species formed two branches, one of which contained all cultivars of the subgenus Leptostemonum. The cp genome data and phylogenetic analysis provides molecular evidence revealing the origin and evolutionary relationships of S. melongena and its wild relatives. Our findings suggest precise intra- and interspecies relatedness within the subgenus Leptostemonum, which has positive implications for work on improvements in eggplant breeding, particularly in producing heterosis, expanding the source of species variation, and breeding new varieties.

Doubled Haploids in Eggplant

Eggplant is a solanaceous crop cultivated worldwide for its edible fruit. Eggplant breeding programs are mainly aimed to the generation of F1 hybrids by crossing two highly homozygous, pure lines, which are traditionally obtained upon several self crossing generations, which is an expensive and time consuming process. Alternatively, fully homozygous, doubled haploid (DH) individuals can be induced from haploid cells of the germ line in a single generation. Several attempts have been made to develop protocols to produce eggplant DHs principally using anther culture and isolated microspore culture. Eggplant could be considered a moderately recalcitrant species in terms of ability for DH production. Anther culture stands nowadays as the most valuable technology to obtain eggplant DHs. However, the theoretical possibility of having plants regenerated from somatic tissues of the anther walls cannot be ruled out. For this reason, the use of isolated microspores is recommended when possible. This approach still has room for improvement, but it is largely genotype-dependent. In this review, we compile the most relevant advances made in DH production in eggplant, their application to breeding programs, and the future perspectives for the development of other, less genotype-dependent, DH technologies.

Development of Interspecific Hybrids between a Cultivated Eggplant Resistant to Bacterial Wilt (Ralstonia solanacearum) and Eggplant Wild Relatives for the Development of Rootstocks

Bacterial wilt caused by Ralstonia solanacerum is one of the most economically and destructive eggplant diseases in many tropical and subtropical areas of the world. The objectives of this study were to develop interspecific hybrids, as potential rootstocks, between the eggplant (Solanum melongena) bacterial wilt resistant line EG203 and four wild accessions (S. incanum UPV1, S. insanum UPV2, S.anguivi UPV3, and S. sisymbriifolium UPV4), and to evaluate interspecific hybrids along with parents for resistance to bacterial wilt strains Pss97 and Pss2016. EG203 was crossed successfully with wild accessions UPV2 and UPV3 and produced viable seeds that germinated when wild accessions were used as a maternal parent in the crosses. In addition, viable interspecific hybrids between EG203 and UPV1 were obtained in both directions of the hybridization, although embryo rescue had to be used. Hybridity was confirmed in the four developed interspecific hybrid combinations with three SSR markers. EG203 was resistant to both strains Pss97 and Pss2016, while UPV1 and UPV3 were, respectively, resistant and moderately resistant to Pss2016. The four interspecific hybrids with UPV2, UPV3, and UPV1 were susceptible to both bacterial wilt strains, indicating that the resistance of EG203, UPV1, and UPV3 behaves as recessive in interspecific crosses. However, given the vigor of interspecific hybrids between eggplant and the three cultivated wild species, these hybrids may be of interest as rootstocks. However, the development of interspecific hybrid rootstocks resistant to bacterial wilt will probably require the identification of new sources of dominant resistance to this pathogen in the eggplant wild relatives.

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

Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.

Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

Background

Solanum incanum is a close wild relative of S. melongena with high contents of bioactive phenolics and drought tolerance. S. aethiopicum is a cultivated African eggplant cross-compatible with S. melongena. Despite their great interest in S. melongena breeding programs, the genomic resources for these species are scarce.

Results

RNA-Seq was performed with NGS from pooled RNA of young leaf, floral bud and young fruit tissues, generating more than one hundred millions raw reads per species. The transcriptomes were assembled in 83,905 unigenes for S. incanum and in 87,084 unigenes for S. aethiopicum with an average length of 696 and 722 bp, respectively. The unigenes were structurally and functionally annotated based on comparison with public databases by using bioinformatic tools. The single nucleotide variant calling analysis (SNPs and INDELs) was performed by mapping our S. incanum and S. aethiopicum reads, as well as reads from S. melongena and S. torvum available on NCBI database (National Center for Biotechnology Information), against the eggplant genome. Both intraspecific and interspecific polymorphisms were identified and subsets of molecular markers were created for all species combinations. 36 SNVs were selected for validation in the S. incanum and S. aethiopicum accessions and 96 % were correctly amplified confirming the polymorphisms. In addition, 976 and 1,278 SSRs were identified in S. incanum and S. aethiopicum transcriptomes respectively, and a set of them were validated.

Conclusions

This work provides a broad insight into gene sequences and allelic variation in S. incanum and S. aethiopicum. This work is a first step toward better understanding of target genes involved in metabolic pathways relevant for eggplant breeding. The molecular markers detected in this study could be used across all the eggplant genepool, which is of interest for breeding programs as well as to perform marker-trait association and QTL analysis studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2631-4) contains supplementary material, which is available to authorized users.

Crop wild relatives of the brinjal eggplant (Solanum melongena): Poorly represented in genebanks and many species at risk of extinction

PREMISE OF THE STUDY

Crop wild relatives (CWR) provide important traits for plant breeding, including pest, pathogen, and abiotic stress resistance. Therefore, their conservation and future availability are essential for food security. Despite this need, the world's genebanks are currently thought to conserve only a small fraction of the total diversity of CWR.

METHODS

We define the eggplant genepool using the results of recent taxonomic and phylogenetic studies. We identify the gaps in germplasm accessions for eggplant (Solanum melongena L.) CWR by comparing georeferenced herbarium records and germplasm accessions using a gap analysis methodology implementing species distribution models (SDM). Preliminary conservation assessments using IUCN criteria were done for all species and were combined with the gap analysis to pinpoint where under-collected and threatened CWR species coincide with high human disturbance and occur outside of protected areas.

KEY RESULTS

We show that many eggplant CWR are poorly represented in genebanks compared to their native ranges. Priority areas for future collecting are concentrated in Africa, especially along the Kenya-Tanzania border. Fourteen species of eggplant CWR are assessed as threatened or near-threatened; these are also concentrated in eastern Africa.

CONCLUSIONS

The knowledge base upon which conservation of wild relative germplasm depends must take into account both taxonomic and phylogenetic advances. Beyond traditional research focus on close relatives of crops, we emphasize the benefits of defining a broad CWR genepool, and the importance of assessing threats to wild species when targeting localities for future collection of CWR to improve crop breeding in the face of environmental change.

Genetic variation in cultivated Rheum tanguticum populations

To examine whether cultivation reduced genetic variation in the important Chinese medicinal plant Rheum tanguticum, the levels and distribution of genetic variation were investigated using ISSR markers. Fifty-eight R. tanguticum individuals from five cultivated populations were studied. Thirteen primers were used and a total of 320 DNA bands were scored. High levels of genetic diversity were detected in cultivated R. tanguticum (PPB = 82.19, H = 0.2498, H_B = 0.3231, I = 0.3812) and could be explained by the outcrossing system, as well as long-lived and human-mediated seed exchanges. Analysis of molecular variance (AMOVA) showed that more genetic variation was found within populations (76.1%) than among them (23.9%). This was supported by the coefficient of gene differentiation (G_st = 0.2742) and Bayesian analysis (θ_B = 0.1963). The Mantel test revealed no significant correlation between genetic and geographic distances among populations (r = 0.1176, p = 0.3686). UPGMA showed that the five cultivated populations were separated into three clusters, which was in good accordance with the results provided by the Bayesian software STRUCTURE (K = 3). A short domestication history and no artificial selection may be an effective way of maintaining and conserving the gene pools of wild R. tanguticum.