Genetic diversity of NBS–LRR class disease-resistance gene analogs in cultivated and wild eggplants

The genes encoding the nucleotide-binding site (NBS) and leucine-rich repeat (LRR) motifs constitute a large gene family in plants and have attracted much interest, because most of the plant disease-resistance genes that have been cloned are from this gene family. In this study, degenerate oligonucleotide primers, designed on the basis of conserved regions of the NBS domains from known plant resistance genes, were used to isolate resistance gene analogs (RGAs) from cultivated and wild eggplants, i.e., S. melongena, S. aethiopicum gr. Gilo, S. linnaeanum, S. integrifolium, S. sisymbriifolium, and S. khasianum. Sequence analysis indicated that the cloned eggplant RGAs belong to the non-TIR–NBS–LRR type, which are very similar to the R genes or the RGAs identified in other plant species, especially Solanaceae plants, suggesting the existence of common ancestors. Wide genetic diversity of eggplant RGAs was observed both in interspecific and intraspecific sequences, and eight distinct families of eggplant RGAs were identified. Further studies revealed a high average ratio of synonymous to non-synonymous substitution and a low level of recombination. These results suggest that NBS-encoding sequences of RGAs in cultivated and wild eggplants are subject to gradual accumulation of mutations leading to purifying selection. This is the first report of NBS–LRR class RGAs in eggplants.     

Diversity in commercial varieties and landraces of black eggplants and implications for broadening the breeders' gene pool

Black‐coloured eggplants (Solanum melongena) represent the commercially most important group of eggplants in Europe and North America. Most of the modern varieties of black eggplants correspond to F₁ hybrids, which at the same time constitute an elite gene pool for the development of new varieties. However, there are many black landraces and old varieties, which could be useful as sources of variation for black eggplant breeding programmes as well as for the broadening of the genetic diversity of the breeders’ gene pool. We have studied the morphological and molecular [amplified fragment length polymorphism and simple sequence repeat (SSR)] diversity in a collection of 38 black eggplant accessions, including commercial (modern F₁ hybrid and old nonhybrid) varieties and landraces as well as in six nonblack control eggplants, from different origins. The results show that black eggplants contain a considerable morphological and molecular diversity, but commercial varieties, and in particular F₁ hybrids, display a reduced morphological and molecular diversity when compared with landraces. The principal components analysis morphological and principal coordinates analysis molecular analyses show that commercial F₁ hybrids group together, indicating that they share a common and narrow gene pool. Commercial F₁ hybrids present a series of productive advantages, like early production, intense black colour (low L*, a* and b*) values and absence of fruit calyx prickles. However, several of the landraces and old nonhybrid varieties studied present a high yield as well as other traits of interest for eggplant breeding. Furthermore, given the low genetic diversity of F₁ hybrids and the moderate level of SSR heterozygosity found in these materials (0.382), introduction of black landraces and old varieties in the present breeding programmes could contribute to broadening the gene pool used by breeders and this could help increase the heterosis for yield of F₁ hybrids, which is greatly favoured by high heterozygosity levels.     

Using genetic diversity information to establish core collections of Stylosanthes capitata and Stylosanthes macrocephala

Stylosanthes species are important forage legumes in tropical and subtropical areas. S. macrocephala and S. capitata germplasm collections that consist of 134 and 192 accessions, respectively, are maintained at the Brazilian Agricultural Research Corporation Cerrados (Embrapa-Cerrados). Polymorphic microsatellite markers were used to assess genetic diversity and population structure with the aim to assemble a core collection. The mean values of H_O and H_E for S. macrocephala were 0.08 and 0.36, respectively, whereas the means for S. capitata were 0.48 and 0.50, respectively. Roger’s genetic distance varied from 0 to 0.83 for S. macrocephala and from 0 to 0.85 for S. capitata. Analysis with STRUCTURE software distinguished five groups among the S. macrocephala accessions and four groups among those of S. capitata. Nei’s genetic diversity was 27% in S. macrocephala and 11% in S. capitata. Core collections were assembled for both species. For S. macrocephala, all of the allelic diversity was represented by 23 accessions, whereas only 13 accessions were necessary to represent all allelic diversity for S. capitata. The data presented herein evidence the population structure present in the Embrapa-Cerrados germplasm collections of S. macrocephala and S. capitata, which may be useful for breeding programs and germplasm conservation.     

Leaf cuticular n-alkanes as markers in the chemotaxonomy of the eggplant (Solanum melongena L.) and related species

The complex of species formed by eggplant (Solanum melongena L.) and its wild and weedy relatives (mainly S. incanum L. and S. insanum L.) is characterised by an extreme morphological divergence that is not always associated with genetic variation. The taxonomy of so‐called ‘spiny Solanum’ species (subgenus Leptostemonum) is therefore extremely unclear. Cultivated eggplant lacks resistance to pests that frequently occur among the wild forms and species. As these wild plants are a potential gene pool for improvement of eggplant cultivars, knowledge of the characteristics of taxonomic relations between plants of different origin is crucial. We suggest using the leaf cuticular n‐alkane chain length distribution pattern as an alternative taxonomic marker for eggplant and related species. The results are in good agreement with current knowledge of the systematics of these plants; at the same time, the method developed here is useful for verifying plant identification based on morphological traits. Analysis of 13 eggplant cultivars, five accessions of S. incanum and two lines of S. macrocarpon enabled the intraspecific variation within eggplant to be assessed as low. There was wide variability among S. incanum accessions, probably because plants described as S. incanum are members of a number of different species. Some Asian accessions (sometimes described as S. insanum) were found to be almost identical to S. melongena, while a truly wild African S. incanum plant showed extensive similarity. The usefulness of the chemotaxonomic approach in dealing with the S. melongena–S. incanum complex is discussed.     

Genetic Diversity,Population Structure,and Resistance to Phytophthora capsici of a Worldwide Collection of Eggplant Germplasm

Eggplant (Solanum melongena L.) is an important solanaceous crop with high phenotypic diversity and moderate genotypic diversity. Ninety-nine genotypes of eggplant germplasm (species (S. melongena, S. incanum, S. linnaeanum and S. gilo), landraces and heirloom cultivars) from 32 countries and five continents were evaluated for genetic diversity, population structure, fruit shape, and disease resistance to Phytophthora fruit rot. Fruits from each line were measured for fruit shape and evaluated for resistance to two Phytophthora capsici isolates seven days post inoculation. Only one accession (PI 413784) was completely resistant to both isolates evaluated. Partial resistance to Phytophthora fruit rot was found in accessions from all four eggplant species evaluated in this study. Genetic diversity and population structure were assessed using 22 polymorphic simple sequence repeats (SSRs). The polymorphism information content (PIC) for the population was moderate (0.49) in the population. Genetic analyses using the program STRUCTURE indicated the existence of four genetic clusters within the eggplant collection. Population structure was detected when eggplant lines were grouped by species, continent of origin, country of origin, fruit shape and disease resistance.     

Genetic Diversity of Some Pear Cultivars and Genotypes Using Simple Sequence Repeat (SSR) Markers

The genetic diversity and relationships among 47 pear cultivars and genotypes (Pyrus spp.), including 4 Japanese pears (Pyrus pyrifolia), 40 European pears (Pyrus communis), 1 Chinese pear (Pyrus bretschneideri) as well as 2 wild relatives (Pyrus salicifolia and Pyrus mazandaranica) were studied using 28 microsatellite primer pairs. A total of 174 alleles were produced at the 28 SSR loci with their sizes ranging from 81 to 290?bp. The number of observed alleles for each locus ranged from 3 (TsuENH014 and TsuENH046) to 12 (NB103a), with an average of 6.21 alleles per locus. In some SSR loci, more than two alleles were amplified in some cultivars and genotypes, suggesting that duplication has occurred in those accessions. This information suggests that at least two genomic regions exist for these loci in the pear genome. The observed heterozygosity (H _o) values of amplified loci ranged from 0.17 (TsuENH006) to 0.97 (NB103a). Shannon's information index (I) value was observed to be highest (2.14) in the NB103a locus, while the TsuENH006 locus had the lowest value with an average of 1.37 among SSR loci. The Dice genetic similarity coefficient ranged from 0.29 (??Nijisseiki?? and P. mazandaranica) to 0.91 (??Chojuro?? and ??Nijisseiki??) among samples. UPGMA cluster analysis showed two major groups corresponding to the Japanese and European pears.     

High Resolution Melting (HRM) analysis in eggplant (Solanum melongena L.): A tool for microsatellite genotyping and molecular characterization of a Greek Genebank collection

The conservation and characterization of eggplant (Solanum melongena L.) genetic resources in germplasm banks has been the basis of their use in breeding projects, which has resulted in the development of new cultivars. High Resolution Melting (HRM) analysis, combined with eight microsatellite markers, has been integrated in order to facilitate the molecular identification and characterization of the eggplant germplasm, collected from the National Genebank Collection of Greece. The eight microsatellite loci used were highly informative and generated sixty three HRM profiles, which were sufficient to discriminate all eggplant landraces and cultivars studied, highlighting its potential use for cultivar genotyping. The thirty six eggplant genotypes were classified into four clusters. Hence, this assay provided a fast, cost-effective and closed-tube microsatellite genotyping method, well suited for molecular characterization of eggplant cultivars.     

Inheritance of Fusarium wilt resistance introgressed from Solanum aethiopicum Gilo and Aculeatum groups into cultivated eggplant (S. melongena) and development of associated PCR-based markers

The two eggplant relatives Solanum aethiopicum gr. Gilo and Solanum aethiopicum gr. Aculeatum (=Solanum integrifolium) carry resistance to the fungal wilt disease caused by Fusarium oxysporum f. sp. melongenae, a worldwide soil-borne disease of eggplant. To introgress the resistance trait into cultivated eggplant, the tetraploid somatic hybrids S. melongena + S. aethiopicum and S. melongena + S. integrifolium were used. An inheritance study of the resistance was performed on advanced anther culture-derived androgenetic backcross progenies from the two somatic hybrids. The segregation fitted a 3 resistant (R): 1 susceptible (S) ratio in the selfed populations and a 1R:1S ratio in the backcross progenies for the trait derived from S. aethiopicum and S. integrifolium. These ratios are consistent with a single gene, which we designated as Rfo-sa1, controlling the resistance to Fusarium oxysporum f. sp. melongenae. The allelic relationship between the resistance genes from S. aethiopicum and S. integrifolium indicate that these two genes are alleles of the same locus. Bulked Segregant Analysis (BSA) was performed with RAPD markers on the BC₃/BC₅ resistant advanced backcross progenies, and three RAPD markers associated with the resistance trait were identified. Cleaved Amplified Polymorphic Sequences (CAPSs) were subsequently obtained on the basis of the amplicon sequences. The evaluation of the efficiency of these markers in predicting the resistant phenotype in segregating progenies revealed that they represent useful tools for indirect selection of Fusarium resistance in eggplant.     

Current status in production and utilization of dihaploids from somatic hybrids between eggplant (Solanum melongena L.) and its wild relatives

The major constrains for practical exploitation of the somatic hybrids between eggplant and its wild relatives have been their sterility and tetraploidy which prevented their incorporation into breeding programs. Here we demonstrate that anther culture was successfully utilized to bring back the ploidy level to the diploid status in tetraploid interspecific hybrids between eggplant and the allied species S. integrifolium and S. aethiopicum gr. gilo. Both the relative species are resistant to Fusarium oxysporum f. sp. melongenae and to some strains of bacterial wilt (Ralstonia solanacearum) which are very destructive diseases of eggplant. Dihaploid androgenetic plants were obtained from the somatic hybrids, from the “double somatic hybrid” obtained by sexual cross of the two somatic hybrids [(eggplant + S. aethiopicum) × (eggplant + S. integrifolium)], and from tetraploid backcrossed plants between the somatic hybrid with S. aethiopicum and eggplant. Phenotypical, molecular, biological and biochemical characterization, and also artificial inoculation with Fusarium oxysporum are consistent with a recombination between the genomes of the species involved in the hybridizations. Dihaploids resistant to Fusarium were successfully backcrossed with eggplant. Besides their utility as potential valuable breeding materials, the introgressed lines obtained may be utilized in genetic and molecular studies about the resistance to Fusarium from S. integrifolium and S. aethiopicum gr. gilo.     

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.     

Association Mapping for Fruit,Plant and Leaf Morphology Traits in Eggplant

An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders’ traits.     

Morphological and allozyme variation in a collection of Cucumeropsis mannii Naudin (Cucurbitaceae) from Côte d'Ivoire

To set up a rational collecting strategy for germplasm of the edible-seeded cucurbit Cucumeropsis mannii, a study was conducted using 24 morphological and seven putative enzyme markers to determine the intra-specific variability from 16 and 22 accessions (representing three cultivars), respectively. The analysis of variance, showed a significant difference between the three cultivars. Principal component analysis pointed out a variation among individuals, mainly on the basis of flower, fruit, and seed size. Dendrogram with UPGMA method allowed clustering of the cultivars. Genetic diversity indices estimated equalled: 9.96% for the proportion of polymorphic loci (P), 1.10 for the number of alleles (A) and 0.023 for observed heterozygosity (H_o). The level of the within accessions genetic diversity (H_S = 0.078) was higher than among accessions (D_ST = 0.042). Nei's genetic distances between the three cultivars were also low (0.079–0.147), indicating a high degree of similarity of the analysed cultivars.     

Clonal diversity and genetic differentiation revealed by SSR markers in wild Vaccinium macrocarpon and Vaccinium oxycoccos

American cranberry (Vaccinium macrocarpon) is a perennial, woody plant species, native to North American bogs and wetlands. Cranberries represent one of the few agriculturally important native plants in which wild gene pools are still readily available within the undeveloped wetlands of the northern US and Canada. Earlier studies have reported low genetic variation in V. macrocarpon at the species and population level. However, in this study, we characterised 229 individuals of wild V. macrocarpon and V. oxycoccos (small cranberry) from Wisconsin and 22 accessions using microsatellite markers and observed substantial genetic variation and differentiation within and among populations and species. While V. macrocarpon was analysed using 108 alleles from 11 microsatellite loci revealing 42 unique genotypes, V. oxycoccos was analysed using 156 alleles from eight loci revealing 28 unique genotypes. There were a total of 182 alleles found in both species combined with 156 of those alleles present in V. oxycoccos and 84 alleles found in V. macrocarpon. All eight loci possessed species‐specific alleles with V. oxycoccos possessing 98 private alleles versus 26 private alleles found V. macrocarpon, and 58 alleles were found in common between both species. Our data will be valuable not only for future wild cranberry diversity and population genetics research, but for other cranberry breeding and genetics studies.     

Development of a set of genomic microsatellite markers in tea (Camellia L.) (Camelliaceae)

Tea (Camellia L.) is the world’s most consumed health drink and is also important economically. Due to its self-incompatible and outcrossing nature, tea is composed of highly heterogeneous germplasm. It is a perennial, slow-growing crop and hence the successful release of new improved cultivars following conventional breeding methods takes years. In this context, a DNA marker-based molecular breeding approach holds great promise in accelerating genetic improvement programs in tea. Here we describe the isolation of a set of highly polymorphic genomic microsatellite markers using the enrichment approach, which may be useful for phylogenetic and marker-assisted breeding programs in tea. The enriched library comprising 3,205 clones was screened for the presence of microsatellites using a three-primer-based colony PCR method. Four hundred positive clones were selected and sequenced, to reveal 153 sequences containing simple sequence repeats. Seventy-eight primer pairs were designed from repeat-positive sequences, out of which 40 primer pairs produced successful amplifications. Twenty-two of these primer pairs, when tested on a panel of 21 diverse tea clones and accessions, were found to be highly polymorphic, resulting in 137 alleles with an average of 6.76 alleles per primer pair. The polymorphic information content (PIC), expected heterozygosity (H _e) and observed heterozygosity (H _o) of the polymorphic markers ranged from 0.1 to 0.9, 0.1–0.9 and 0.0–0.8, with average values of 0.6 ± 0.18, 0.7 ± 0.17 and 0.5 ± 0.22, respectively. These markers can be applied for various diversity analyses, mapping programs and genotyping of tea crop.     

Role of hydrogen peroxide and ascorbate-glutathione pathway in host resistance to bacterial wilt of eggplant

Ralstonia solanacearum, a soil-borne bacterium causes bacterial wilt, is a lethal disease of eggplant (Solanum melongena L.). However, the first line of defense mechanism of R. solanacearum infection remains unclear. The present study focused on the role of induced H₂O₂, defense-related enzymes of ascorbate-glutathione pathway variations in resistant and susceptible cultivars of eggplant under biotic stress. Fifteen cultivars of eggplant were screened for bacterial wilt resistance, and the concentration of antioxidant enzymes were estimated upon infection with R. solanacearum. A quantitative real-time PCR was also carried out to study the expression of defense genes. The concentration of H₂O₂ in the pathogen inoculated seedlings was two folds higher at 12 h after pathogen inoculation compared to control. Antioxidant enzymes of ascorbate-glutathione pathway were rapidly increased in resistant cultivars followed by susceptible and highly susceptible cultivars upon pathogen inoculation. The enzyme activity of ascorbate-glutathione pathway correlates by amplification of their defense genes along with pathogenesis-related protein-1a (PR-1a). The expressions of defense genes increased 2.5?3.5 folds in resistant eggplant cultivars after pathogen inoculation. The biochemical and molecular markers provided an insight to understand the first line of defense responses in eggplant cultivars upon inoculation with the pathogen.     

Isozyme analysis of genetic variability and population structure of Lactuca L. germplasm

Isozymes were used to investigate the genetic variability, population structure, and relationships of Lactuca germplasm. The isozyme systems revealed 16 putative loci of a total of 31 alleles. Out of these 16 loci, 11 were polymorphic. The average values of expected heterozygosity (H_e), observed heterozygosity (H_o), mean number of alleles per locus (A) and effective number of alleles per locus (A_e) were 0.2227, 0.266, 1.3005 and 1.369, respectively. The average fixation indices were lower than zero for most of the accessions studied, indicating an excess of heterozygotes. Genetic differentiation among accessions (F_ST) exhibited that 51.3% of the isozyme variation was recorded among accessions, and 48.7% of the genetic variation resided within accessions. The average values of total heterozygosity (H_T) and intra-accessional genetic diversity (H_S) were 0.352 and 0.171, respectively. Moreover, the inter-accessional genetic diversity (D_ST) ranged from 0 to 0.424 with an average of 0.18. Cluster analysis revealed that L. sativa cultivars were distributed throughout different Lactuca species. Thereby, isozymes results confirms the hypothesis of the polyphyletic origin of L. sativa. This high level of genetic variation proved that isozymes are efficient for polymorphism analysis of Lactuca germplasm.     

Random amplified polymorphic DNA variation in the eggplant,Solanum melongena L. (Solanaceae)

RAPD analysis was carried out on 52 accessions of Solanum melongena (eggplant) and related weedy forms known as insanum. Twenty-two primers amplified 130 fragments. Solanum melongena exhibited 117 of the fragments, all of which were also present in insanum. Insanum displayed an additional 13 fragments not found in S. melongena. Overall, the insanum accessions were more diverse than those of S. melongena. The calculated similarity between them was 0.947. The RAPD results were closely concordant with the results of an electrophoretic isozyme survey performed on the same accessions. The concordance of the results shows that even though S. melongena and insanum are highly diverse morphologically, it is no longer appropriate to distinguish them taxonomically.