Genetic mapping of simply inherited categorical traits, including anthocyanin accumulation profiles and fruit appearance, in eggplant (Solanum melongena).

BACKGROUND: The appearance quality of the eggplant (Solanum melongena L.) fruit is an important trait that influences its commercial value. It is known that quality traits such as anthocyanin composition and fruit surface pattern are categorical and are inherited simply. However, research examples of gene mapping for the composition (anthocyanin accumulation profile) and the surface pattern in eggplant fruit are limited. METHODS AND RESULTS: To map loci for these traits including the accumulation profiles of two anthocyanins, a widely spreading anthocyanin, delphinidin 3-(p-coumaroyl) rutinoside-5-glucoside (nasunin), and the relatively rare delphinidin 3-glucoside (D3G), we used two F2 intracrossed populations (LWF2 and N28F2). For the LWF2 population, mapping was achieved by reconstructing the linkage map created by Fukuoka et al. [1]. In the case of the N28F2 population, we constructed a linkage map consisting of 13 linkage groups using 238 simple sequence repeats, 75 single-nucleotide polymorphisms. Using the two F2 populations, the nasunin accumulating profile, the striped pattern on the fruit surface, the colors of flowers, fruit, and calyxes, and the D3G accumulating profile were genetically mapped. Furthermore, by utilizing the eggplant reference genome information, mutations in the causative candidate genes for those loci were identified. CONCLUSION: Overall, the results of this study suggest that inactivation of key enzymes of anthocyanin metabolism and the gene orthologous to the tomato u gene are potential causes of observed variety in eggplant appearance traits.

Correction: Wang et al. LC-MS/MS Analysis of Choline Compounds in Japanese-Cultivated Vegetables and Fruits. Foods 2020, 9, 1029.

The authors wish to make a correction to the published version of their paper [...].

Correction: Wang et al. Investigation of the Distribution and Content of Acetylcholine, a Novel Functional Compound in Eggplant. Foods 2021, 10, 81.

The authors wish to make a correction to the published version of their paper [...].

Identification and characterization of resistance quantitative trait loci against bacterial wilt caused by the Ralstonia solanacearum species complex in potato.

Bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) represents one of the most serious diseases affecting potato cultivation. The development of BW-resistant cultivars represents the most efficient strategy to control this disease. The resistance-related quantitative trait loci (QTLs) in plants against different RSSC strains have not been studied extensively. Therefore, we performed QTL analysis for evaluating BW resistance using a diploid population derived from Solanum phureja, S. chacoense, and S. tuberosum. Plants cultivated in vitro were inoculated with different strains (phylotype I/biovar 3, phylotype I/biovar 4, and phylotype IV/biovar 2A) and incubated at 24 °C or 28 °C under controlled conditions. Composite interval mapping was performed for the disease indexes using a resistant parent-derived map and a susceptible parent-derived map consisting of single-nucleotide polymorphism markers. We identified five major and five minor resistance QTLs on potato chromosomes 1, 3, 5, 6, 7, 10, and 11. The major QTLs PBWR-3 and PBWR-7 conferred stable resistance against Ralstonia pseudosolanacearum (phylotype I) and Ralstonia syzygii (phylotype IV), whereas PBWR-6b was a strain-specific major resistance QTL against phylotype I/biovar 3 and was more effective at a lower temperature. Therefore, we suggest that broad-spectrum QTLs and strain-specific QTLs can be combined to develop the most effective BW-resistant cultivars for specific areas. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01321-9.

Investigation of the Distribution and Content of Acetylcholine, a Novel Functional Compound in Eggplant.

Eggplants are rich in acetylcholine (ACh), which can improve high blood pressure and negative psychological states. However, information on ACh content in individual parts of eggplant and the changes in ACh content during eggplant development is limited. Therefore, we investigated the ACh content in various parts of eggplant, namely, the leaf, root, bud, calyx, ovary, fruit, exocarp, mesocarp, partition, placenta, core, fruit base, fruit center, and fruit top in 26 eggplant varieties. Furthermore, the effect of heat treatment on ACh content was investigated. The ACh content significantly differed among the eggplant varieties. The difference between the varieties with the highest and lowest ACh content was 100-fold (Tosataka: 11 ± 0.61 mg/100 g fresh weight (FW) and Ryoma: 0.11 ± 0.046 mg/100 g FW, respectively). Eggplant fruit presented the highest ACh content (4.8 mg/100 g FW); it was three times higher than that in other parts combined (1.6 mg/100 g FW). The root contained the lowest ACh content among all parts. The ACh content increased with growth after flowering. The ACh content in the fruit 1.5 months after flowering was 400 times that in the ovary. ACh was uniformly distributed in eggplant flesh. Heat treatment did not cause ACh loss in eggplant. Thus, eggplant is an excellent raw material for functional foods.

Fine mapping of a major locus representing the lack of prickles in eggplant revealed the availability of a 0.5-kb insertion/deletion for marker-assisted selection.

As prickles cause labour inefficiency during cultivation and scratches on the skin of fruits during transportation, they are considered undesirable traits of eggplant (Solanum melongena L.). Because the molecular basis of prickle emergence has not been entirely revealed in plants, we mapped an eggplant semi-dominant Prickle (Pl) gene locus, which causes the absence of prickles, on chromosome 6 of a linkage map of the F2 population derived from crossing the no-prickly cultivar 'Togenashi-senryo-nigo' and the prickly line LS1934. By performing synteny mapping with tomato, the genomic region corresponding to the eggplant Pl locus was identified. Through bacterial artificial chromosome (BAC) screening, positive BAC clones and the contig sequence that harbour the Pl locus in the prickly eggplant genome were revealed. The BAC contig length was 133 kb, and it contained 16 predicted genes. Among them, a characteristic 0.5-kb insertion/deletion was detected. As the 0.5-kb insertion was commonly identified with the prickly phenotype worldwide, a primer pair that amplifies the insertion/deletion could be used for marker-assisted selection of the no-prickly phenotype. Such findings contribute to map-based-cloning of the Pl gene and the understanding of gene function, ultimately providing new insights into the regulatory molecular mechanisms underlying prickle emergence in plants.

LC-MS/MS Analysis of Choline Compounds in Japanese-Cultivated Vegetables and Fruits.

Choline is an essential nutrient and choline esters are potential functional food ingredients. We aimed to analyze the choline compound content in 19 cultivated fruits and vegetables and identify those with high acetylcholine content. We utilized liquid chromatography with tandem mass spectrometry to quantify choline compounds according to the standard addition method. Choline compounds were extracted from lyophilized fruit/vegetable powders and passed through a weakly acidic cation exchange column, resulting in a concentrated solution of choline compounds. The compounds were separated on a pentafluorophenyl column and then analyzed using positive mode electrospray ionization. Results showed that acetylcholine and choline were the primary choline compounds in all agricultural products; propionylcholine and butyrylcholine were minor compounds in 17 and 12 agricultural products, respectively. The acetylcholine concentration was 2900-fold higher in eggplants (6.12 mg/100 g fresh weight [FW]) than in other agricultural products (average: 2.11 × 10-3 mg/100 g FW). The concentration of acetylcholine differed only 2-fold between eggplant cultivars with the highest ('Higomurasaki': 5.53 mg/100 g FW) and lowest ('Onaga nasu': 2.79 mg/100 g FW) concentrations. The half-life of acetylcholine in eggplants was approximately 16 days, which is longer the shelf life of eggplants. Thus, eggplants can be a good source of acetylcholine.

Loss of function of the Pad-1 aminotransferase gene, which is involved in auxin homeostasis, induces parthenocarpy in Solanaceae plants.

Fruit development normally occurs after pollination and fertilization; however, in parthenocarpic plants, the ovary grows into the fruit without pollination and/or fertilization. Parthenocarpy has been recognized as a highly attractive agronomic trait because it could stabilize fruit yield under unfavorable environmental conditions. Although natural parthenocarpic varieties are useful for breeding Solanaceae plants, their use has been limited, and little is known about their molecular and biochemical mechanisms. Here, we report a parthenocarpic eggplant mutant, pad-1, which accumulates high levels of auxin in the ovaries. Map-based cloning showed that the wild-type (WT) Pad-1 gene encoded an aminotransferase with similarity to Arabidopsis VAS1 gene, which is involved in auxin homeostasis. Recombinant Pad-1 protein catalyzed the conversion of indole-3-pyruvic acid (IPyA) to tryptophan (Trp), which is a reverse reaction of auxin biosynthetic enzymes, tryptophan aminotransferases (TAA1/TARs). The RNA level of Pad-1 gene increased during ovary development and reached its highest level at anthesis stage in WT. This suggests that the role of Pad-1 in WT unpollinated ovary is to prevent overaccumulation of IAA resulting in precocious fruit-set. Furthermore, suppression of the orthologous genes of Pad-1 induced parthenocarpic fruit development in tomato and pepper plants. Our results demonstrated that the use of pad-1 genes would be powerful tools to improve fruit production of Solanaceae plants.

Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes.

A core collection of eggplant (Solanum melongena L.) was developed based on a dataset of genome-wide 831 SNP and 50 SSR genotypes analyzed in 893 accessions of eggplant genetic resources collected in the NARO Genebank using the Core Hunter II program. The 893 accessions were collected worldwide, mainly Asia. Genetic variation and population structure among the 893 eggplant accessions were characterized. The genetic diversity of the Asian accessions, especially the South Asian and Southeast Asian accessions, forming the center of diversity in eggplant, was higher than that of the other regions. The resulting core collection, World Eggplant Core (WEC) collection consisted of 100 accessions basically collected from the high genetic diversity countries. Based on the results of the cluster and STRUCTURE analyses with SNP genotypes, the WEC collection was divided into four clusters (S1-S4). Each cluster corresponds to a geographical group as below, S1; the European, American and African countries, S2; the East Asian countries, S3; the Southeast Asian countries, S4; the South Asian and Southeast Asian countries. The genotype and phenotype data of the WEC collection are available from the VegMarks database (https://vegmarks.nivot.affrc.go.jp/resource/), and seed samples are available from the NARO Genebank (https://www.gene.affrc.go.jp/databases-core_collections.php).

QTL analysis of resistance to bacterial wilt caused by Ralstonia solanacearum in potato.

Ralstonia solanacearum causes bacterial wilt, a soil-borne disease and one of the most important maladies of potato and other Solanaceae crops. We analyzed the resistance of a potato clone to bacterial wilt by quantitative trait locus (QTL) analysis. A resistant diploid potato clone 10-03-30 was crossed with a susceptible diploid clone F1-1 to generate a diploid, two-way pseudo-testcross F1 population comprised of 94 genotypes. Dense linkage maps, containing 4,139 single nucleotide polymorphism markers with an average distance of 0.6 and 0.3 cM between markers, were constructed for both parents. The resistance level was evaluated by in vitro inoculation test with R. solanacearum (phylotype I/biovar 4/race 1). Five QTLs (qBWR-1 to -5) were identified on potato chromosomes 1, 3, 7, 10, and 11, and they explained 9.3-18.4% of the phenotypic variance. The resistant parent had resistant alleles in qBWR-2, qBWR-3, and qBWR-4 and susceptible alleles in qBWR-1 and qBWR-5. Accumulation of the resistant alleles in all five QTLs increased the level of resistance compared with that of the resistant parent. This is the first study to identify novel QTLs for bacterial wilt resistance in potato by using genome-wide markers.

Antihypertensive effects of orally administered eggplant (Solanum melongena) rich in acetylcholine on spontaneously hypertensive rats.

Our previous results (Nakamura et al., 2013, 2016) indicated that acetylcholine (ACh) in orally administered foods exerts antihypertensive effects. Eggplants (Solanum melongena) contain abundant ACh (Horiuchi et al., 2003), and their food functionality was discovered, using spontaneously hypertensive rats, by measuring blood pressure after oral administration of a suspension of lyophilized eggplant powder. We found that lyophilized eggplant powder induced significantly lowered acute and chronic blood pressure levels at very low doses of 0.0650 mg/kg body weight (b.w.) and 0.821 mg/(kg b.w.·day), respectively. Chronic administration suppressed adrenaline and noradrenaline excretion in the urine, and aorta assays showed that eggplant acted on the M3 muscarinic ACh receptor (M3 mAChR). ACh was conclusively shown to function as the main component of eggplant contributing to antihypertensive activity by suppressing sympathetic nervous activity via M3 mAChR. This report reveals a new food functionality of eggplant and its potential as a novel antihypertensive food.

An NB-LRR gene, TYNBS1, is responsible for resistance mediated by the Ty-2 Begomovirus resistance locus of tomato.

KEY MESSAGE: An NB-LRR gene, TYNBS1, was isolated from Begomovirus-resistance locus Ty-2. Transgenic plant analysis revealed that TYNBS1 is a functional resistance gene. TYNBS1 is considered to be synonymous with Ty-2. Tomato yellow leaf curl disease caused by Tomato yellow leaf curl virus (TYLCV) is a serious threat to tomato (Solanum lycopersicum L.) production worldwide. A Begomovirus resistance gene, Ty-2, was introduced into cultivated tomato from Solanum habrochaites by interspecific crossing. To identify the Ty-2 gene, we performed genetic analysis. Identification of recombinant line 3701 confirmed the occurrence of a chromosome inversion in the Ty-2 region of the resistant haplotype. Genetic analysis revealed that the Ty-2 gene is linked to an introgression encompassing two markers, SL11_25_54277 and repeat A (approximately 200 kb). Genomic sequences of the upper and lower border of the inversion section of susceptible and resistant haplotypes were determined. Two nucleotide-binding domain and leucine-rich repeat-containing (NB-LRR) genes, TYNBS1 and TYNBS2, were identified around the upper and lower ends of the inversion section, respectively. TYNBS1 strictly co-segregated with TYLCV resistance, whereas TYNBS2 did not. Genetic introduction of genomic fragments containing the TYNBS1 gene into susceptible tomato plants conferred TYLCV resistance. These results demonstrate that TYNBS1 is a functional resistance gene for TYLCV, and is synonymous with the Ty-2 gene.

Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato.

KEY MESSAGE: Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F2 population derived from a cross between two commercial F1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

A simulation-based breeding design that uses whole-genome prediction in tomato.

Efficient plant breeding methods must be developed in order to increase yields and feed a growing world population, as well as to meet the demands of consumers with diverse preferences who require high-quality foods. We propose a strategy that integrates breeding simulations and phenotype prediction models using genomic information. The validity of this strategy was evaluated by the simultaneous genetic improvement of the yield and flavour of the tomato (Solanum lycopersicum), as an example. Reliable phenotype prediction models for the simulation were constructed from actual genotype and phenotype data. Our simulation predicted that selection for both yield and flavour would eventually result in morphological changes that would increase the total plant biomass and decrease the light extinction coefficient, an essential requirement for these improvements. This simulation-based genome-assisted approach to breeding will help to optimise plant breeding, not only in the tomato but also in other important agricultural crops.

Detailed mapping of a resistance locus against Fusarium wilt in cultivated eggplant (Solanum melongena).

KEY MESSAGE: This is the first report on genetic mapping of a resistance locus against Fusarium wilt caused by the plant pathogen Fusarium oxysporum f. sp. melongenae in cultivated eggplant. ABSTRACT: Fusarium wilt, caused by the plant pathogen Fusarium oxysporum f. sp. melongenae, is a major soil-borne disease threatening stable production in eggplant (Solanum melongena). Although three eggplant germplasms, LS1934, LS174, and LS2436, are known to be highly resistant to the pathogen, their resistance loci have not been mapped. In this study, we performed quantitative trait locus analyses in F2:3 populations and detected a resistance locus, FM1, at the end of chromosome 2, with two alleles, Fm1(L) and Fm1(E), in the F2 populations LWF2 [LS1934 × WCGR112-8 (susceptible)] and EWF2 [EPL-1 (derived from LS174) × WCGR112-8], respectively. The percentage of phenotypic variance explained by Fm1(L) derived from LS1934 was 75.0% [Logarithm of the odds (LOD) = 29.3], and that explained by Fm1(E) derived from EPL-1 was 92.2% (LOD = 65.8). Using backcrossed inbred lines, we mapped FM1 between two simple sequence repeat markers located ~4.881 cM apart from each other. Comparing the location of the above locus to those of previously reported ones, the resistance locus Rfo-sa1 from an eggplant ally (Solanum aethiopicum gr. Gilo) was mapped very close to FM1, whereas another resistance locus, from LS2436, was mapped to the middle of chromosome 4. This is the first report of mapping of a Fusarium resistance locus in cultivated eggplant. The availability of resistance-linked markers will enable the application of marker-assisted selection to overcome problems posed by self-incompatibility and introduction of negative traits because of linkage drag, and will lead to clear understanding of genetic mechanism of Fusarium resistance.

Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world.

Unlike other important Solanaceae crops such as tomato, potato, chili pepper, and tobacco, all of which originated in South America and are cultivated worldwide, eggplant (Solanum melongena L.) is indigenous to the Old World and in this respect it is phylogenetically unique. To broaden our knowledge of the genomic nature of solanaceous plants further, we dissected the eggplant genome and built a draft genome dataset with 33,873 scaffolds termed SME_r2.5.1 that covers 833.1 Mb, ca. 74% of the eggplant genome. Approximately 90% of the gene space was estimated to be covered by SME_r2.5.1 and 85,446 genes were predicted in the genome. Clustering analysis of the predicted genes of eggplant along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer eggplant-specific traits. Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant scaffolds could be mapped onto the tomato genome. Furthermore, 56 conserved synteny blocks were identified between the two species. The detailed comparative analysis of the eggplant and tomato genomes will facilitate our understanding of the genomic architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.

Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets.

We constructed an integrated DNA marker linkage map of eggplant (Solanum melongena L.) using DNA marker segregation data sets obtained from two independent intraspecific F(2) populations. The linkage map consisted of 12 linkage groups and encompassed 1,285.5 cM in total. We mapped 952 DNA markers, including 313 genomic SSR markers developed by random sequencing of simple sequence repeat (SSR)-enriched genomic libraries, and 623 single-nucleotide polymorphisms (SNP) and insertion/deletion polymorphisms (InDels) found in eggplant-expressed sequence tags (ESTs) and related genomic sequences [introns and untranslated regions (UTRs)]. Because of their co-dominant inheritance and their highly polymorphic and multi-allelic nature, the SSR markers may be more versatile than the SNP and InDel markers for map-based genetic analysis of any traits of interest using segregating populations derived from any intraspecific crosses of practical breeding materials. However, we found that the distribution of microsatellites in the genome was biased to some extent, and therefore a considerable part of the eggplant genome was first detected when gene-derived SNP and InDel markers were mapped. Of the 623 SNP and InDel markers mapped onto the eggplant integrated map, 469 were derived from eggplant unigenes contained within Solanum orthologous (SOL) gene sets (i.e., sets of orthologous unigenes from eggplant, tomato, and potato). Out of the 469 markers, 326 could also be mapped onto the tomato map. These common markers will be informative landmarks for the transfer of tomato's more saturated genomic information to eggplant and will also provide comparative information on the genome organization of the two solanaceous species. The data are available from the DNA marker database of vegetables, VegMarks (http://vegmarks.nivot.affrc.go.jp).

Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.).

Parthenocarpy, the ability to set fruits without pollination, is a useful trait for setting fruit under unfavorable conditions. To identify the loci controlling parthenocarpy in eggplant (Solanum melongena L.), we constructed linkage maps by using co-dominant simple sequence repeat and single nucleotide polymorphism markers in F(2) populations derived from intraspecific crosses between two non-parthenocarpic lines (LS1934 and Nakate-Shinkuro) and a parthenocarpic line (AE-P03). Total map distances were 1,414.6 cM (ALF2: LS1934 x AE-P03) and 1,153.8 cM (NAF2: Nakate-Shinkuro x AE-P03), respectively. Quantitative trait locus (QTL) analyses revealed two QTLs on chromosomes 3 and 8, which we denoted as Controlling parthenocarpy3.1 (Cop3.1) and Cop8.1, respectively. The percentage of phenotypic variance explained (PVE) of Cop3.1 was 6.3% in ALF2 (LOD = 4.2) and 10.6% in NAF2 (LOD = 3.0). The PVE of Cop8.1 was 45.7% in ALF2 (LOD = 23.8) and 29.7% in NAF2 (LOD = 7.9). Using a population of backcross inbred lines, we confirmed the effect of Cop8.1, but there was no evidence to support the contribution of Cop3.1. We need to verify the effect of Cop3.1 under various temperature conditions. In addition, we clarified the effectiveness of selective SSR markers, emf21H22 and emh11J10, mapped on each side of Cop8.1 in other F(2) populations derived from various parental combinations. This is the first report concerning QTL analysis of parthenocarpy in eggplant using molecular markers. It will be useful in marker-assisted selection and in revealing the genomic mechanism underlying parthenocarpy in eggplant.