1
|
Gramazio P, Alonso D, Arrones A, Villanueva G, Plazas M, Toppino L, Barchi L, Portis E, Ferrante P, Lanteri S, Rotino GL, Giuliano G, Vilanova S, Prohens J. Conventional and new genetic resources for an eggplant breeding revolution. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6285-6305. [PMID: 37419672 DOI: 10.1093/jxb/erad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/05/2023] [Indexed: 07/09/2023]
Abstract
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.
Collapse
Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Paola Ferrante
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| |
Collapse
|
2
|
Viana AR, Bottari NB, Oviedo VR, Santos D, Londero JEL, Schetinger MRC, Flores EMM, Pigatto A, Schuch AP, Krause A, Krause LMF. Phytochemical and biological characterization of aqueous extract of Vassobia breviflora on proliferation and viability of melanoma cells: involvement of purinergic pathway. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2023; 86:632-652. [PMID: 37434435 DOI: 10.1080/15287394.2023.2233989] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Vassobia breviflora belongs to the Solanaceae family, possessing biological activity against tumor cells and is a promising alternative for therapy. The aim of this investigation was to determine the phytochemical properties V. breviflora using ESI-ToF-MS. The cytotoxic effects of this extract were examined in B16-F10 melanoma cells and the relationship if any to purinergic signaling was involved. The antioxidant activity of total phenols, (2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) was analyzed, as well as production of reactive oxygen species (ROS) and nitric oxide (NO) was determined. Genotoxicity was assessed by DNA damage assay. Subsequently, the structural bioactive compounds were docked against purinoceptors P2X7 and P2Y1 receptors. The bioactive compounds found in V. breviflora were N-methyl-(2S,4 R)-trans-4-hydroxy-L-proline, calystegine B, 12-O-benzoyl- tenacigenin A and bungoside B. In vitro cytotoxicity was demonstrated at concentration ranges of 0.1-10 mg/ml, and plasmid DNA breaks only at the concentration of 10 mg/ml. V. breviflora extracts affected hydrolysis by ectoenzymes, such as ectonucleoside triphosphate diphosphohydrolase (E-NTPDase) and ectoadenosine deaminase (E-ADA) which control levels of degradation and formation of nucleosides and nucleotides. In the presence of substrates ATP, ADP, AMP and adenosine, the activities of E-NTPDase, 5´-NT or E-ADA were significantly modulated by V. breviflora. N-methyl-(2S,4 R)-trans-4-hydroxy-L-proline presented higher binding affinity (according to receptor-ligand complex estimated binding affinity as evidenced by ∆G values) to bind to both P2X7 and P2Y1purinergic receptors.Our results suggest a putative interaction of V. breviflora bioactive compounds with growth inhibitory potential in B16-F10 melanoma and suggest that may be considered as promising compounds in melanoma and cancer treatment.
Collapse
Affiliation(s)
- Altevir Rossato Viana
- Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, Brazil
| | | | | | - Daniel Santos
- Chemistry, Federal University of Santa Maria, Santa Maria, Brazil
| | | | | | | | - Aline Pigatto
- Postgraduate Program in Teaching Science and Mathematics, Franciscan University, Santa Maria, Brazil
| | - André Passaglia Schuch
- Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Alexandre Krause
- Veterinary Medicine, Federal University of Santa Maria, Santa Maria, Brazil
| | | |
Collapse
|
3
|
Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
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.
Collapse
|
4
|
T. V. N, S. RP, R. L. R. Population structure and genetic diversity characterization of soybean for seed longevity. PLoS One 2022; 17:e0278631. [PMID: 36472991 PMCID: PMC9725150 DOI: 10.1371/journal.pone.0278631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/19/2022] [Indexed: 12/12/2022] Open
Abstract
Seed longevity is an important trait in the context of germplasm conservation and economics of seed production. The identification of populations with high level of genetic variability for seed longevity and associated traits will become a valuable resource for superior alleles for seed longevity. In this study, Genotyping-by-sequencing (GBS)-single nucleotide polymorphism (SNP) approach, simple sequence repeats (SSR) markers and agro-morphological traits have been explored to investigate the diversity and population structure of assembled 96 genotypes. The GBS technique performed on 96 genotypes of soybean (Glycine max (L.) Merrill) resulted in 37,897 SNPs on sequences aligned to the reference genome sequence. The average genome coverage was 6.81X with a mapping rate of 99.56% covering the entire genome. Totally, 29,955 high quality SNPs were identified after stringent filtering and most of them were detected in non-coding regions. The 96 genotypes were phenotyped for eight quantitative and ten qualitative traits by growing in field by following augmented design. The STRUCTURE (Bayesian-model based algorithm), UPGMA (Un-weighed Pair Group Method with Arithmetic mean) and principal component analysis (PCA) approaches using SSR, SNP as well as quantitative and qualitative traits revealed population structure and diversity in assembled population. The Bayesian-model based STRUCTURE using SNP markers could effectively identify clusters with higher seed longevity associated with seed coat colour and size which were subsequently validated by UPGMA and PCA based on SSR and agro-morphological traits. The results of STRUCTURE, PCA and UPGMA cluster analysis showed high degree of similarity and provided complementary data that helped to identify genotypes with higher longevity. Six black colour genotypes, viz., Local black soybean, Kalitur, ACC Nos. 39, 109, 101 and 37 showed higher seed longevity during accelerated ageing. Higher coefficient of variability observed for plant height, number of pods per plant, seed yield per plant, 100 seed weight and seed longevity confirms the diversity in assembled population and its suitability for quantitative trait loci (QTL) mapping.
Collapse
Affiliation(s)
- Naflath T. V.
- Department of Seed Science and Technology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
| | - Rajendra Prasad S.
- Department of Seed Science and Technology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
| | - Ravikumar R. L.
- Department of Plant Biotechnology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
- * E-mail:
| |
Collapse
|
5
|
Shoji T, Saito K. A Jasmonate-Responsive ERF Transcription Factor Regulates Steroidal Glycoalkaloid Biosynthesis Genes in Eggplant. PLANTS (BASEL, SWITZERLAND) 2022; 11:3336. [PMID: 36501375 PMCID: PMC9736504 DOI: 10.3390/plants11233336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Steroidal glycoalkaloids (SGAs) are a class of cholesterol-derived anti-nutritional defense compound that are produced in species of the genus Solanum, such as tomato (S. lycopersicum), potato (S. tuberosum), and eggplant (S. melongena). However, the regulation of defense-related metabolites in eggplant remains underexplored. In tomato and potato, the JASMONATE-RESPONSIVE ETHYLENE RESPONSE FACTOR 4 (JRE4) transcription factor positively regulates a large number of genes involved in SGA biosynthesis. Here, we report that the overexpression of eggplant JRE4 (SmJRE4) induces numerous metabolic genes involved in SGA biosynthesis in leaves. We demonstrate the jasmonate-dependent induction of SmJRE4 and its downstream metabolic genes and show that ethylene treatment attenuates this induction. Our findings thus provide molecular insights into SGA biosynthesis and its regulation in this major crop.
Collapse
|
6
|
Ro N, Haile M, Kim B, Cho GT, Lee J, Lee YJ, Hyun DY. Genome-Wide Association Study for Agro-Morphological Traits in Eggplant Core Collection. PLANTS (BASEL, SWITZERLAND) 2022; 11:2627. [PMID: 36235493 PMCID: PMC9571982 DOI: 10.3390/plants11192627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Eggplant is one of the most economically and nutritionally important vegetables worldwide. The study of the association of phenotypic traits with genetic factors is vital for the rapid and efficient identification and selection of eggplant genetic resources for breeding purposes with desired traits. The eggplant resources (587) collected from different countries, including Korea, were used for establishing the core collection. A total of 288 accessions were selected from 587 Solanum accessions based on 52 single nucleotide polymorphisms (SNPs) markers together with 17 morphological traits. This core collection was further used to analyze the genetic associations of eggplant morphological variations. A large variation was found among the evaluated eggplant accessions for some agro-morphological traits. Stem prickles and leaf prickles showed a significant positive correlation (r = 0.83***), followed by days to flowering and days to maturity (r = 0.64***). A total of 114,981 SNPs were filtered and used for phylogenetic tree analysis, population structure analysis, and genome-wide association study (GWAS). Among the agro-morphological traits, significantly associated SNPs were found for six traits. A total of 377 significantly associated SNPs with six agro-morphological traits were identified. These six traits and the number of SNPs were: days to maturity (51), flower size (121), fruit width (20), harvest fruit color (42), leaf prickles (38), and stem prickles (105). The largest fraction of significant SNPs (11.94%) was obtained on chromosome Ch01, followed by Ch07 and Ch06 with 11.67% and 10.08%, respectively. This study will help to develop markers linked to the most important agro-morphological traits of eggplant genetic resources and support the selection of desirable traits for eggplant breeding programs.
Collapse
Affiliation(s)
- Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Mesfin Haile
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Bichsaem Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Jungro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Yoon-Jung Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Do Yoon Hyun
- Department of Crops and Forestry, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea;
| |
Collapse
|
7
|
Rau D, Attene G, Rodriguez M, Baghino L, Pisanu AB, Sanna D, Acquadro A, Portis E, Comino C. The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes. FRONTIERS IN PLANT SCIENCE 2022; 13:898740. [PMID: 35865281 PMCID: PMC9294547 DOI: 10.3389/fpls.2022.898740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
Collapse
Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Limbo Baghino
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Anna Barbara Pisanu
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Davide Sanna
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| |
Collapse
|
8
|
Aubriot X, Knapp S. A revision of the "spiny solanums" of Tropical Asia ( Solanum, the Leptostemonum Clade, Solanaceae). PHYTOKEYS 2022; 198:1-270. [PMID: 36760991 PMCID: PMC9849010 DOI: 10.3897/phytokeys.198.79514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 04/20/2022] [Indexed: 06/18/2023]
Abstract
The Leptostemonum Clade, or the "spiny solanums", is the most species-rich monophyletic clade of the large cosmopolitan genus Solanum (Solanaceae) and represents almost half the species diversity of the genus. Species diversity in the clade is highest in the Americas, but significant clusters of endemic taxa occur in the Eastern Hemisphere. We present here a taxonomic revision of the 51 species of spiny solanums occurring in tropical Asia (excluding the island of New Guinea, and the lowlands of Nepal and Bhutan). Three species are described as new: Solanumkachinense X.Aubriot & S.Knapp, sp. nov. from northern Myanmar, S.peikuoense S.S.Ying, sp. nov. from Taiwan, and S.sulawesi X.Aubriot & S.Knapp, sp. nov. from northern Sulawesi, Indonesia. Of the spiny solanums occurring in the region, 38 are native and 13 are introduced from the Americas or Africa, either as adventive weeds or as cultivated plants. Phylogenetic resolution amongst these taxa is still a work in progress, so we have chosen to treat these taxa in a geographical context to aid with identification and further taxon discovery. For the native species we provide complete nomenclatural details for all recognised species and their synonyms, complete descriptions, distributions including maps, common names and uses, and preliminary conservation assessments. For the introduced taxa that have been treated in detail elsewhere we provide details of types, synonyms based on tropical Asian material, general distributions, and common names for the region. We provide lecto- or neotypifications for 67 names; 63 for native and 4 for introduced taxa. All taxa are discussed and compared to similar species; keys are provided for all taxa. We illustrate all native species with herbarium and field photographs and introduced species with field photographs only. All specimens examined for this treatment are included in Suppl. materials 1-3 as searchable files.
Collapse
Affiliation(s)
- Xavier Aubriot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, FranceThe Natural History MuseumLondonUnited Kingdom
- The Natural History Museum, Cromwell Road, London SW7 5BD, UKUniversité Paris-SaclayParisFrance
| | - Sandra Knapp
- The Natural History Museum, Cromwell Road, London SW7 5BD, UKUniversité Paris-SaclayParisFrance
| |
Collapse
|
9
|
Al-Rowaily SL, Alghamdi AO, Alghamdi SS, Assaeed AM, Hegazy A, Afzal M, Migdadi HM. Assessment of morphological and molecular variability of some Solanum melongena L. cultivars and wild Solanum incanum L. in Saudi Arabia. Biol Futur 2021; 72:187-199. [PMID: 34554472 DOI: 10.1007/s42977-020-00052-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
The genus Solanum exhibits a wide range of variability in morphology, flavor, and tolerance to biotic and abiotic stresses. Phenotypic and genetic variability using ISSR and RAPD markers of Solanum incanum distributed in Al-Baha province of the Kingdom of Saudi Arabia is assessed. Thirty samples are representing three different locations: Baljershy, Aqeeq, and Tohama, besides twenty-five samples representing five different commercial cultivars tested. Growth type, the number of leaves per plant, fruit size (phenotypic traits), crude protein, carbohydrates, digestive organic matter, and Mg, Ca, P were the principal contributors in the PCA. Molecular analysis showed that 114 ISSR and 80 RAPD alleles with a 100% polymorphism were recorded. The polymorphism information content (PIC) values ranged from 0.84 to 0.91 for ISSR and from 0.59 to 0.89 for RAPD data. Similarity values ranged from 0.16 to 1.00, with an average of 0.47 for ISSR and from 0.01 to 0.97, with an average of 0.36 for RAPD. It resulted in a positive and significant correlation between morphological, molecular, nutritional, and chemical analysis of fruits using Mantel analysis. UPGMA and PCA for morphological traits and molecular data discriminated commercial cultivars and wild relatives. Solanum incanum was more diverse than commercial varieties. This study revealed a wide genetic diversity among and within collected eggplant accessions and may use in breeding programs of eggplants. There is a need to increase the present eggplant collection to widen the genetic diversity of cultivated eggplant varieties in Saudi Arabia.
Collapse
Affiliation(s)
- Saud L Al-Rowaily
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Abdullah O Alghamdi
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Abdulaziz M Assaeed
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Ahmad Hegazy
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Muhammad Afzal
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Hussein M Migdadi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia. .,National Agricultural Research Centre, P. O Box: 639, Baq'a, 19381, Jordan.
| |
Collapse
|
10
|
Martínez-Ispizua E, Calatayud Á, Marsal JI, Mateos-Fernández R, Díez MJ, Soler S, Valcárcel JV, Martínez-Cuenca MR. Phenotyping Local Eggplant Varieties: Commitment to Biodiversity and Nutritional Quality Preservation. FRONTIERS IN PLANT SCIENCE 2021; 12:696272. [PMID: 34276746 PMCID: PMC8281111 DOI: 10.3389/fpls.2021.696272] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/07/2021] [Indexed: 05/05/2023]
Abstract
Given the little variability among commercialised eggplants mainly in developed countries, exploring, and structuring of traditional varieties germplasm collections have become a key element for extending ecotypes and promoting biodiversity preservation and consumption. Thirty-one eggplant landraces from Spain were characterised with 22 quantitative and 14 qualitative conventional morphological descriptors. Landraces were grouped based on their fruit skin colour (black-purple, striped, white, and reddish). Landraces B7, B20, and B24 were left out for their distinctive fruit characteristics. Wide variation for plant, leaf, flower, and fruit phenology traits was observed across the local landraces, and fruit descriptors were considered the most important ones. In a second experiment, landraces, B14, B16, and B17 were selected to determine fruit quality. By contemplating the benefits provided by antioxidants and sugars for human health, pulp antioxidant capacity, total phenolic, ascorbic acid, carotenoid, flavonoid, and total sugar content were determined. Significant differences were observed across these three landraces, and B14 was highlighted for its antioxidant properties, while B17 stood out for its high sugar content. B16 did not stand out for any traits. The results indicate the wide variability in eggplants for their phenotypic and nutritional characteristics, which emphasises the importance of traditional varieties as the main source of agricultural biodiversity.
Collapse
Affiliation(s)
- Eva Martínez-Ispizua
- Horticulture Department, Valencian Institute for Agricultural Research (IVIA), Valencia, Spain
| | - Ángeles Calatayud
- Horticulture Department, Valencian Institute for Agricultural Research (IVIA), Valencia, Spain
| | - José Ignacio Marsal
- Horticulture Department, Valencian Institute for Agricultural Research (IVIA), Valencia, Spain
| | - Rubén Mateos-Fernández
- Plants Genomics and Biotechnology Department, Institute for Plant Molecular and Cell Biology (IBMCP), Valencia, Spain
| | - María José Díez
- Biotechnology Department, Valencian Institute for the Conservation and Improvement of Agrobiodiversity (COMAV), Polytechnic University of Valencia, Valencia, Spain
| | - Salvador Soler
- Biotechnology Department, Valencian Institute for the Conservation and Improvement of Agrobiodiversity (COMAV), Polytechnic University of Valencia, Valencia, Spain
| | - José Vicente Valcárcel
- Biotechnology Department, Valencian Institute for the Conservation and Improvement of Agrobiodiversity (COMAV), Polytechnic University of Valencia, Valencia, Spain
| | | |
Collapse
|
11
|
Comparative analysis of the nutritional profiles of selected Solanum species grown in Sri Lanka. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
Mauceri A, Abenavoli MR, Toppino L, Panda S, Mercati F, Aci MM, Aharoni A, Sunseri F, Rotino GL, Lupini A. Transcriptomics reveal new insights into molecular regulation of nitrogen use efficiency in Solanum melongena. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4237-4253. [PMID: 33711100 DOI: 10.1093/jxb/erab121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen-use efficiency (NUE) is a complex trait of great interest in breeding programs because through its improvement, high crop yields can be maintained whilst N supply is reduced. In this study, we report a transcriptomic analysis of four NUE-contrasting eggplant (Solanum melongena) genotypes following short- and long-term exposure to low N, to identify key genes related to NUE in the roots and shoots. The differentially expressed genes in the high-NUE genotypes are involved in the light-harvesting complex and receptor, a ferredoxin-NADP reductase, a catalase and WRKY33. These genes were then used as bait for a co-expression gene network analysis in order to identify genes with the same trends in expression. This showed that up-regulation of WRKY33 triggered higher expression of a cluster of 21 genes and also of other genes, many of which were related to N-metabolism, that were able to improve both nitrogen uptake efficiency and nitrogen utilization efficiency, the two components of NUE. We also conducted an independent de novo experiment to validate the significantly higher expression of WRKY33 and its gene cluster in the high-NUE genotypes. Finally, examination of an Arabidopsis transgenic 35S::AtWRKY33 overexpression line showed that it had a bigger root system and was more efficient at taking up N from the soil, confirming the pivotal role of WRKY33 for NUE improvement.
Collapse
Affiliation(s)
- Antonio Mauceri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Laura Toppino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Mercati
- Istituto di Bioscienze e Biorisorse CNR - Consiglio Nazionale Ricerche, Corso Calatafimi 414, Palermo, Italy
| | - Meriem Miyassa Aci
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Sunseri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Giuseppe Leonardo Rotino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Antonio Lupini
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| |
Collapse
|
13
|
Sulli M, Barchi L, Toppino L, Diretto G, Sala T, Lanteri S, Rotino GL, Giuliano G. An Eggplant Recombinant Inbred Population Allows the Discovery of Metabolic QTLs Controlling Fruit Nutritional Quality. FRONTIERS IN PLANT SCIENCE 2021; 12:638195. [PMID: 34079565 PMCID: PMC8166230 DOI: 10.3389/fpls.2021.638195] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/22/2021] [Indexed: 06/02/2023]
Abstract
Eggplant (Solanum melongena L.) represents the third most important crop of the Solanaceae family and is an important component of our daily diet. A population of 164 F6 recombinant inbred lines (RILs), derived from two eggplant lines differing with respect to several key agronomic traits, "305E40" and "67/3," was grown to the commercial maturation stage, and fruits were harvested, separated into peel and flesh, and subjected to liquid chromatography Liquid Chromatography/Mass Spectrometry (LC/MS) analysis. Through a combination of untargeted and targeted metabolomics approaches, a number of metabolites belonging to the glycoalkaloid, anthocyanin, and polyamine classes and showing a differential accumulation in the two parental lines and F1 hybrid were identified. Through metabolic profiling of the RILs, we identified several metabolomic quantitative trait loci (mQTLs) associated with the accumulation of those metabolites. Each of the metabolic traits proved to be controlled by one or more quantitative trait loci (QTLs); for most of the traits, one major mQTL (phenotypic variation explained [PVE] ≥ 10%) was identified. Data on mQTL mapping and dominance-recessivity relationships of measured compounds in the parental lines and F1 hybrid, as well as an analysis of the candidate genes underlying the QTLs and of their sequence differences in the two parental lines, suggested a series of candidate genes underlying the traits under study.
Collapse
Affiliation(s)
- Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Laura Toppino
- CREA, Council for Agricultural and Economics Research, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Tea Sala
- CREA, Council for Agricultural and Economics Research, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Sergio Lanteri
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Giuseppe Leonardo Rotino
- CREA, Council for Agricultural and Economics Research, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| |
Collapse
|
14
|
Schrenk D, Bignami M, Bodin L, Chipman JK, del Mazo J, Hogstrand C, Hoogenboom L(R, Leblanc J, Nebbia CS, Nielsen E, Ntzani E, Petersen A, Sand S, Schwerdtle T, Vleminckx C, Wallace H, Brimer L, Cottrill B, Dusemund B, Mulder P, Vollmer G, Binaglia M, Ramos Bordajandi L, Riolo F, Roldán‐Torres R, Grasl‐Kraupp B. Risk assessment of glycoalkaloids in feed and food, in particular in potatoes and potato-derived products. EFSA J 2020; 18:e06222. [PMID: 32788943 PMCID: PMC7417869 DOI: 10.2903/j.efsa.2020.6222] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The European Commission asked EFSA for a scientific opinion on the risks for animal and human health related to the presence of glycoalkaloids (GAs) in feed and food. This risk assessment covers edible parts of potato plants and other food plants containing GAs, in particular, tomato and aubergine. In humans, acute toxic effects of potato GAs (α-solanine and α-chaconine) include gastrointestinal symptoms such as nausea, vomiting and diarrhoea. For these effects, the CONTAM Panel identified a lowest-observed-adverse-effect level of 1 mg total potato GAs/kg body weight (bw) per day as a reference point for the risk characterisation following acute exposure. In humans, no evidence of health problems associated with repeated or long-term intake of GAs via potatoes has been identified. No reference point for chronic exposure could be identified from the experimental animal studies. Occurrence data were available only for α-solanine and α-chaconine, mostly for potatoes. The acute dietary exposure to potato GAs was estimated using a probabilistic approach and applying processing factors for food. Due to the limited data available, a margin of exposure (MOE) approach was applied. The MOEs for the younger age groups indicate a health concern for the food consumption surveys with the highest mean exposure, as well as for the P95 exposure in all surveys. For adult age groups, the MOEs indicate a health concern only for the food consumption surveys with the highest P95 exposures. For tomato and aubergine GAs, the risk to human health could not be characterised due to the lack of occurrence data and the limited toxicity data. For horses, farm and companion animals, no risk characterisation for potato GAs could be performed due to insufficient data on occurrence in feed and on potential adverse effects of GAs in these species.
Collapse
|
15
|
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. Genes (Basel) 2020; 11:genes11070745. [PMID: 32635424 PMCID: PMC7397344 DOI: 10.3390/genes11070745] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/16/2022] Open
Abstract
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.
Collapse
|
16
|
Mauceri A, Bassolino L, Lupini A, Badeck F, Rizza F, Schiavi M, Toppino L, Abenavoli MR, Rotino GL, Sunseri F. Genetic variation in eggplant for Nitrogen Use Efficiency under contrasting NO 3 - supply. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:487-508. [PMID: 31087763 DOI: 10.1111/jipb.12823] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/08/2019] [Indexed: 05/03/2023]
Abstract
Eggplant (Solanum melongena L.) yield is highly sensitive to N fertilization, the excessive use of which is responsible for environmental and human health damage. Lowering N input together with the selection of improved Nitrogen-Use-Efficiency (NUE) genotypes, more able to uptake, utilize, and remobilize N available in soils, can be challenging to maintain high crop yields in a sustainable agriculture. The aim of this study was to explore the natural variation among eggplant accessions from different origins, in response to Low (LN) and High (HN) Nitrate (NO3 - ) supply, to identify NUE-contrasting genotypes and their NUE-related traits, in hydroponic and greenhouse pot experiments. Two eggplants, AM222 and AM22, were identified as N-use efficient and inefficient, respectively, in hydroponic, and these results were confirmed in a pot experiment, when crop yield was also evaluated. Overall, our results indicated the key role of N-utilization component (NUtE) to confer high NUE. The remobilization of N from leaves to fruits may be a strategy to enhance NUtE, suggesting glutamate synthase as a key enzyme. Further, omics technologies will be used for focusing on C-N metabolism interacting networks. The availability of RILs from two other selected NUE-contrasting genotypes will allow us to detect major genes/quantitative trait loci related to NUE.
Collapse
Affiliation(s)
- Antonio Mauceri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| | - Laura Bassolino
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Antonio Lupini
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| | - Franz Badeck
- CREA Centro di ricerca Genomica e Bioinformatica, I-29017, Fiorenzuola d'Arda, Italy
| | - Fulvia Rizza
- CREA Centro di ricerca Genomica e Bioinformatica, I-29017, Fiorenzuola d'Arda, Italy
| | - Massimo Schiavi
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Laura Toppino
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| | - Giuseppe L Rotino
- CREA Centro di ricerca Genomica e Bioinformatica, I-26836, Montanaso Lombardo, Italy
| | - Francesco Sunseri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, I-89124, Reggio Calabria, Italy
| |
Collapse
|
17
|
Zhang J, Yang J, Zhang L, Luo J, Zhao H, Zhang J, Wen C. A new SNP genotyping technology Target SNP-seq and its application in genetic analysis of cucumber varieties. Sci Rep 2020; 10:5623. [PMID: 32221398 PMCID: PMC7101363 DOI: 10.1038/s41598-020-62518-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 03/11/2020] [Indexed: 01/18/2023] Open
Abstract
To facilitate the utility of SNP-based genotyping, we developed a new method called target SNP-seq which combines the advantages of multiplex PCR amplification and high throughput sequencing. Compared with KASP, Microarrays, GBS and other SNP genotyping methods, target SNP-seq is flexible both in SNPs and samples, yields high accuracy, especially when genotyping genome wide perfect SNPs with high polymorphism and conserved flanking sequences, and is cost-effective, requiring 3 days and $7 for per DNA sample to genotype hundreds of SNP loci. The present study established a DNA fingerprint of 261 cucumber varieties by target SNP-seq with 163 perfect SNPs from 4,612,350 SNPs based on 182 cucumber resequencing datasets. Four distinct subpopulations were found in 261 Chinese cucumber varieties: the north China type, the south China type, the Europe type, and the Xishuangbanna type. The north China type and Xishuangbanna type harbored lower genetic diversity, indicating greater risk of genetic erosion in these two subpopulations. Furthermore, a core set of 24 SNPs was able to distinguish 99% of the 261 cucumber varieties. 29 core cucumber backbone varieties in China were identified. Therefore, target SNP-seq provides a new way to screen out core SNP loci from the whole genome for DNA fingerprinting of crop varieties. The high efficiency and low cost of target SNP-seq is more competitive than the current SNP genotyping methods, and it has excellent application prospects in genetic research, as well as in promoting plant breeding processes in the near future.
Collapse
Affiliation(s)
- Jian Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Like Zhang
- National Agricultural Technology Extension and Service Center, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jiang Luo
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Hong Zhao
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jianan Zhang
- Molbreeding Biotechnology Company, Shijiazhuang, 050000, China
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
| |
Collapse
|
18
|
Wei Q, Wang W, Hu T, Hu H, Wang J, Bao C. Construction of a SNP-Based Genetic Map Using SLAF-Seq and QTL Analysis of Morphological Traits in Eggplant. Front Genet 2020; 11:178. [PMID: 32218801 PMCID: PMC7078336 DOI: 10.3389/fgene.2020.00178] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/13/2020] [Indexed: 01/09/2023] Open
Abstract
Eggplant (Solanum melongena; 2n = 24) is an economically important fruit crop of the family Solanaceae that was domesticated in India and Southeast Asia. Construction of a high-resolution genetic map and map-based gene mining in eggplant have lagged behind other crops within the family such as tomato and potato. In this study, we conducted high-throughput single nucleotide polymorphism (SNP) discovery in the eggplant genome using specific length amplified fragment (SLAF) sequencing and constructed a high-density genetic map for the quantitative trait locus (QTL) analysis of multiple traits. An interspecific F2 population of 121 individuals was developed from the cross between cultivated eggplant "1836" and the wild relative S. linnaeanum "1809." Genomic DNA extracted from parental lines and the F2 population was subjected to high-throughput SLAF sequencing. A total of 111.74 Gb of data and 487.53 million pair-end reads were generated. A high-resolution genetic map containing 2,122 SNP markers and 12 linkage groups was developed for eggplant, which spanned 1530.75 cM, with an average distance of 0.72 cM between adjacent markers. A total of 19 QTLs were detected for stem height and fruit and leaf morphology traits of eggplant, explaining 4.08-55.23% of the phenotypic variance. These QTLs were distributed on nine linkage groups (LGs), but not on LG2, 4, and 9. The number of SNPs ranged from 2 to 11 within each QTL, and the genetic interval varied from 0.15 to 10.53 cM. Overall, the results establish a foundation for the fine mapping of complex QTLs, candidate gene identification, and marker-assisted selection of favorable alleles in eggplant breeding.
Collapse
Affiliation(s)
| | | | | | | | | | - Chonglai Bao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
19
|
Miyatake K, Shinmura Y, Matsunaga H, Fukuoka H, Saito T. Construction of a core collection of eggplant ( Solanum melongena L.) based on genome-wide SNP and SSR genotypes. BREEDING SCIENCE 2019; 69:498-502. [PMID: 31598083 PMCID: PMC6776151 DOI: 10.1270/jsbbs.18202] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/17/2019] [Indexed: 05/24/2023]
Abstract
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).
Collapse
Affiliation(s)
- Koji Miyatake
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO),
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Yoshimi Shinmura
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO),
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Hiroshi Matsunaga
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO),
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Hiroyuki Fukuoka
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO),
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
- Takii & Company, Limited,
1360 Hari, Konan, Shiga 520-3231,
Japan
| | - Takeo Saito
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO),
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| |
Collapse
|
20
|
Barchi L, Pietrella M, Venturini L, Minio A, Toppino L, Acquadro A, Andolfo G, Aprea G, Avanzato C, Bassolino L, Comino C, Molin AD, Ferrarini A, Maor LC, Portis E, Reyes-Chin-Wo S, Rinaldi R, Sala T, Scaglione D, Sonawane P, Tononi P, Almekias-Siegl E, Zago E, Ercolano MR, Aharoni A, Delledonne M, Giuliano G, Lanteri S, Rotino GL. A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Sci Rep 2019; 9:11769. [PMID: 31409808 PMCID: PMC6692341 DOI: 10.1038/s41598-019-47985-w] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/05/2019] [Indexed: 11/30/2022] Open
Abstract
With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.
Collapse
Affiliation(s)
- Lorenzo Barchi
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Marco Pietrella
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Res Ctr, Via Anguillarese 301, 00123, Roma, Italy.,Council for Agricultural Research and Economics (CREA), Research Centre for Olive, Citrus and Tree Fruit, 47121, Forlì, Italy
| | - Luca Venturini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.,Department of Life Sciences, Natural History Museum, Cromwell Rd, Kensington, London, United Kingdom
| | - Andrea Minio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Laura Toppino
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| | - Alberto Acquadro
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, Italy
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Res Ctr, Via Anguillarese 301, 00123, Roma, Italy
| | - Carla Avanzato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Laura Bassolino
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| | - Cinzia Comino
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Alessandra Dal Molin
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Alberto Ferrarini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Louise Chappell Maor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ezio Portis
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Sebastian Reyes-Chin-Wo
- UC Davis Genome Center-GBSF, 451 Health Sciences Drive, University of California, Davis, CA, 95616, USA
| | - Riccardo Rinaldi
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy
| | - Tea Sala
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| | - Davide Scaglione
- IGA Technology Services, Via J. Linussio, 51, 33100, Udine, Italy
| | - Prashant Sonawane
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Paola Tononi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Efrat Almekias-Siegl
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Elisa Zago
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | | | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Casaccia Res Ctr, Via Anguillarese 301, 00123, Roma, Italy.
| | - Sergio Lanteri
- University of Torino - DISAFA - Plant Genetics and Breeding, Largo Braccini 2, 10095, Grugliasco, Torino, Italy.
| | - Giuseppe Leonardo Rotino
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, 26836, Montanaso Lombardo, LO, Italy
| |
Collapse
|
21
|
Barchi L, Acquadro A, Alonso D, Aprea G, Bassolino L, Demurtas O, Ferrante P, Gramazio P, Mini P, Portis E, Scaglione D, Toppino L, Vilanova S, Díez MJ, Rotino GL, Lanteri S, Prohens J, Giuliano G. Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm. FRONTIERS IN PLANT SCIENCE 2019; 10:1005. [PMID: 31440267 PMCID: PMC6693525 DOI: 10.3389/fpls.2019.01005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/18/2019] [Indexed: 05/20/2023]
Abstract
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.
Collapse
Affiliation(s)
| | | | - David Alonso
- COMAV, Universitat Politècnica de Valencia, Valencia, Spain
| | - Giuseppe Aprea
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Laura Bassolino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Olivia Demurtas
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Paola Ferrante
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | - Paola Mini
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | | | - Laura Toppino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | | | | | | | | | - Jaime Prohens
- COMAV, Universitat Politècnica de Valencia, Valencia, Spain
| | - Giovanni Giuliano
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| |
Collapse
|
22
|
|
23
|
Gramazio P, Yan H, Hasing T, Vilanova S, Prohens J, Bombarely A. Whole-Genome Resequencing of Seven Eggplant ( Solanum melongena) and One Wild Relative ( S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement. FRONTIERS IN PLANT SCIENCE 2019; 10:1220. [PMID: 31649694 PMCID: PMC6791922 DOI: 10.3389/fpls.2019.01220] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/04/2019] [Indexed: 05/20/2023]
Abstract
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.
Collapse
Affiliation(s)
- Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
- *Correspondence: Pietro Gramazio,
| | - Haidong Yan
- School of Plant and Environmental Sciences (SPES), Virginia Tech, Blacksburg, VA, United States
| | - Tomas Hasing
- School of Plant and Environmental Sciences (SPES), Virginia Tech, Blacksburg, VA, United States
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Aureliano Bombarely
- School of Plant and Environmental Sciences (SPES), Virginia Tech, Blacksburg, VA, United States
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
24
|
Untargeted Metabolomics Analysis of Eggplant ( Solanum melongena L.) Fruit and Its Correlation to Fruit Morphologies. Metabolites 2018; 8:metabo8030049. [PMID: 30200482 PMCID: PMC6160926 DOI: 10.3390/metabo8030049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022] Open
Abstract
Eggplant is one of the most widely cultivated vegetables in the world and has high biodiversity in terms of fruit shape, size, and color. Therefore, fruit morphology and nutrient content become important considerations for both consumers and breeders who develop new eggplant-based products. To gain insight on the diversity of eggplant metabolites, twenty-one eggplant accessions were analyzed by untargeted metabolomics using GC-MS and LC-MS. The dataset of eggplant fruit morphologies, and metabolites specific to different eggplant fruit accessions were used for correlation analysis. Untargeted metabolomics analysis using LC-MS and GC-MS was able to detect 136 and 207 peaks, respectively. Fifty-one (51) metabolites from the LC-MS analysis and 207 metabolites from the GC-MS analysis were putatively identified, which included alkaloids, terpenes, terpenoids, fatty acids, and flavonoids. Spearman correlation analysis revealed that 14 fruit morphologies were correlated with several metabolites. This information will be very useful for the development of strategies for eggplant breeding.
Collapse
|
25
|
Kaushik P, Plazas M, Prohens J, Vilanova S, Gramazio P. Diallel genetic analysis for multiple traits in eggplant and assessment of genetic distances for predicting hybrids performance. PLoS One 2018; 13:e0199943. [PMID: 29949625 PMCID: PMC6021119 DOI: 10.1371/journal.pone.0199943] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/15/2018] [Indexed: 11/22/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Mariola Plazas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| |
Collapse
|
26
|
Portis E, Lanteri S, Barchi L, Portis F, Valente L, Toppino L, Rotino GL, Acquadro A. Comprehensive Characterization of Simple Sequence Repeats in Eggplant ( Solanum melongena L.) Genome and Construction of a Web Resource. FRONTIERS IN PLANT SCIENCE 2018; 9:401. [PMID: 29643862 PMCID: PMC5883146 DOI: 10.3389/fpls.2018.00401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/13/2018] [Indexed: 05/21/2023]
Abstract
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.
Collapse
Affiliation(s)
- Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, Italy
- *Correspondence: Sergio Lanteri,
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, Italy
| | | | | | - Laura Toppino
- CREA-GB, Research Centre for Genomics and Bioinformatics, Lodi, Italy
| | | | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari – Plant Genetics and Breeding, Università degli Studi di Torino, Turin, Italy
| |
Collapse
|
27
|
Taher D, Solberg SØ, Prohens J, Chou YY, Rakha M, Wu TH. World Vegetable Center Eggplant Collection: Origin, Composition, Seed Dissemination and Utilization in Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:1484. [PMID: 28970840 PMCID: PMC5609569 DOI: 10.3389/fpls.2017.01484] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/10/2017] [Indexed: 05/19/2023]
Abstract
Eggplant is the fifth most economically important solanaceous crop after potato, tomato, pepper, and tobacco. Apart from the well-known brinjal eggplant (Solanum melongena L.), two other under-utilized eggplant species, the scarlet eggplant (S. aethiopicum L.) and the gboma eggplant (S. macrocarpon L.) are also cultivated. The taxonomy and identification of eggplant wild relatives is challenging for breeders due to the large number of related species, but recent phenotypic and genetic data and classification in primary, secondary, and tertiary genepools, as well as information on the domestication process and wild progenitors, facilitates their utilization in breeding. The World Vegetable Center (WorldVeg) holds a large public germplasm collection of eggplant, which includes the three cultivated species and more than 30 eggplant wild relatives, with more than 3,200 accessions collected from 90 countries. Over the last 15 years, more than 10,000 seed samples from the Center's eggplant collection have been shared with public and private sector entities, including other genebanks. An analysis of the global occurrences and genebank holdings of cultivated eggplants and their wild relatives reveals that the WorldVeg genebank holds the world's largest public collection of the three cultivated eggplant species. The composition, seed dissemination and utilization of germplasm from the Center's collection are highlighted. In recent years more than 1,300 accessions of eggplant have been characterized for yield and fruit quality parameters. Further screening for biotic and abiotic stresses in eggplant wild relatives is a priority, as is the need to amass more comprehensive knowledge regarding wild relatives' potential for use in breeding. However, as is the case for many other crops, wild relatives are highly under-represented in the global conservation system of eggplant genetic resources.
Collapse
Affiliation(s)
- Dalia Taher
- World Vegetable CenterTainan, Taiwan
- Vegetable Crops Research Department, Agriculture Research Center, Horticulture Research InstituteGiza, Egypt
| | - Svein Ø. Solberg
- World Vegetable CenterTainan, Taiwan
- Faculty of Applied Ecology and Agricultural Sciences, Inland Norway University of Applied SciencesElverum, Norway
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | | | - Mohamed Rakha
- World Vegetable CenterTainan, Taiwan
- Horticulture Department, Faculty of Agriculture, University of KafrelsheikhKafr El-Sheikh, Egypt
| | | |
Collapse
|
28
|
Acquadro A, Barchi L, Gramazio P, Portis E, Vilanova S, Comino C, Plazas M, Prohens J, Lanteri S. Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLoS One 2017; 12:e0180774. [PMID: 28686642 PMCID: PMC5501601 DOI: 10.1371/journal.pone.0180774] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Alberto Acquadro
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Lorenzo Barchi
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Ezio Portis
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Cinzia Comino
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Mariola Plazas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Sergio Lanteri
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| |
Collapse
|
29
|
Taranto F, D'Agostino N, Greco B, Cardi T, Tripodi P. Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing. BMC Genomics 2016; 17:943. [PMID: 27871227 PMCID: PMC5117568 DOI: 10.1186/s12864-016-3297-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 11/15/2016] [Indexed: 01/03/2023] Open
Abstract
Background Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes. Results GBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features. Conclusions GBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3297-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- F Taranto
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - N D'Agostino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - B Greco
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - T Cardi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - P Tripodi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy.
| |
Collapse
|
30
|
Docimo T, Francese G, De Palma M, Mennella D, Toppino L, Lo Scalzo R, Mennella G, Tucci M. Insights in the Fruit Flesh Browning Mechanisms in Solanum melongena Genetic Lines with Opposite Postcut Behavior. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:4675-85. [PMID: 27198496 DOI: 10.1021/acs.jafc.6b00662] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Color, taste, flavor, nutritional value, and shelf life are important factors determining quality and healthiness of food and vegetables. These factors are strongly affected by browning processes, occurring after fruit or vegetable cutting. Characterization of ten eggplant genotypes for chlorogenic acid (CGA) content, total phenols (TP), polyphenoloxidase (PPO) activity, and browning tendency corroborated a lack of significant correlations between biochemical factors and fruit flesh browning. Further in-depth molecular and biochemical analyses of two divergent eggplant genetic lines, AM199 (high browning) and AM086 (low browning), within 30 min from cutting, highlighted differences in the physiological mechanisms underlying the browning process. qRT-PCR analysis revealed distinct activation mechanisms of CGA biosynthetic and PPO genes in the two genetic lines. Metabolic data on CGA, sugars, and ascorbic acid contents confirmed that their different browning tendency matched with different metabolic responses to cutting. Our findings suggest that the complex mechanism of flesh browning in the two eggplant genetic lines might be mediated by multiple specific factors.
Collapse
Affiliation(s)
- T Docimo
- Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e BioRisorse, UOS Portici , Via Università 133, 80055 Portici, Italy
| | - G Francese
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per l'Orticoltura (CREA-ORT) , Via dei Cavalleggeri 25, 84098 Pontecagnano, Italy
| | - M De Palma
- Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e BioRisorse, UOS Portici , Via Università 133, 80055 Portici, Italy
| | - D Mennella
- Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e BioRisorse, UOS Portici , Via Università 133, 80055 Portici, Italy
| | - L Toppino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di Ricerca per l'Orticoltura (CREA-ORL) , Via Paullese 28, 26836 Montanaso Lombardo, Italy
| | - R Lo Scalzo
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Unità di ricerca per i processi dell'industria agroalimentare (CREA-IAA) , Via Venezian 26, 20133 Milano, Italy
| | - G Mennella
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per l'Orticoltura (CREA-ORT) , Via dei Cavalleggeri 25, 84098 Pontecagnano, Italy
| | - M Tucci
- Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e BioRisorse, UOS Portici , Via Università 133, 80055 Portici, Italy
| |
Collapse
|
31
|
Toppino L, Barchi L, Lo Scalzo R, Palazzolo E, Francese G, Fibiani M, D'Alessandro A, Papa V, Laudicina VA, Sabatino L, Pulcini L, Sala T, Acciarri N, Portis E, Lanteri S, Mennella G, Rotino GL. Mapping Quantitative Trait Loci Affecting Biochemical and Morphological Fruit Properties in Eggplant (Solanum melongena L.). FRONTIERS IN PLANT SCIENCE 2016; 7:256. [PMID: 26973692 PMCID: PMC4777957 DOI: 10.3389/fpls.2016.00256] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/15/2016] [Indexed: 05/19/2023]
Abstract
Eggplant berries are a source of health-promoting metabolites including antioxidant and nutraceutical compounds, mainly anthocyanins and chlorogenic acid; however, they also contain some anti-nutritional compounds such as steroidal glycoalkaloids (SGA) and saponins, which are responsible for the bitter taste of the flesh and with potential toxic effects on humans. Up to now, Quantitative Trait Loci (QTL) for the metabolic content are far from being characterized in eggplant, thus hampering the application of breeding programs aimed at improving its fruit quality. Here we report on the identification of some QTL for the fruit metabolic content in an F2 intraspecific mapping population of 156 individuals, obtained by crossing the eggplant breeding lines "305E40" × "67/3." The same population was previously employed for the development of a RAD-tag based linkage map and the identification of QTL associated to morphological and physiological traits. The mapping population was biochemically characterized for both fruit basic qualitative data, like dry matter, °Brix, sugars, and organic acids, as well as for health-related compounds such chlorogenic acid, (the main flesh monomeric phenol), the two peel anthocyanins [i.e., delphinidin-3-rutinoside (D3R) and delphinidin-3-(p- coumaroylrutinoside)-5-glucoside (nasunin)] and the two main steroidal glycoalkaloids, solasonine, and solamargine. For most of the traits, one major QTL (PVE ≥10%) was spotted and putative orthologies with other Solanaceae crops are discussed. The present results supply valuable information to eggplant breeders on the inheritance of key fruit quality traits, thus providing potential tools to assist future breeding programs.
Collapse
Affiliation(s)
- Laura Toppino
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORL, Unità di Ricerca per l'OrticolturaMontanaso Lombardo, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Plant Genetics and Breeding, University of TurinTurin, Italy
| | - Roberto Lo Scalzo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-IAA, Unità di Ricerca per i Processi dell'Industria AgroalimentareMilano, Italy
| | - Eristanna Palazzolo
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di PalermoPalermo, Italy
| | - Gianluca Francese
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORT, Centro di Ricerca per l'OrticolturaPontecagnano-Faiano, Italy
| | - Marta Fibiani
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-IAA, Unità di Ricerca per i Processi dell'Industria AgroalimentareMilano, Italy
| | - Antonietta D'Alessandro
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORT, Centro di Ricerca per l'OrticolturaPontecagnano-Faiano, Italy
| | - Vincenza Papa
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-IAA, Unità di Ricerca per i Processi dell'Industria AgroalimentareMilano, Italy
| | - Vito A. Laudicina
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di PalermoPalermo, Italy
| | - Leo Sabatino
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di PalermoPalermo, Italy
| | - Laura Pulcini
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORA, Unità di Ricerca per l'OrticolturaMonsampolo del Tronto, Italy
| | - Tea Sala
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORL, Unità di Ricerca per l'OrticolturaMontanaso Lombardo, Italy
| | - Nazzareno Acciarri
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORA, Unità di Ricerca per l'OrticolturaMonsampolo del Tronto, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Plant Genetics and Breeding, University of TurinTurin, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Plant Genetics and Breeding, University of TurinTurin, Italy
| | - Giuseppe Mennella
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORT, Centro di Ricerca per l'OrticolturaPontecagnano-Faiano, Italy
| | - Giuseppe L. Rotino
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORL, Unità di Ricerca per l'OrticolturaMontanaso Lombardo, Italy
- *Correspondence: Giuseppe L. Rotino
| |
Collapse
|
32
|
Portis E, Cericola F, Barchi L, Toppino L, Acciarri N, Pulcini L, Sala T, Lanteri S, Rotino GL. Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant. PLoS One 2015; 10:e0135200. [PMID: 26284782 PMCID: PMC4540451 DOI: 10.1371/journal.pone.0135200] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/18/2015] [Indexed: 11/18/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Fabio Cericola
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Laura Toppino
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Nazzareno Acciarri
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Laura Pulcini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Tea Sala
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
- * E-mail:
| |
Collapse
|
33
|
Meyer RS, Whitaker BD, Little DP, Wu SB, Kennelly EJ, Long CL, Litt A. Parallel reductions in phenolic constituents resulting from the domestication of eggplant. PHYTOCHEMISTRY 2015; 115:194-206. [PMID: 25813879 DOI: 10.1016/j.phytochem.2015.02.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 12/21/2014] [Accepted: 02/04/2015] [Indexed: 05/19/2023]
Abstract
Crop domestication is often accompanied by changes in metabolite compositions that alter traits such as flavor, color, or other beneficial properties. Fruits of eggplants (Solanum melongena L.) and related species are abundant and diverse in pharmacologically interesting phenolic compounds, particularly hydroxycinnamic acid (HCA) conjugates such as the antioxidant caffeoylquinic acids (CQA) and HCA-polyamine amides (HCAA). To understand metabolite variability through the lens of natural and artificial selection, HPLC-DAD was used to generate phenolic profiles for 32 compounds in fruits from 93 accessions representing 9 Solanum species. Profiles were used for identification of species-level and infraspecific chemical patterns across both genetic distance and landscape. Sampling of plant lines included the undomesticated progenitor of eggplant and Asian landraces with a genetic background associated with three Asian regions near proposed separate centers of domestication to test whether chemical changes were convergent despite different origins. Results showed ten compounds were unique to species, and ten other compounds varied significantly in abundance among species. Five CQAs and three HCA-polyamine conjugates were more abundant in wild (undomesticated) versus domesticated eggplant, indicating that artificial selection may have led to reduced phenolic levels. No chemical abundance patterns were associated with site-origin. However, one genetically distinct lineage of geographically-restricted SE Asian eggplants (S. melongena subsp. ovigerum) had a higher HCAA content and diversity than other lineages, which is suggested to be related to artificial selection for small, firm fruit. Overall, patterns show that fruit size, palatability and texture were preferentially selected over health-beneficial phytochemical content during domestication of several nightshade crops.
Collapse
Affiliation(s)
- Rachel S Meyer
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458, United States; The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States; New York University, Center for Genomics and Systems Biology, 12 Waverly Place, New York, NY 10003, United States.
| | - Bruce D Whitaker
- Food Quality Laboratory, Building 002, Room 117, Beltsville Agricultural Research Center-West, Agricultural Research Service, USDA, 10300 Baltimore Avenue, Beltsville, MD 20705, United States
| | - Damon P Little
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458, United States
| | - Shi-Biao Wu
- Department of Biological Sciences, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, United States
| | - Edward J Kennelly
- The Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, United States; Department of Biological Sciences, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, NY 10468, United States
| | - Chun-Lin Long
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, PR China
| | - Amy Litt
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458, United States
| |
Collapse
|
34
|
High Resolution Melting (HRM) analysis in eggplant (Solanum melongena L.): A tool for microsatellite genotyping and molecular characterization of a Greek Genebank collection. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
35
|
Mutegi E, Snow AA, Rajkumar M, Pasquet R, Ponniah H, Daunay MC, Davidar P. Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum, Solanaceae) in southern India: implications for conservation. AMERICAN JOURNAL OF BOTANY 2015; 102:140-8. [PMID: 25587156 DOI: 10.3732/ajb.1400403] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Crop wild relatives represent important genetic resources for crop improvement and the preservation of native biodiversity. Eggplant (Solanum melongena), known as brinjal in India, ranks high among crops whose wild gene pools are underrepresented in ex situ collections and warrant urgent conservation. Knowledge of outcrossing rates and patterns of genetic variation among wild populations can aid in designing strategies for both in situ and ex situ preservation.• METHODS We used 14 microsatellite (simple sequence repeat) markers to examine genetic diversity, population structure, and outcrossing in 10 natural populations of wild/weedy eggplant (S. insanum = S. melongena var. insanum) and three cultivated populations in southern India.• KEY RESULTS Multilocus FST analyses revealed strong differentiation among populations and significant isolation by distance. Bayesian model-based clustering, principal coordinate analysis, and hierarchical cluster analysis grouped the wild/weedy populations into three major clusters, largely according to their geographic origin. The three crop populations were similar to each other and grouped with two wild/weedy populations that occurred nearby. Outcrossing rates among the wild/weedy populations ranged from 5-33%, indicating a variable mixed-mating system.• CONCLUSION Geographic isolation has played a significant role in shaping the contemporary patterns of genetic differentiation among these populations, many of which represent excellent candidates for in situ conservation. In two cases, close genetic affinity between cultivars and nearby wild/weedy populations suggests that gene flow has occurred between them. To our knowledge, this is the first study investigating population-level patterns of genetic diversity in wild relatives of eggplant.
Collapse
Affiliation(s)
- Evans Mutegi
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12 St., Columbus, Ohio 43210 USA
| | - Allison A Snow
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12 St., Columbus, Ohio 43210 USA
| | - Muthu Rajkumar
- Department of Ecology and Environmental Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
| | - Remy Pasquet
- IRD, UR 072, LEGS 91198 Gif-sur-yvette, France; Université Paris-Sud 11 91400 Orsay, France
| | - Hopeland Ponniah
- Department of Ecology and Environmental Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
| | - Marie-Christine Daunay
- INRA, Unité de Génétique & Amélioration des Fruits et Légumes, UR1052, Domaine St Maurice, CS 60094 F-84143 Montfavet cedex, France
| | - Priya Davidar
- Department of Ecology and Environmental Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
| |
Collapse
|
36
|
Portis E, Cericola F, Barchi L, Toppino L, Acciarri N, Pulcini L, Sala T, Lanteri S, Rotino GL. Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant. PLoS One 2015. [PMID: 26284782 DOI: 10.1371/jounal.pone.0135200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Fabio Cericola
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy; Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Laura Toppino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Nazzareno Acciarri
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Laura Pulcini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Tea Sala
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| |
Collapse
|
37
|
Cericola F, Portis E, Lanteri S, Toppino L, Barchi L, Acciarri N, Pulcini L, Sala T, Rotino GL. Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant. BMC Genomics 2014; 15:896. [PMID: 25311640 PMCID: PMC4210512 DOI: 10.1186/1471-2164-15-896] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/06/2014] [Indexed: 11/26/2022] Open
Abstract
Background The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the genome, and seek to establish correlations between phenotype and genotype. The major advantages of GWA lie in being able to sample a much wider range of the phenotypic and genotypic variation present, in being able to exploit multiple rounds of historical recombination in many different lineages and to include multiple accessions of direct relevance to crop improvement. Results A 191 accessions eggplant (Solanum melongena L.) association panel, comprising a mixture of breeding lines, old varieties and landrace selections originating from Asia and the Mediterranean Basin, was SNP genotyped and scored for anthocyanin pigmentation and fruit color at two locations over two years. The panel formed two major clusters, reflecting geographical provenance and fruit type. The global level of linkage disequilibrium was 3.4 cM. A mixed linear model appeared to be the most appropriate for GWA. A set of 56 SNP locus/phenotype associations was identified and the genomic regions harboring these loci were distributed over nine of the 12 eggplant chromosomes. The associations were compared with the location of known QTL for the same traits. Conclusion The GWA mapping approach was effective in validating a number of established QTL and, thanks to the wide diversity captured by the panel, was able to detect a series of novel marker/trait associations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-896) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, Largo P, Braccini 2, I-10095 Grugliasco, Torino, Italy.
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Portis E, Barchi L, Toppino L, Lanteri S, Acciarri N, Felicioni N, Fusari F, Barbierato V, Cericola F, Valè G, Rotino GL. QTL mapping in eggplant reveals clusters of yield-related loci and orthology with the tomato genome. PLoS One 2014; 9:e89499. [PMID: 24586828 PMCID: PMC3931786 DOI: 10.1371/journal.pone.0089499] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
In spite of its widespread cultivation and nutritional and economic importance, the eggplant (Solanum melongena L.) genome has not been extensively explored. A lack of knowledge of the patterns of inheritance of key agronomic traits has hindered the exploitation of marker technologies to accelerate its genetic improvement. An already established F2 intraspecific population of eggplant bred from the cross ‘305E40’ x ‘67/3’ was phenotyped for 20 agronomically relevant traits at two sites. Up to seven quantitative trait loci (QTL) per trait were identified and the percentage of the phenotypic variance (PV) explained per QTL ranged from 4 to 93%. Not all the QTL were detectable at both sites, but for each trait at least one major QTL (PV explained ≥10%) was identified. Although no detectable QTL x environment interaction was found, some QTL identified were location-specific. Many of the fruit-related QTL clustered within specific chromosomal regions, reflecting either linkage and/or pleiotropy. Evidence for putative tomato orthologous QTL/genes was obtained for several of the eggplant QTL. Information regarding the inheritance of key agronomic traits was obtained. Some of the QTL, along with their respective linked markers, may be useful in the context of marker-assisted breeding.
Collapse
Affiliation(s)
- Ezio Portis
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Lorenzo Barchi
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Laura Toppino
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORL, Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| | - Sergio Lanteri
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Nazzareno Acciarri
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORA, Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Nazzareno Felicioni
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORA, Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Fabio Fusari
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORA, Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Valeria Barbierato
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORL, Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| | - Fabio Cericola
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Giampiero Valè
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-GPG, Genomic Research Centre, Fiorenzuola d'Arda, Piacenza, Italy ; Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-RIS, Rice Research Unit, Vercelli, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORL, Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| |
Collapse
|