journal article
Open Access
Aug 16, 2022
A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant
Abstract
Eggplant (Solanum melongena L.), similar to many other crops, suffers from soil-borne diseases, including Fusarium oxysporum f. sp. melongenae (Fom), causing wilting and heavy yield loss. To date, the genetic factors underlying plant responses to Fom are not well known. We previously developed a Recombinant Inbred Lines (RILs) population using as a female parent the fully resistant line ‘305E40’ and as a male parent the partially resistant line ‘67/3’. The fully resistant trait to Fom was introgressed from the allied species S. aethiopicum. In this work, the RIL population was assessed for the responses to Fom and by using a genomic mapping approach, two major QTLs on chromosomes CH02 and CH11 were identified, associated with the full and partial resistance trait to Fom, respectively. A targeted BSAseq procedure in which Illumina reads bulks of RILs grouped according to their resistance score was aligned to the appropriate reference genomes highlighted differentially enriched regions between resistant/susceptible progeny in the genomic regions underlying both QTLs. The characterization of such regions allowed us to identify the most reliable candidate genes for the two resistance traits. With the aim of revealing exclusive species-specific contigs and scaffolds inherited from the allied species and thus associated with the full resistance trait, a draft de-novo assembly of available Illumina sequences of the ‘305E40’ parent was developed to better resolve the non-recombining genomic region on its CH02 carrying the introgressed Fom resistance locus from S. aethiopicum.
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References
79
[1]
Weese "Eggplant origins: Out of Africa, into the Orient" Taxon (2010) 10.1002/tax.591006
[2]
Meyer "Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication" Mol. Phylogenet. Evol. (2012) 10.1016/j.ympev.2012.02.006
[3]
Knapp, S., Vorontsova, M.S., and Prohens, J. (2013). Wild Relatives of the Eggplant (Solanum melongenan L.: Solanaceae): New Understanding of Species Names in a Complex Group. PLoS ONE, 8.
10.1371/journal.pone.0057039
[4]
Page "Eggplant Domestication: Pervasive Gene Flow, Feralization, and Transcriptomic Divergence" Mol. Biol. Evol. (2019) 10.1093/molbev/msz062
[5]
Arnoux "Genomic inference of complex domestication histories in three Solanaceae species" J. Evol. Biol. (2021) 10.1111/jeb.13723
[6]
(2022, March 10). Faostat Data. Available online: http://www.fao.org/faostat/en/#data/QC.
[7]
Stravato "Attacchi di Fusarium oxysporum f. sp. melongenae agente della tracheofusariosi della melanzana in Italia centrale" Inf. Fitopatol. (1993)
[8]
Bajaj, Y.P.S. (1994). Somatic hybridization of eggplant (Solanum melongena L), with its close and wilt relatives. Biotechnology in Agriculture and Forestry, Somatic Hybridization in Crop Improvement, Springer.
10.1007/978-3-642-57945-5
[9]
"Fusarium wilt on eggplant in Almeria (Spain)" Bol. Sanid. Veg. Plagas (2004)
[10]
Altinok "First report of fusarium wilt of eggplant caused by Fusarium oxysporum f. sp. melongenae in Turkey" Plant Pathol. (2005) 10.1111/j.1365-3059.2005.01235.x
[11]
"Fusarium wilt of eggplant in the Netherlands" Neth. J. Plant Pathol. (1976) 10.1007/bf03041375
[12]
Hawkes, J.G., Lester, R.N., Nee, M., and Estrada-R., N. (1991). The use of wild species for the genetic improvement of brinjal-eggplant (Solanum melongena) and tomato (Lycopersicon esculentum). Solanaceae III: Taxonomy, Chemistry, Evolution, Royal Botanic Gardens.
[13]
Pratap "Eggplant" Alien Gene Transfer in Crop Plants, Achievements and Impacts (2014)
[14]
Abdullaheva "Resistance of eggplant to fusar ium wilt" Sel. Semenovod. (1988)
[15]
Komochi "Evaluation of resistance to bacterial wilt and verticillium wilt in eggplants (Solanum melongena L.) collected in Malaysia" J. Jpn. Soc. Hortic. Sci. (1996) 10.2503/jjshs.65.81
[16]
Monma "‘Diataro’, a bacterial wilt- and Fusarium wilt-resistant hybrid eggplant for rootstock" Bull. Natl. Res. Inst. Veg. Orn. Plants Tea Ser. A (1997)
[17]
Mandhare "Varietal screening and efficacy of fungicides against Fusarium wilt of brinjal" J. Maharashtra Agric. Univ. (1993)
[18]
Barchi "QTL analysis reveals new eggplant loci involved in resistance to fungal wilts" Euphytica (2018) 10.1007/s10681-017-2102-2
[19]
Mutlu "Development of SRAP, SRAP-RGA, RAPD, and SCAR markers linked with a Fusarium wilt resistance gene in eggplant" Theor. Appl. Genet. (2008) 10.1007/s00122-008-0864-6
[20]
Miyatake "Detailed mapping of a resistance locus against Fusarium wilt in cultivated eggplant Solanum melongena" Theor. Appl. Genet. (2016) 10.1007/s00122-015-2632-8
[21]
Daunay, M.C., Lester, R.N., Gebhardt, C., Hennart, J.W., Jahn, M., Frary, A., and Doganlar, S. (2001). Genetic resources of eggplant (Solanum melongena L.) and allied species: A new challenge for molecular geneticists and eggplant breeders. Solanaceae V; Advances in Taxonomy and Utilization, Nijmegen University Press.
[22]
Interspecific Hybridization between Eggplant and Wild Relatives from Different Genepools
Mariola Plazas, Santiago Vilanova, Pietro Gramazio et al.
Journal of the American Society for Horticultural...
2016
10.21273/jashs.141.1.34
[23]
Syfert "Crop wild relatives of the brinjal eggplant (Solanum melongena): Poorly represented in genebanks and many species at risk of extinction" Am. J. Bot. (2016) 10.3732/ajb.1500539
[24]
Carputo, D., Aversano, R., and Ercolano, M.R. (2021). Pepper and Eggplant Genetic Resources. The wild Solanum genomes, Springer. Chapter 6.
10.1007/978-3-030-30343-3
[25]
Kaushik "Phenotyping of eggplant wild relatives and interspecific hybrids with conventional and phenomics descriptors provides insight for their potential utilization in breeding" Front. Plant Sci. (2016) 10.3389/fpls.2016.00677
[26]
Rizza "Androgenic dihaploids from somatic hybrids between Solanum melongena and S. aethiopicum group gilo as a source of resistance to Fusarium oxysporum f. sp. melongenae" Plant Cell Rep. (2002) 10.1007/s00299-001-0429-5
[27]
Rotino, G.L., Mennella, G., Fusari, F., Vitelli, G., Tacconi, M.G., D’Alessandro, A., and Acciarri, N. (2001, January 9). Towards introgression of resistance to Fusarium oxysporum F. sp. melongenae from Solanum integrifolium into eggplant. Proceedings of the 11th Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Antalya, Turkey.
[28]
Rotino, G.L., Rizza, F., Mennella, G., Tacconi, M.G., Alberti, P., D’Alessandro, A., Acciarri, N., and Toppino, L. (2004, January 17–19). Production and utilization of sexual “doubled hybrid” between the somatic hybrids S. melongena (+) S. integrifolium and S. melongena (+) S. aethiopicum gr. gilo. Proceedings of the EUCARPIA, XIIth Meeting on Genetics and Breeding of Capsicum & Eggplant, Noordwijkerhout, The Netherlands.
[29]
Rotino "Current status in production and utilization of dihaploids from somatic hybrids between eggplant (Solanum melongena L.) and its wild relatives" Acta Physiol. Plant. (2005) 10.1007/s11738-005-0077-4
[30]
Toppino "Inheritance of Fusarium wilt resistance introgressed from Solanum aethiopicum Gilo and Aculeatum groups into cultivated eggplant S. melongena and development of associated PCR-based markers" Mol. Breed. (2008) 10.1007/s11032-008-9170-x
[31]
Boyaci, F., Unlu, A., and Abak, K. (2010, January 22). Screening for resistance to Fusarium wilt of some cultivated eggplants and wild Solanum accessions. Proceedings of the XXVIII International Horticultural Congress on Science and Horticulture for People IHC2010: International Symposium on New 935, Lisbon, Portugal.
[32]
Boyaci "Genetic analysis of resistance to wilt caused by Fusarium (Fusarium oxysporum melongenae) in eggplant (Solanum melongena)" Indian J. Agric. Sci. (2011)
[33]
Michelmore "Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations" Proc. Natl. Acad. Sci. USA (1991) 10.1073/pnas.88.21.9828
[34]
Barchi, L., Lanteri, S., Portis, E., Valè, G., Volante, A., Pulcini, L., Ciriaci, T., Acciarri, N., Barbierato, V., and Toppino, L. (2012). A RAD Tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation. PLoS ONE, 7.
10.1371/journal.pone.0043740
[35]
Barchi "A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution" Sci. Rep. (2019) 10.1038/s41598-019-47985-w
[36]
Portis, E., Barchi, L., Toppino, L., Lanteri, S., Acciarri, N., Felicioni, N., Fusari, F., Barbierato, V., Cericola, F., and Valè, G. (2014). QTL mapping in eggplant reveals clusters of yield-related loci and orthology with the tomato genome. PLoS ONE, 9.
10.1371/journal.pone.0089499
[37]
Fukuoka "Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets" Theor. Appl. Genet. (2012) 10.1007/s00122-012-1815-9
[38]
Hirakawa "Draft genome sequence of eggplant (Solanum melongena L.): The representative Solanum species indigenous to the Old World" DNA Res. (2014) 10.1093/dnares/dsu027
[39]
Barbierato "Phenotype and gene expression analyses of the Rfo-sa1 resistant aubergine interaction with Fusarium oxysporum f. sp. melongenae and Verticillium dahliae" Plant Pathol. (2016) 10.1111/ppa.12518
[40]
Toppino, L., Barchi, L., Mercati, F., Acciarri, N., Perrone, D., Martina, M., Gattolin, S., Sala, T., Fadda, S., and Mauceri, A. (2020). 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, 11.
10.3390/genes11070745
[41]
Florio, F.E., Gattolin, S., Toppino, L., Bassolino, L., Fibiani, M., Lo Scalzo, R., and Rotino, G.L. (2021). A SmelAAT Acyltransferase Variant Causes a Major Difference in Eggplant (Solanum melongena L.) Peel Anthocyanin Composition. Int. J. Mol. Sci., 22.
10.3390/ijms22179174
[42]
Sulli "An Eggplant Recombinant Inbred Population Allows the Discovery of Metabolic QTLs Controlling Fruit Nutritional Quality" Front. Plant Sci. (2021) 10.3389/fpls.2021.638195
[43]
Barchi, L., Portis, E., Toppino, L., and Rotino, G.L. (2019). Molecular Mapping, QTL Identification, and GWA Analysis. The Eggplant Genome, Springer International Publishing.
10.1007/978-3-319-99208-2_5
[44]
Barchi "Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding" Plant J. (2021) 10.1111/tpj.15313
[45]
Toppino "Mapping Quantitative Trait Loci Affecting Biochemical and Morphological Fruit Properties in Eggplant (Solanum melongena L.)" Front. Plant Sci. (2016) 10.3389/fpls.2016.00256
[46]
Andràsfalvi, A., Moòr, A., and Zatykò, L. (1995). Sources of resistance among Solanum spp. to an Italian isolate of Fusarium oxysporum f. sp. melongenae. EUCARPIA, Proceedings of the 9th Meeting of Genetics and Breeding of Capsicum and Eggplant, SINCOP.
[47]
Sall, J., Stephens, M.L., Lehman, A., and Loring, S. (2017). JMP Start Statistics: A Guide to Statistics and Data Analysis Using JMP, Sas Institute.
[48]
Broman "R/qtl: QTL mapping in experimental crosses" Bioinformatics (2003) 10.1093/bioinformatics/btg112
[49]
Lander "Mapping mendelian factors underlying quantitative traits using RFLP linkage maps" Genetics (1989) 10.1093/genetics/121.1.185
[50]
Churchill "Empirical threshold values for quantitative trait mapping" Genetics (1994) 10.1093/genetics/138.3.963
Showing 50 of 79 references
Cited By
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Characterisation of Fusarium and Neocosmospora Species Associated With Crown Rot and Wilt of African Eggplant (Solanum aethiopicum) in Ghana
Journal of Phytopathology
Benjamin Azu Okorley, Sabine Ravnskov · 2024
Metrics
21
Citations
79
References
Details
- Published
- Aug 16, 2022
- Vol/Issue
- 11(16)
- Pages
- 2548
- License
- View
Authors
Funding
MIPAAF
Award: 18271
Cite This Article
Maria Rosaria Tassone, Paolo Bagnaresi, Francesca Desiderio, et al. (2022). A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant. Cells, 11(16), 2548. https://doi.org/10.3390/cells11162548
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