Abstract
Both inter- and intraspecific maps have been developed in eggplant. The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. The first maps developed could be defined as ‘first generation,’ built up by means of pre-NGS (next-generation sequencing) molecular biology techniques (AFLP, RAPD, SSR, etc.). Unfortunately, the reduced polymorphism detected in intraspecific mapping populations in the ‘first-generation’ maps, along with the relatively low commercial importance in the ‘seed market’ of the species, hampered the construction of dense eggplant genetic maps. Recently, thanks to NGS-derived molecular markers, new marker-rich maps (‘second-generation maps’) were constructed. To assist selection in breeding programs, in particular to identify QTLs underlying key agronomic traits, biparental approaches as well as genome-wide association (GWA) mapping studies were conducted in this species, using the available linkage maps. Among the traits studied, great importance was given to the identification of QTLs linked to morphological and biological traits, including leaf, flower, plant, and fruit characteristics, as well as QTLs associated with parthenocarpy and to resistances to fungal (Fusarium oxysporum f. sp. melongenae and Verticillium dahliae) and bacterial (Ralstonia solanacearum) wilts. QTL studies to elucidate the genetic basis of biochemical composition, content in bioactive and antinutritional compounds, as well as other fruit quality traits were also carried out.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376. https://doi.org/10.1371/journal.pone.0003376
Barbierato V, Toppino L, Rinaldi P, Sala T, Bassolino L, Valè G, Ferrarini A, Delledonne M, Bagnaresi P, Rotino GL (2016) Phenotypical and gene expression analyses of Rfo-sa1 resistant eggplant interaction with Fusarium oxysporum f. sp. melongenae and Verticillium dahliae. Plant Pathol 65:1297–1309. https://doi.org/10.1111/ppa.12518
Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genom 12:304. https://doi.org/10.1186/1471-2164-12-304
Barchi L, Lanteri S, Portis E, Stàgel A, Valè G, Toppino L, Leonardo Rotino GL (2010) Segregation distortion and linkage analysis in eggplant (Solanum melongena L.). Genome 53:805–815. https://doi.org/10.1139/G10-073
Barchi L, Lanteri S, Portis E, Valè G, Volante A, Pulcini L, Ciriaci T, Acciarri N, Barbierato V, Toppino L, Rotino GL (2012) A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation. PLoS ONE 7:e43740. https://doi.org/10.1371/journal.pone.0043740
Barchi L, Toppino L, Valentino D, Bassolino L, Portis E, Lanteri S, Rotino GL (2018) QTL analysis reveals new eggplant loci involved in resistance to fungal wilts. Euphytica 214:20. https://doi.org/10.1007/s10681-017-2102-2
Bernatzky R, Tanksley SD (1986) Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898
Cericola F, Portis E, Lanteri S, Toppino L, Barchi L, Acciarri N, Pulcini L, Sala T, Rotino GL (2014) Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant. BMC Genom 15:896. https://doi.org/10.1186/1471-2164-15-896
Cericola F, Portis E, Toppino L, Barchi L, Acciarri N, Ciriaci T, Sala T, Rotino GL, Lanteri S (2013) The population structure and diversity of eggplant from Asia and the Mediterranean basin. PLoS ONE 8:e73702. https://doi.org/10.1371/journal.pone.0073702
Doğanlar S, Frary A, Daunay M-C, Huvenaars K, Mank R, Frary A (2014) High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae. Euphytica 198:231–241. https://doi.org/10.1007/s10681-014-1096-2
Doganlar S, Frary A, Daunay M-CC, Lester RN, Tanksley SD (2002a) A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the Solanaceae. Genetics 161:1697–1711
Doganlar S, Frary A, Daunay M-CC, Lester RN, Tanksley SD (2002b) Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 161:1713–1726
Frary A, Doganlar S, Daunay MC, Tanksley SD (2003) QTL analysis of morphological traits in eggplant and implications for conservation of gene function during evolution of solanaceous species. TAG Theor Appl Genet 107:359–370. https://doi.org/10.1007/s00122-003-1257-5
Frary A, Frary A, Daunay M-C, Huvenaars K, Mank R, Doğanlar S (2014) QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis. Euphytica 197:211–228. https://doi.org/10.1007/s10681-013-1060-6
Frary A, Xu YM, Liu JP, Mitchell S, Tedeschi E, Tanksley S (2005) Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments. Theor Appl Genet 111:291–312
Fukuoka H, Miyatake K, Nunome T, Negoro S, Shirasawa K, Isobe S, Asamizu E, Yamaguchi H, Ohyama A (2012) Development of gene-based markers and construction of an integrated linkage map in eggplant by using Solanum orthologous (SOL) gene sets. TAG Theor Appl Genet 125:47–56. https://doi.org/10.1007/s00122-012-1815-9
Fukuoka H, Yamaguchi H, Nunome T, Negoro S, Miyatake K, Ohyama A (2010) Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato. Gene 450:76–84. https://doi.org/10.1016/j.gene.2009.10.006
Ge H, Liu Y, Jiang M, Zhang J, Han H, Chen H (2013) Analysis of genetic diversity and structure of eggplant populations (Solanum melongena L.) in China using simple sequence repeat markers. Sci Hortic (Amsterdam) 162:71–75. https://doi.org/10.1016/j.scienta.2013.08.004
Gebhardt C (2016) The historical role of species from the Solanaceae plant family in genetic research. Theor Appl Genet 129:2281–2294. https://doi.org/10.1007/s00122-016-2804-1
Gramazio P, Prohens J, Plazas M, Andújar I, Herraiz FJ, Castillo E, Knapp S, Meyer RS, Vilanova S (2014) Location of chlorogenic acid biosynthesis pathway and polyphenol oxidase genes in a new interspecific anchored linkage map of eggplant. BMC Plant Biol 14:350. https://doi.org/10.1186/s12870-014-0350-z
Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A, Yamaguchi H, Sato S, Isobe S, Tabata S, Fukuoka H (2014) Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res 21:649–660. https://doi.org/10.1093/dnares/dsu027
Jansen RC, Stam P (1994) High-resolution of quantitative traits into multiple loci via interval mapping. Genetics 136:1447–1455
Lebeau A, Gouy M, Daunay MC, Wicker E, Chiroleu F, Prior P, Frary A, Dintinger J (2013) Genetic mapping of a major dominant gene for resistance to Ralstonia solanacearum in eggplant. Theor Appl Genet 126:143–158. https://doi.org/10.1007/s00122-012-1969-5
Miyatake K, Saito T, Negoro S, Yamaguchi H, Nunome T, Ohyama A, Fukuoka H (2012) Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.). TAG Theor Appl Genet 124:1–11. https://doi.org/10.1007/s00122-012-1796-8
Miyatake K, Saito T, Negoro S, Yamaguchi H, Nunome T, Ohyama A, Fukuoka H (2016) Detailed mapping of a resistance locus against Fusarium wilt in cultivated eggplant (Solanum melongena). Theor Appl Genet 129:357–367. https://doi.org/10.1007/s00122-015-2632-8
Mutlu N, Boyaci FH, Gocmen M, Abak K (2008) Development of SRAP, SRAP-RGA, RAPD and SCAR markers linked with a Fusarium wilt resistance gene in eggplant. Theor Appl Genet 117:1303–1312
Nunome T, Ishiguro K, Yoshida T, Hirai M (2001) Mapping of fruit shape and color development traits in eggplant (Solanum melongena L.) based on RAPD and AFLP markers. Breed Sci 51:19–26
Nunome T, Negoro S, Kono I, Kanamori H, Miyatake K, Yamaguchi H, Ohyama A, Fukuoka H (2009) Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theor Appl Genet 119:1143–1153. https://doi.org/10.1007/s00122-009-1116-0
Nunome T, Suwabe K, Iketani H, Hirai M (2003a) Identification and characterization of microsatellites in eggplant. Plant Breed 122:256–262
Nunome T, Suwabe K, Ohyama A, Fukuoka H (2003b) Characterization of trinucleotide microsatellites in Eggplant. Breed Sci 53:77–83
Portis E, Barchi L, Toppino L, Lanteri S, Acciarri N, Felicioni N, Fusari F, Barbierato V, Cericola F, Valè G, Rotino GL (2014) QTL mapping in eggplant reveals clusters of yield-related loci and orthology with the tomato genome. PLoS ONE 9:e89499. https://doi.org/10.1371/journal.pone.0089499
Portis E, Cericola F, Barchi L, Toppino L, Acciarri N, Pulcini L, Sala T, Lanteri S, Rotino GL (2015) Association mapping for fruit, plant and leaf morphology traits in eggplant. PLoS ONE 10:e0135200. https://doi.org/10.1371/journal.pone.0135200
Rinaldi R, Van Deynze A, Portis E, Rotino GL, Toppino L, Hill T, Ashrafi H, Barchi L, Lanteri S (2016) New insights on eggplant/tomato/pepper synteny and identification of eggplant and pepper orthologous QTL. Front Plant Sci 7:1031
Robbins MD, Sim S-C, Yang W, Van Deynze A, van der Knaap E, Joobeur T, Francis DM (2011) Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato. J Exp Bot 62:1831–1845
Salgon S, Jourda C, Sauvage C, Daunay M-C, Reynaud B, Wicker E, Dintinger J (2017) Eggplant resistance to the Ralstonia solanacearum species complex involves both broad-spectrum and strain-specific Quantitative Trait Loci. Front Plant Sci 8:828. https://doi.org/10.3389/fpls.2017.00828
Salgon S, Raynal M, Lebon S, Baptiste JM, Daunay MC, Dintinger J, Jourda C (2018) Genotyping by sequencing highlights a polygenic resistance to Ralstonia pseudosolanacearum in eggplant (Solanum melongena L.). Int J Mol Sci 19:357. https://doi.org/10.3390/ijms19020357
Stàgel A, Portis E, Toppino L, Rotino GL, Lanteri S (2008) Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genom 9:357. https://doi.org/10.1186/1471-2164-9-357
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 (2016) Mapping quantitative trait loci affecting biochemical and morphological fruit properties in eggplant (Solanum melongena L.). Front Plant Sci 7:256. https://doi.org/10.3389/fpls.2016.00256
Toppino L, Vale G, Rotino GL (2008) 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 22:237–250
Vilanova S, Manzur JP, Prohens J (2012) Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins. Mol Breed 30:647–660. https://doi.org/10.1007/s11032-011-9650-2
Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ (2003) High-Resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 49:853–860. https://doi.org/10.1373/49.6.853
Wu FN, Eannetta NT, Xu YM, Tanksley SD (2009) A detailed synteny map of the eggplant genome based on conserved ortholog set II (COSII) markers. Theor Appl Genet 118:927–935. https://doi.org/10.1007/s00122-008-0950-9
Wu FN, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single copy, orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174:1407–1420
Xi’ou X, Bihao C, Guannan L, Jianjun L, Qinghua C, Jin J, Yujing C (2015) Functional characterization of a putative bacterial wilt resistance gene (RE-bw) in eggplant. Plant Mol Biol Report 33:1058–1073. https://doi.org/10.1007/s11105-014-0814-1
Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208
Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1469
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Barchi, L., Portis, E., Toppino, L., Rotino, G.L. (2019). Molecular Mapping, QTL Identification, and GWA Analysis. In: Chapman, M. (eds) The Eggplant Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-99208-2_5
Download citation
DOI: https://doi.org/10.1007/978-3-319-99208-2_5
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-99207-5
Online ISBN: 978-3-319-99208-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)