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Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding

TitleImproved genome assembly and pan-genome provide key insights into eggplant domestication and breeding
Publication TypeArticolo su Rivista peer-reviewed
Year of Publication2021
AuthorsBarchi, L., Rabanus-Wallace M.T., Prohens J., Toppino L., Padmarasu S., Portis E., Rotino G.L., Stein N., Lanteri S., and Giuliano Giovanni
JournalPlant Journal
Volume107
Pagination579-596
ISSN09607412
KeywordsChalcone isomerase, Fruits, Genes, Genetic diversity, Genetic Variation, Horticultural crops, Orthologous genes, Plants (botany), Reference lines, Selective sweep, Solanum melongena
Abstract

Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant ‘67/3’ reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant. © 2021 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd

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URLhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85107282475&doi=10.1111%2ftpj.15313&partnerID=40&md5=2c530b77e1a7d002484d238b68db9aaa
DOI10.1111/tpj.15313
Citation KeyBarchi2021