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Article|11 Aug 2019|OPEN
Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits
Aliki Xanthopoulou1, Javier Montero-Pau2, Ifigeneia Mellidou3, Christos Kissoudis4, José Blanca5, Belén Picó5, Aphrodite Tsaballa3, Eleni Tsaliki3, Athanasios Dalakouras3, Harry S. Paris6, Maria Ganopoulou3, Theodoros Moysiadis7, Maslin Osathanunkul8,9, Athanasios Tsaftaris4, Panagiotis Madesis7,, Apostolos Kalivas3 & Ioannis Ganopoulos3,
1Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
2Department of Biochemistry and Molecular Biology, Universitat de València, 46022 Valencia, Spain
3Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001, Greece
4Perrotis College, American Farm School, Thessaloniki 57001, Greece
5Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
6Department of Vegetable Crops and Plant Genetics, Agricultural Research Organization, Newe Ya’ar Research Center, Ramat Yishay, Israel
7Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki 57001, Greece
8Department of Biology, Faculty of Science Chiang Mai University, Chiang Mai, Thailand
9Center of Excellence in Bioresources for Agriculture, Industry and MedicineChiang Mai University, Chiang Mai, Thailand

Horticulture Research 6,
Article number: 19094 (2019)
doi: 10.1038/hortres.2019.94
Views: 16

Received: 28 Feb 2019
Revised: 18 Jun 2019
Accepted: 19 Jun 2019
Published online: 11 Aug 2019

Abstract

Cucurbita pepo contains two cultivated subspecies, each of which encompasses four fruit-shape morphotypes (cultivar groups). The Pumpkin, Vegetable Marrow, Cocozelle, and Zucchini Groups are of subsp. pepo and the Acorn, Crookneck, Scallop, and Straightneck Groups are of subsp. ovifera. Recently, a de novo assembly of the C. pepo subsp. pepo Zucchini genome was published, providing insights into its evolution. To expand our knowledge of evolutionary processes within C. pepo and to identify variants associated with particular morphotypes, we performed whole-genome resequencing of seven of these eight C. pepo morphotypes. We report for the first time whole-genome resequencing of the four subsp. pepo (Pumpkin, Vegetable Marrow, Cocozelle, green Zucchini, and yellow Zucchini) morphotypes and three of the subsp. ovifera365bet体育投注吧 (Acorn, Crookneck, and Scallop) morphotypes. A high-depth resequencing approach was followed, using the BGISEQ-500 platform that enables the identification of rare variants, with an average of 33.5X. Approximately 94.5% of the clean reads were mapped against the reference Zucchini genome. In total, 3,823,977 high confidence single-nucleotide polymorphisms (SNPs) were identified. Within each accession, SNPs varied from 636,918 in green Zucchini to 2,656,513 in Crookneck, and were distributed homogeneously along the chromosomes. Clear differences between subspecies pepo and ovifera in genetic variation and linkage disequilibrium are highlighted. In fact, comparison between subspecies pepo and ovifera indicated 5710 genes (22.5%) with Fst?>?0.80 and 1059 genes (4.1%) with Fst?=?1.00 as potential candidate genes that were fixed during the independent evolution and domestication of the two subspecies. Linkage disequilibrium was greater in subsp. ovifera than in subsp. pepo, perhaps reflective of the earlier differentiation of morphotypes within subsp. ovifera. Some morphotype-specific genes have been localized. Our results offer new clues that may provide an improved understanding of the underlying genomic regions involved in the independent evolution and domestication of the two subspecies. Comparisons among SNPs unique to particular subspecies or morphotypes may provide candidate genes responsible for traits of high economic importance.