Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits  

作　　者：Aliki Xanthopoulou Javier Montero-Pau Ifigeneia Mellidou Christos Kissoudis JoséBlanca Belén Picó Aphrodite Tsaballa Eleni Tsaliki Athanasios Dalakouras Harry S.Paris Maria Ganopoulou Theodoros Moysiadis Maslin Osathanunkul Athanasios Tsaftaris Panagiotis Madesis Apostolos Kalivas Ioannis Ganopoulos 

机构地区：[1]Department of Genetics and Plant Breeding,Aristotle University of Thessaloniki,Thessaloniki 54124,Greece [2]Department of Biochemistry and Molecular Biology,Universitat de València,46022 Valencia,Spain [3]Institute of Plant Breeding and Genetic Resources,Hellenic Agricultural Organization DEMETER(ex NAGREF),Thermi,Macedonia 57001,Greece [4]Perrotis College,American Farm School,Thessaloniki 57001,Greece [5]Institute for the Conservation and Breeding of Agricultural Biodiversity(COMAV-UPV),Universitat Politècnica de València,Camino de Vera s/n,46022 Valencia,Spain [6]Department of Vegetable Crops and Plant Genetics,Agricultural Research Organization,Newe Ya’ar Research Center,Ramat Yishay,Israel [7]Institute of Applied Biosciences(INAB),CERTH,Thermi-Thessaloniki 57001,Greece [8]Department of Biology,Faculty of Science Chiang Mai University,Chiang Mai,Thailand [9]Center of Excellence in Bioresources for Agriculture,Industry and MedicineChiang Mai University,Chiang Mai,Thailand

出　　处：《Horticulture Research》2019年第1期568-584,共17页园艺研究（英文）

基　　金：supported by Hellenic Agricultural Organization(ELGO)Demeter.

摘　　要：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 wholegenome 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.ovifera(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

关 键 词：CULTIVAR TRAITS Whole 

分 类 号：S91[农业科学—水产科学]