Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight

作     者：Stefano Pavan Chiara Delvento Rosa Mazzeo Francesca Ricciardi Pasquale Losciale Liliana Gaeta Nunzio D’Agostino Francesca Taranto Raquel Sanchez-Perez Luigi Ricciardi Concetta Lotti Stefano Pavan;Chiara Delvento;Rosa Mazzeo;Francesca Ricciardi;Pasquale Losciale;Liliana Gaeta;Nunzio D'Agostino;Francesca Taranto;Raquel Sánchez-Pérez;Luigi Ricciardi;Concetta Lotti

作者机构：Department of SoilPlant and Food ScienceUniversity of Bari Aldo MoroVia Amendola 165/ABari 70126Italy Institute of Biomedical TechnologiesNational Research Council(CNR)Via Amendola 122/DBari 70126Italy Department of the Sciences of AgricultureFood and EnvironmentUniversity of FoggiaVia Napoli 25Foggia 71100Italy Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment(CREA-AA)Bari 70125Italy Department of Agricultural SciencesUniversity of Naples Federico IIPortici 80055Italy Institute of Biosciences and BioresourcesNational Research Council of ItalyPortici 80055Italy CEBAS-CSIC.Campus Universitario de Espinardo30100 EspinardoSpain 

出 版 物：《Horticulture Research》 (园艺研究（英文）)

年 卷 期：2021年第8卷第1期

页      面：223-234页

核心收录：

学科分类：0710[理学-生物学] 0831[工学-生物医学工程（可授工学、理学、医学学位）] 1001[医学-基础医学(可授医学、理学学位)] 09[农学] 0901[农学-作物学] 0703[理学-化学] 0902[农学-园艺学] 0836[工学-生物工程] 090201[农学-果树学] 0834[工学-风景园林学（可授工学、农学学位）] 

主　　题：linkage structure Italian 

摘      要：Almond[Prunus dulcis Miller(D.A.Webb)]is the main tree nut species worldwide.Here,genotyping-by-sequencing(GBS)was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research(CREA)and the Spanish National Research Council(CSIC),leading to the detection of 93,119 single-nucleotide polymorphisms(SNPs).The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools.Data on SNP diversity and runs of homozygosity(ROHs)allowed the definition of kinship,inbreeding,and linkage disequilibrium(LD)decay in almond cultivated germplasm.Four-year phenotypic observations,gathered on 98 cultivars of the CREA collection,were used to perform a genome-wide association study(GWAS)and,for the first time in a crop species,homozygosity mapping(HM),resulting in the identification of genomic associations with nut,shell,and seed weight.Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent.Overall,this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding.In a broader perspective,our results encourage the use of ROHs in crop science to estimate inbreeding,choose parental combinations minimizing the risk of inbreeding depression,and identify genomic footprints of selection for specific traits.