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 

机构地区：[1]Department of Soil,Plant and Food Science,University of Bari Aldo Moro,Via Amendola 165/A,Bari 70126,Italy [2]Institute of Biomedical Technologies,National Research Council(CNR),Via Amendola 122/D,Bari 70126,Italy [3]Department of the Sciences of Agriculture,Food and Environment,University of Foggia,Via Napoli 25,Foggia 71100,Italy [4]Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment(CREA-AA),Bari 70125,Italy [5]Department of Agricultural Sciences,University of Naples Federico II,Portici 80055,Italy [6]Institute of Biosciences and Bioresources,National Research Council of Italy,Portici 80055,Italy [7]CEBAS-CSIC.Campus Universitario de Espinardo,30100 Espinardo,Spain

出　　处：《Horticulture Research》2021年第1期223-234,共12页园艺研究（英文）

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.

关 键 词：linkage structure Italian 

分 类 号：S662.9[农业科学—果树学]