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Article|10 Jan 2021|OPEN
Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight
Stefano Pavan1,2, Chiara Delvento1, Rosa Mazzeo3, Francesca Ricciardi3, Pasquale Losciale1, Liliana Gaeta4, Nunzio D’Agostino5, Francesca Taranto6, Raquel Sánchez-Pérez7, Luigi Ricciardi1 & Concetta Lotti3,
1Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via Amendola 165/A, Bari 70126, Italy
2Institute of Biomedical Technologies, National Research Council (CNR), Via Amendola 122/D, Bari 70126, Italy
3Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, Foggia 71100, Italy
4Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment (CREA-AA), Bari 70125, Italy
5Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy
6Institute of Biosciences and Bioresources, National Research Council of Italy, Portici 80055, Italy
7CEBAS-CSIC. Campus Universitario de Espinardo, 30100 Espinardo, Spain

Horticulture Research 8,
Article number: 15 (2021)
doi: 10.1038/hortres.2021.15
Views: 477

Received: 22 Jun 2020
Revised: 04 Nov 2020
Accepted: 13 Nov 2020
Published online: 10 Jan 2021

Abstract

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.