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Article|01 Jan 2021|OPEN
Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars
Felipe Pérez de los Cobos1,2, Pedro J. Martínez-García3, Agustí Romero1, Xavier Miarnau4, Iban Eduardo2, Werner Howad2, Mourad Mnejja2, Federico Dicenta3, Rafel Socias i Company5, Maria J. Rubio-Cabetas5, Thomas M. Gradziel6, Michelle Wirthensohn7, Henri Duval8, Doron Holland9, Pere Arús2, Francisco J. Vargas1 & Ignasi Batlle1,
1Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120 Constantí, Tarragona, Spain
2Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
3Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), P.O. Box 164, 30100 Espinardo, Murcia, Spain
4Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Fruitcentre, PCiTAL, Gardeny Park, Fruitcentre Building, 25003 Lleida, Spain
5Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059, Zaragoza, Instituto Agroalimentario de Aragón IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
6University of California, 1 Shields Avenue, Davis, CA 95616, USA
7University of Adelaide, Waite Research, School of Agriculture, Food and Wine, PMB 1, Glen Osmond, Adelaide, SA 5064, Australia
8Institut National de la Recherche Agronomique (INRA), Domain St. Maurice CS 60094, 84143 Montfavet Cedex, France
9Agricultural Research Organization, Newe-Ya’ar Research Center, P.O. Box 1021, Ramat Yishad 30095, Israel

Horticulture Research 8,
Article number: 11 (2021)
doi: 10.1038/hortres.2021.11
Views: 378

Received: 17 Jun 2020
Revised: 07 Nov 2020
Accepted: 13 Nov 2020
Published online: 01 Jan 2021


Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.