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Article|25 Sep 2023|OPEN
Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time
Felipe Pérez de los Cobos1,2,3,5 , Eva Coindre4,5 , Naima Dlalah4 and Bénédicte Quilot-Turion4 , Ignasi Batlle1 , Pere Arús2,3 , Iban Eduardo2,3 , Henri Duval,4 ,
1Fruticultura, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8 43120 Constantí Tarragona, Spain
2Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
3Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
4INRAE, GAFL, F-84143, Montfavet, France
5Both authors contributed equally
*Corresponding author. E-mail:

Horticulture Research 10,
Article number: uhad193 (2023)
Views: 129

Received: 17 Jul 2023
Accepted: 14 Sep 2023
Published online: 25 Sep 2023


Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype–phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.