Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time
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Author
Coindre, Eva
Dlalah, Naïma
Quilot-Turion, Bénédicte
Arús, Pere
Duval, Henri
Publication date
2023-09-25ISSN
2052-7276
Abstract
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
575 - General genetics. General cytogenetics
633 - Field crops and their production
Pages
11
Publisher
Oxford University Press
Is part of
Horticulture Research
Citation
De Los Cobos, Felipe Pérez, Eva Coindre, Naïma Dlalah, Bénédicte Quilot-Turion, I. Batlle, Pere Arús, Iban Eduardo, and Henri Duval. 2023. “Almond Population Genomics and Non-Additive GWAS Reveal New Insights into Almond Dissemination History and Candidate Genes for Nut Traits and Blooming Time.” Horticulture Research. 10 (10): uhad193. doi: 10.1093/hr/uhad193.
Grant agreement number
MINECO/Programa Estatal de fomento de la investigación científica y técnica de excelencia/SEV-2015-0533/ES/ /
MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I/CEX2019-000902-S/ES/ /
MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I y Programa Estatal de I+D+I orientada a los retos de la sociedad/PID2019-110599RR-I00/ES/Aplication of Marker Assisted Introgression and Resynthesis in peach/MAIRES
MICIU/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I y Programa Estatal de I+D+I orientada a los retos de la sociedad/PID2020-118612RR-I00/ES/Mejora genética de variedades de almendro/
INIA/Programa Estatal de I+D+I orientada a los retos de la sociedad/RTA2017-00084-00-00/ES/Mejora genética de variedades de almendro/
MICIU/Programa Estatal de I+D+I orientada a los retos de la sociedad/PCI2019-103670/ES/Resiliencia de los cultivos de frutas al cambio climático en la cuenca mediterránea/FREECLIMB
FEDER/ / /EU/ /
Program
Fructicultura
Genòmica i Biotecnologia
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