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Communication Dans Un Congrès Année : 2023

Diversity analysis of the INRAE and IRTA collection from the Axiom 60K SNP almond array

Résumé

Following the works of the “almond genome” consortium, and the publication of the almond genome reference “Texas”, we developed a 60K SNPs axiom almond array as tools for almond breeders and genetic studies. From a pool of 80 resequenced varieties, a set of 70k SNPs markers was filtered for the development of the array and the Affymetryx score retained 60581 SNPs markers. These SNP were well distributed along the eight chromosomes. The mean and the median for the distance between following SNPs were 2891 bp and 901 bp respectively and there were two gaps with more than 300 000 bp on chromosomes 1 and 2. With this array, we genotyped 219 almond accessions available in the two collections of INRAE in Avignon and IRTA in Reus. We excluded from our statistical analysis wild and hybrid accessions and SNPs with more than 10% of missing data. At the end of the process, we had an initial matrix with 152 individuals and 54K SNPs. Analysis with the SNMF R package showed that two models with five or seven ancestral groups were most probable. The model with five groups contained 21, 14, 19, 14, 12 varieties, and the first three groups included mainly Spanish, Italian and Chinese varieties respectively, while the two other groups and the admixture group contained different origins. The Kinship analysis highlighted the relationships between the varieties and we observed that the identified clusters corresponded well with to origin of the countries. This was particularly the case for the Italian, Chinese, Californian and Spanish varieties. The French varieties were more scattered. Our analysis showed that data provided by the axiom almond array were of good quality. The future steps of our analysis will be the GWAS analysis with some phenological and nut quality traits.
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Dates et versions

hal-04127020 , version 1 (13-06-2023)

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  • HAL Id : hal-04127020 , version 1

Citer

Henri Duval, Felipe Perez de Los Cobos, Eva Coindre, Ignasi Batlle, Iban Eduardo Muñoz, et al.. Diversity analysis of the INRAE and IRTA collection from the Axiom 60K SNP almond array. VIII International Symposium on Almonds and Pistachios, University of California, May 2023, Davis, United States. ⟨hal-04127020⟩
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