Articles
Diversity analysis of the INRAE and IRTA almond collections from the Axiom 60K SNP almond chip
Article number
1406_6
Pages
43 – 46
Language
English
Abstract
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 60581 SNPs markers was filtered for the development of the array.
These SNP were well distributed along the eight chromosomes.
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 origin of the countries; most notably with 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 and could be used for genome-wide association studies (GWASs)
From a pool of 80 resequenced varieties, a set of 60581 SNPs markers was filtered for the development of the array.
These SNP were well distributed along the eight chromosomes.
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 origin of the countries; most notably with 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 and could be used for genome-wide association studies (GWASs)
Authors
H. Duval, F. Pérez de los Cobos, E. Coindre, N. Dlalah, I. Batlle, I.E. Muñoz, P. Arús
Keywords
almond diversity, SNP, axiom array, structure, kinship
Groups involved
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