Articles
Genetic structure and GWAS in an international pomegranate collection including Sardinian germplasm
Article number
1464_30
Pages
227 – 234
Language
English
Abstract
Pomegranate (Punica granatum L.) is a strategic crop for Mediterranean and Mediterranean-like environments.
We assembled an integrated panel of 163 accessions (109 international; 54 Sardinian) resequenced at ~20×, yielding >20,000 high-quality SNPs.
Population-structure analyses (Ward, DAPC, network) resolved 10-11 clusters.
The Sardinian set included a low-diversity cluster comprising the majority of Sardinian accessions, many of which formed clone-like pairs.
Inter-cluster divergence was moderate (AMOVA FST=0.150). Sliding-window scans (1 Mb) identified highly differentiated regions (FST>0.50) on Chr1, Chr2 and Chr6. Mean values for fruit colour, aril colour and seed hardness differed significantly among clusters, with seed hardness being the most discriminant trait.
As a proof of concept, a preliminary multi-locus GWAS for seed hardness and taste (BLINK; FarmCPU), correcting for structure, revealed multiple loci, including a robust cross-method signal for taste on chromosome 7 and additional model-dependent signals for seed hardness (Chr1, Chr2, Chr5, and Chr7) and taste (Chr3 and Chr6). A representative subset has been established as a common garden in Sardinia for long-term validation and deployment.
These results illustrate how integrating regional landraces with international germplasm can support conservation and guide breeding for fruit-quality targets in Mediterranean contexts.
We assembled an integrated panel of 163 accessions (109 international; 54 Sardinian) resequenced at ~20×, yielding >20,000 high-quality SNPs.
Population-structure analyses (Ward, DAPC, network) resolved 10-11 clusters.
The Sardinian set included a low-diversity cluster comprising the majority of Sardinian accessions, many of which formed clone-like pairs.
Inter-cluster divergence was moderate (AMOVA FST=0.150). Sliding-window scans (1 Mb) identified highly differentiated regions (FST>0.50) on Chr1, Chr2 and Chr6. Mean values for fruit colour, aril colour and seed hardness differed significantly among clusters, with seed hardness being the most discriminant trait.
As a proof of concept, a preliminary multi-locus GWAS for seed hardness and taste (BLINK; FarmCPU), correcting for structure, revealed multiple loci, including a robust cross-method signal for taste on chromosome 7 and additional model-dependent signals for seed hardness (Chr1, Chr2, Chr5, and Chr7) and taste (Chr3 and Chr6). A representative subset has been established as a common garden in Sardinia for long-term validation and deployment.
These results illustrate how integrating regional landraces with international germplasm can support conservation and guide breeding for fruit-quality targets in Mediterranean contexts.
Authors
M. Santona, F. Cossio, L. De Pau, D. Satta, G. Schirru, G. Tacconi, C.M. Posadinu, D. Fois, A. Porceddu, D. Rau
Keywords
population genetics, genetic diversity, germplasm valorisation, Punica granatum, GWAS, FST genome-scan
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