Abstract
The characterization and construction of genetic diversity panels provide valuable information for developing germplasm conservation strategies and applying advanced breeding techniques. Thus, we performed analysis of diversity and genetic structure in Cocos nucifera L. with a collection of dwarf and tall accessions belonging to the International Coconut Genebank for Latin America in the Caribbean. The collection comprises six dwarf accessions (represented by 36 individuals) and six tall (represented by 48 individuals). The analysis of clustering and DAPC performed from a set of 4044 SNP markers showed the existence of three clusters, one of which was formed exclusively by all dwarf coconut accessions. The tall accessions were separated into two distinct clusters, one formed by accessions from regions bathed by the Pacific Ocean (Southeast Asia and Oceania) and another formed by accessions from regions bathed by the Atlantic Ocean (Brazilian coastline and West Africa). The analysis allowed us to observe that the cluster formed by the accessions of dwarf coconut is closer genetically to the cluster formed by the accessions of tall coconut from the Pacific than the others from the Atlantic. Both groups presented similar genetic diversity (GD) values, 0.25 and 0.26, respectively. The inbreeding coefficient (F) revealed the presence of greater heterozygosity than expected in the dwarf coconut accessions and the inbreeding in the tall accessions. Consequently, we provide important information for maintaining those accessions in the germplasm bank and for future implementation of genomic-wide association studies (GWAS) and genomic selection (GS) with the evaluated accessions.
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Data availability
“The raw SNPs markers generated during and analyzed during the current study are available in the Mendeley Data repository, https://data.mendeley.com/datasets/42p5djgtjs.”
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Acknowledgements
"The author(s) utilized the University of Wisconsin—Madison Biotechnology Center's DNA Sequencing Facility (Research Resource Identifier—RRID:SCR_017759) to generate GBS libraries and sequence GBS libraries. The UWBC is a Licensed Service Provider for internal and external clients, providing GBS services under license from Keygene N.V. which owns patents and patent applications protecting its Sequence Based Genotyping technologies."
Funding
This work was supported by EMBRAPA (Project number: 03.15.00.127.00.00 and 01.06.01.007.06.00).
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All author contributed with the study development. Marial preparation and data collection were performed by EFNC, LECD and SRRR. Data analysis were performed by RF-N and AVS. The manuscript was written by all the authors since the first draft till the final version. All authors read and approved the final manuscript.
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da Silva, A.V., Costa, E.F.N., Diniz, L.E.C. et al. Genomic and population characterization of a diversity panel of dwarf and tall coconut accessions from the International Coconut Genebank for Latin America and Caribbean. Genet Resour Crop Evol (2023). https://doi.org/10.1007/s10722-023-01652-2
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DOI: https://doi.org/10.1007/s10722-023-01652-2