Genomic Characterization of SNPs for Genetic Differentiation and Selection in Populations from the American Oil Palm [Elaeis oleifera (Kunth) Cortés] Germplasm Bank from Brazil

In this study, we used SNP markers to access the genetic components occurrence of genetic differentiation resulting from the selection processes applied to collect and maintain the germplasm bank of Elaeis oleifera (Kunth) Cortés from the Brazilian Amazon rainforest. A set of 1667 higher quality SNP...

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Bibliographic Details
Published in:Diversity (Basel) 2022-04, Vol.14 (4), p.270
Main Authors: Leão, André, Filho, Jaire, Pereira, Valquiria, Alves, Alexandre, Souza Júnior, Manoel
Format: Article
Language:English
Subjects:
Alleles
caiaué
conservation strategy
Differentiation
diversity
Elaeis oleifera
Gene frequency
Genetic diversity
Genetic testing
Genetic variability
Genomes
Genomics
Geographical distribution
Germplasm
Loci
Markers
Plant reproduction
Population
Population genetics
Populations
Rainforests
selection
Simulation
Single-nucleotide polymorphism
SNP markers
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Summary:In this study, we used SNP markers to access the genetic components occurrence of genetic differentiation resulting from the selection processes applied to collect and maintain the germplasm bank of Elaeis oleifera (Kunth) Cortés from the Brazilian Amazon rainforest. A set of 1667 higher quality SNPs—derived from a previous GBS study—was used for genomic characterization and calculation of genetic parameters. There is differentiation in the distribution of alleles between populations for 78.52% of the tested loci. Genotypic diversity test results indicated strong evidence of genotypic differentiation between populations. Sixteen out of the nineteen tested deviated significantly from the expected allele frequencies in HWE, reinforcing the hypothesis that there was maybe a selection in the evaluated populations. A group of 568 loci with a higher probability of being under selection effects were selected, both directional and stabilizing. In total, 1546 and 1274 SNPs aligned in the genomes of E. oleifera and E. guineensis Jacq., respectively. These markers showed a wide distribution throughout the genome of the two species. In conclusion, the E. oleifera GB from the Brazilian Amazon rainforest has specific genetic structures and good genetic variability within populations.
ISSN:1424-2818
1424-2818
DOI:10.3390/d14040270