Khemira, H.; Mahdhi, M.; Afzal, M.; Oteef, M.D.Y.; Tounekti, T.; AL-Faifi, Z.; Alsolami, W. Assessment of Genetic Diversity and Phylogenetic Relationship of Local Coffee Populations in Southwestern Saudi Arabia Using DNA Barcoding. PeerJ 2023, 11, e16486, doi:10.7717/peerj.16486.
Khemira, H.; Mahdhi, M.; Afzal, M.; Oteef, M.D.Y.; Tounekti, T.; AL-Faifi, Z.; Alsolami, W. Assessment of Genetic Diversity and Phylogenetic Relationship of Local Coffee Populations in Southwestern Saudi Arabia Using DNA Barcoding. PeerJ 2023, 11, e16486, doi:10.7717/peerj.16486.
Khemira, H.; Mahdhi, M.; Afzal, M.; Oteef, M.D.Y.; Tounekti, T.; AL-Faifi, Z.; Alsolami, W. Assessment of Genetic Diversity and Phylogenetic Relationship of Local Coffee Populations in Southwestern Saudi Arabia Using DNA Barcoding. PeerJ 2023, 11, e16486, doi:10.7717/peerj.16486.
Khemira, H.; Mahdhi, M.; Afzal, M.; Oteef, M.D.Y.; Tounekti, T.; AL-Faifi, Z.; Alsolami, W. Assessment of Genetic Diversity and Phylogenetic Relationship of Local Coffee Populations in Southwestern Saudi Arabia Using DNA Barcoding. PeerJ 2023, 11, e16486, doi:10.7717/peerj.16486.
Abstract
The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and the evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci, namely atpB-rbcl, TrnL-TrnF, TrnT-TrnL, and TrnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while TrnT-TrnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, TrnT-TrnL recorded the highest singleton variable sites, while TrnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.
Keywords
Coffea arabica; chloroplastic DNA; barcode, genetic diversity; population structure; Saudi Arabia
Subject
Biology and Life Sciences, Agricultural Science and Agronomy
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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