Assessment of Genetic Diversity of Local Coffee Populations in Southwestern Saudi Arabia Using SRAP Markers

• Published in: Agronomy (Basel) Vol. 13; no. 2; p. 302
• Main Authors: Al-Ghamedi, Khalef, Alaraidh, Ibrahim, Afzal, Muhammad, Mahdhi, Mosbah, Al-Faifi, Zarraq, Oteef, Mohammed D. Y., Tounekti, Taieb, Alghamdi, Salem S., Khemira, Habib
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.01.2023
• Subjects: Agronomic crops; Analysis; Biological diversity; Cluster analysis; Coffea arabica; Coffee; Divergence; Gene polymorphism; Genes; Genetic analysis; Genetic aspects; Genetic diversity; Genetic engineering; Genetic research; Genomics; Genotypes; Geographical distribution; Germplasm; Mountains; Polymorphism; Population genetics; population structure; Population studies; Populations; Saudi Arabia; Software; SRAP; Structural analysis; Terraces; Saudi Arabia; Ethiopia; Yemen; Red Sea
• ISSN: 2073-4395; 2073-4395
• DOI: 10.3390/agronomy13020302

Coffea arabica, a member of the Rubiaceae family, is the most commercially important species of the genus Coffea. It has been grown on the mountain terraces of southwestern Saudi Arabia for centuries. At present, the species is subject to increased genetic erosion due to the abandonment of many gardens by their owners and the increasingly dry climate. The current study was carried out to determine the genetic diversity of 56 local coffee accessions collected from the southern regions of Saudi Arabia using 30 sequence-related amplified polymorphism (SRAP) markers. Six SRAP markers showed polymorphism among the 56 accessions. A total of 1125 bands, with an average of 187.5, was produced from all six SRAP primers. The polymorphic information content (PIC) ranged from 74.8 to 97.7, with an average of 91.4 for all studied SRAP markers. The high polymorphism percentage seen in this study, along with the high number of alleles produced and the high PIC values of the primers used, demonstrate that the SRAP approach was an effective molecular technique for assessing genetic diversity in the studied populations. The structural analysis showed a sharp peak, with no ambiguity, demonstrating the highest delta K value at K = 3 and K = 6, and the coffee accessions could be grouped into three and six main populations, respectively. The PCoA, cluster analysis, and structural population analysis results suggest considerable genetic diversity among coffee populations growing on the southwestern mountain terraces of Saudi Arabia. The 56 accessions were segregated into five groups, mostly according to geographic distribution. The accessions from the southern districts of Jazan region mostly clustered in groups 2 and 4, while the accessions from the northern districts of Al-Baha and Assir regions formed separate groups. Based on these analyses, accessions KSA1R, KSA6R, KSA21, KSA25, KSA37, KSA38, KSA42, KSA59, KSA60, KSA62, and KSA63 were the most divergent. The genotypes should be conserved for use in coffee-breeding programs to improve the agronomic value of the crop, broaden the genetic base of C. arabica in Saudi Arabia and increase environmental resilience. Additional molecular and functional genomics studies are necessary to further elucidate how this germplasm has evolved and enhance the value of local Arabica coffee diversity in the Kingdom.