In silico screening of the SH3 resistance locus in coffea canephora and coffea arabica for candidate genes involved in coffee leaf rust resistance

• Main Author: Merlin, Marc Lenard T.
• Format: text
• Language: English
• Published: Animo Repository 2023
• Subjects: Coffee rust disease; Coffee; Robusta coffee; Hemileia vastatrix; Biology
• Online Access: https://animorepository.dlsu.edu.ph/etdb_bio/36; https://animorepository.dlsu.edu.ph/context/etdb_bio/article/1055/viewcontent/2023_Merlin_In_silico_screening_of_the_SH3_resistance_locus_in_Coffea_Full_text.pdf
• Institution: De La Salle University

Two commercially cultivated species of coffee include Coffea canephora (Robusta) and Coffea arabica (Arabica). One of the reasons for the decline in volume of production of coffee in the Philippines are pests and diseases–one of which is the coffee leaf rust (CLR), caused by the obligate biotrophic fungus Hemileia vastatrix. Existing literature reports that resistance to CLR is conferred by resistance genes called SH (susceptibility to Hemileia sp.) genes. Currently, there are nine reported SH genes, and the SH3 gene locus was regarded to confer robust resistance to CLR. Ten molecular markers of the SH3 gene locus were gathered from published literature, and were subjected to Primer-BLAST and Nucleotide BLAST to identify the location of this gene cluster both in the C. canephora and C. arabica genomes. The binding sites of six molecular markers, BA-48-21O-f, Sat244, Sat160, SP-M5-SH3, Sat281, and BA-42-21B-r, indicated that the SH3 gene locus was located in Chromosome 3 wherein the region between 3 Mbp-16 Mbp was analyzed. Possible resistance genes within this region were obtained from Ensembl Plants and Coffee Genome Hub. The gathered genes were further filtered using the Orange program to determine which are associated with defense response during infection using their Gene Ontology (GO) term names. In C. canephora, there were 94 possible resistance genes, whereas there were 82 and 65 identified in the C. canephora and C. eugenioides subgenomes, respectively, of the entire C. arabica genome. These genes were subjected to Protein BLAST and Translated BLAST to identify the proteins they encode. Maps indicating the locations of the genes within the chromosome were constructed using the chromoMap app. The findings of this study serve as a reference of which genes can be used in the marker-assisted selection of disease-resistant coffee varieties. It aims to contribute to the development of resistant cultivars through conventional breeding aided by molecular techniques.