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

Clicks: 3
ID: 284768
2023
Free PDF
Article Quality & Performance Metrics
Overall Quality
Not rated
Combines reader engagement with the AI quality analysis. This article has not been analysed, so there is no overall score — reader engagement is measured and shown alongside.
AI Quality Assessment
Not analyzed
Readership in this journal
Steady

Ranked #981 of 3,757 articles by views in Malay Journal

Most read Least read

Bar heights use a square-root scale. Only the 120 most-read articles are drawn; the journal has 3,757 in total.

Mint this article as an NFT
Not yet minted

Create a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.

5 SUSD one-off · no wallet required
Sign in to mint
Abstract
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.
Reference Key
persistent_1760653626_68f1713a3d424 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Merlin, Marc Lenard T.
Journal Malay Journal
Year 2023
DOI
DOI not found
URL
https://animorepository.dlsu.edu.ph/etdb_bio/36
Keywords Keywords not found

Citations

No citations found. To add a citation, contact the admin at info@scimatic.org

Comments

No comments yet. Be the first to comment on this article.