Effectiveness of Single Nucleotide Polymorphism Markers in Genotyping Germplasm Collections of Coffea canephora Using KASP Assay

Authors: AKPERTEY, ABRAHAM - Cocoa Research Institute Of Ghana; PADI, FRANCIS KWAME - Cocoa Research Institute Of Ghana; Meinhardt, Lyndel; Zhang, Dapeng

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/28/2020
Publication Date: 1/25/2021
Citation: Akpertey, A., Padi, F., Meinhardt, L.W., Zhang, D. 2021. Effectiveness of Single Nucleotide Polymorphism Markers in Genotyping Germplasm Collections of Coffea canephora Using KASP Assay. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2020.612593.
DOI: https://doi.org/10.3389/fpls.2020.612593

Interpretive Summary: Development of Robusta coffee Coffea canephora L. requires the inclusion of genetic diversity, looking for incorporating new genes to tolerate or resist important pests and diseases, maintaining or improving yield and cup quality of the new materials. The present study used single nucleotide polymorphism (SNP) fingerprinting at 120 loci to examine the diversity, population structure, parentage and labeling errors in 400 C. canephora genotypes assembled from different sources over different time periods at the Cocoa Research Institute of Ghana (CRIG). Of the 400 genotypes analyzed 18.6% were mislabeled and the coffee germplasm collection at CRIG was separated into two main genetic clusters. This information will be used by scientist, coffee breeders and extension staff to improve Robusta coffee varieties and has significant implications for the establishment of Robusta coffee seed gardens in Ghana.

Technical Abstract: Development of Robusta coffee Coffea canephora L. requires the inclusion of genetic diversity, looking for incorporating new genes to tolerate or resist important pests and diseases, maintaining or improving yield and cup quality of the new materials. The present study used single nucleotide polymorphism (SNP) fingerprinting at 120 loci to examine the diversity, population structure, parentage and labeling errors in 400 C. canephora genotypes assembled from different sources over different time periods at the Cocoa Research Institute of Ghana (CRIG). The 120 SNPs used in analysis were high quality SNPs selected based on call rate, minor allele frequency and linkage disequilibrium through validation of two hundred candidate SNPs. Principal coordinate analysis separated the coffee germplasm collection at CRIG into two main clusters, with the first two coordinates accounting for 36.7% of the total variation. Analysis of molecular variance showed significant variations between populations (41%), though the maximum diversity was within the populations (59%). Of the 400 genotypes analyzed, both synonymous (trees with same SNP profiles but different names, 12.8%) and homonymous (trees with same name but different SNP profiles, 5.8%) mislabeling were identified in addition to trees with unique genotypes. This implicates pre-planting labelling errors and introduction of synonymous clones with different names. For 20 progenies derived from an open pollinated bi-clonal seed garden, only 8 had one parent different from breeders’ records. The data suggests mislabeling of the clones used in the seed garden and pollen contamination from more distant coffee plots. This has significant implications for isolation distance in the establishment of Robusta coffee seed gardens. The impact of genetic diversity and mislabeling on Robusta coffee breeding is discussed.