SNP markers associated with resistance to Frosty Pod and Black Pod diseases in a F1 population of Theobroma cacao L.

Authors: Gutierrez, Osman; Puig, Alina; PHILLIPS-MORA, WILBERT - Catie Tropical Agricultural Research; Bailey, Bryan; ALI, SHANIN - University Of California; MOCKAITIS, KEITHANE - Indiana University; SCHNELL, RAYMOND - Mars, Inc; LIVINGSTONE, DONALD - Mars, Inc; MUSTIGA, GUILIANA - Mars, Inc; ROYAERT, STEFAN - Mars, Inc; MOTAMAYOR, JUAN - Mars, Inc

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2021
Publication Date: 4/30/2021
Citation: Gutierrez, O.A., Puig, A.S., Phillips-Mora, W., Bailey, B.A., Ali, S.S., Mockaitis, K., Schnell, R.J., Livingstone, D., Mustiga, G., Royaert, S., Motamayor, J.C. 2021. SNP markers associated with resistance to Frosty Pod and Black Pod diseases in a F1 population of Theobroma cacao L. . Tree Genetics and Genomes. 17, 28. https://doi.org/10.1007/s11295-021-01507-w.
DOI: https://doi.org/10.1007/s11295-021-01507-w

Interpretive Summary: Cacao (Theobroma cacao L.) is an important crop in the tropical regions of the world. Cacao production worldwide has been severely affected by diseases and pests. In the Americas Frosty Pod and Black Pod are the most important diseases that cause substantial production loses. The use of fungicides to control these diseases is not feasible due to high costs and environmental concerns. The most environmentally sound solutions are the development of resistance varieties. The purpose of this study was to investigate the association of molecular markers with Frosty Pod and Black Pod in cacao in an F1 population with the cross of two cacao cultivars ‘Pound 7’ and ‘UF 273’. Results indicated that association between molecular markers and Frosty Pod as well as Black Pod resistance was observed in this population. The source of Frosty Pod resistance is derived from the ‘UF 273’ parent and the source of Black Pod resistance came from the ‘Pound 7’ variety. These results indicate the prospect of using these markers to accelerate the development of cacao varieties resistant to Frosty Pod and Black Pod.

Technical Abstract: Economically, cacao (Theobroma cacao L.) is a major tropical commodity for the Americas; however, severe losses due to Moniliophthora roreri (Cif. and Par.), which causes frosty pod rot (FPR), and Phytophthora spp., which causes black pod rot (BPR), have reduced cacao production in the Americas. The objectives of this study are to (i) re-confirm the QTL using different marker set; (ii) discover new QTL associated with FPR and BPR resistance using SNP markers; and (iii) find genes in the candidate QTL regions. At CATIE in Turrialba, Costa Rica, an F1 mapping population of cacao was obtained by crossing “POUND 7,” a clone moderately susceptible to FPR and resistant to BPR, with “UF 273,” resistant to FPR and highly susceptible to BPR. A total of 179 F1 progeny were fingerprinted with 5149 SNP markers and a dense linkage map composed of 10 linkage groups was developed using 2910 polymorphic SNP markers. Also segregating F1 trees were screened for resistance to FPR and BPR diseases. Seven QTL previously reported on chromosomes 2, 7, and 8 for FPR resistance and on chromosomes 4, 8, and 10 for BPR resistance were confirmed. Additionally, eight QTL were identified for FPR resistance (chromosomes 4, 9, and 10) and BPR resistance (chromosome 2). The expression of genes commonly associated with plant defense and disease resistance that are located within the identified QTL was confirmed.