Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava

Authors: RABBI, ISMAIL YUSUF - International Institute Of Tropical Agriculture (IITA); KAYONDO, SIRAJ ISMAIL - International Institute Of Tropical Agriculture (IITA); BAUCHET, GUILLAUME - Boyce Thompson Institute; YUSUF, MUYIDEEN - International Institute Of Tropical Agriculture (IITA); AGHOGHO, CYNTHIA IDHIGU - International Institute Of Tropical Agriculture (IITA); OGUNPAIMO, KAYODE - International Institute Of Tropical Agriculture (IITA); UWUGIAREN, RUTH - International Institute Of Tropical Agriculture (IITA); SMITH, IKPAN ANDREW - International Institute Of Tropical Agriculture (IITA); PETERI, PRASAD - International Institute Of Tropical Agriculture (IITA); AGBONA, AFOLABI - International Institute Of Tropical Agriculture (IITA); PARKES, ELIZABETH - International Institute Of Tropical Agriculture (IITA); LYDIA, EZENWAKA - National Root Crops Research Institute (NRCRI); WOLFE, MARNIN - Cornell University; Jannink, Jean-Luc; EGESI, CHIEDOZIE - International Institute Of Tropical Agriculture (IITA); KULAKOW, PETER - International Institute Of Tropical Agriculture (IITA)

Submitted to: Plant Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/20/2020
Publication Date: 7/30/2020
Citation: Rabbi, I., Kayondo, S., Bauchet, G., Yusuf, M., Aghogho, C., Ogunpaimo, K., Uwugiaren, R., Smith, I., Peteri, P., Agbona, A., Parkes, E., Lydia, E., Wolfe, M., Jannink, J., Egesi, C., Kulakow, P. 2020. Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava. Plant Molecular Biology. https://doi.org/10.1007/s11103-020-01038-3.
DOI: https://doi.org/10.1007/s11103-020-01038-3

Interpretive Summary: Cassava (Manihot esculenta) is a critical food security crop in the tropics due to its adaptation to marginal environments. Improving this clonally propagated crop can be accelerated by identifying markers close to genes that affect important crop traits. We used a panel of 5130 cassava clones developed at the International Institute of Tropical Agriculture—Nigeria to find markers that explained variation in traits. The population was genotyped at more than 100,000 markers. Traits were classified broadly: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type). We also included color and shape traits that are strongly genetically determined related to leaves, stems and roots. In total, 41 significant associations were uncovered. While some of the identified markers matched previous reports, we also found new markers. We provide a catalogue of favorable alleles at the markers for each trait-marker combination and genes present nearby. These resources provide a foundation for the development of rapid assays that could be used in cassava breeding programs, and candidate genes for further research.

Technical Abstract: Cassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5130 clones developed at the International Institute of Tropical Agriculture—Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type) were investigated. We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.