High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding

Authors: RABBI, ISMAIL - International Institute Of Tropical Agriculture (IITA); HAMBLIN, MARTHA - Cornell University; KUMAR, P. LAVA - International Institute Of Tropical Agriculture (IITA); GEDIL, MELAKU - International Institute Of Tropical Agriculture (IITA); IKPAN, ANDREW - International Institute Of Tropical Agriculture (IITA); Jannink, Jean-Luc; KULAKOW, PETER - International Institute Of Tropical Agriculture (IITA)

Submitted to: Virus Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/1/2013
Publication Date: 12/31/2013
Citation: Rabbi, I., Hamblin, M., Kumar, P., Gedil, M., Ikpan, A.S., Jannink, J., Kulakow, P. 2013. High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding. Virus Research. 186:87-96.

Interpretive Summary: Cassava mosaic disease (CMD) is the most important viral disease of cassava in Africa and the Indian sub-continent. The cultivated cassava species is protected from CMD by polygenic resistance introgressed from the wild species Manihot glaziovii and a dominant monogenic type of resistance, named CMD2, discovered in African landraces. The ability of the monogenic resistance to confer high levels of resistance in different genetic backgrounds has led recently to its extensive usage in breeding across Africa as well as in Latin America, even though the virus is not present there. Most of the landraces carrying the monogenic resistance are morphologically very similar and come from a geographically restricted area of West Africa, raising the possibility that the diversity of the single-gene resistance could be very limited, possibly originating from a single source. Several mapping studies in different genetic backgrounds have reported molecular markers linked to supposedly new resistance genes. However, it is not possible to tell if these are indeed new genes in the absence an adequate genetic map. To address this important question, a high-density single nucleotide polymorphism (SNP) map of cassava was developed by sequencing in 180 full-sib progeny of a single cross in which resistance to CMD is variable. Virus screening showed that CMD symptoms and presence of virus were strongly correlated (r = 0.98). Genome-wide analysis using 6756 DNA markers from sequencing uncovered a single locus that explained 75% of the variation for CMD symptoms. Projection of the previously published DNA markers linked to CMD resistance showed that they occurred in the same chromosomal location surrounding the resistance locus identified in our study. Cluster analysis of the landraces first shown to have this type of resistance revealed that they are very closely related, if not identical. These findings suggest that there is a single source of monogenic resistance in the crop’s genepool tracing back to a common ancestral clone. In the absence of further resistance diversification, the long-term effectiveness of the single gene resistance is known to be precarious because the virus may evolve virulence.

Technical Abstract: Cassava mosaic disease (CMD), caused by different species of cassava mosaic geminiviruses (CMGs), is the most important disease of cassava in Africa and the Indian sub-continent. The cultivated cassava species is protected from CMD by polygenic resistance introgressed from the wild species Manihot glaziovii and a dominant monogenic type of resistance, named CMD2, discovered in African landraces. The ability of the monogenic resistance to confer high levels of resistance in different genetic backgrounds has led recently to its extensive usage in breeding across Africa as well as pre-emptive breeding in Latin America. However, most of the landraces carrying the monogenic resistance are morphologically very similar and come from a geographically restricted area of West Africa, raising the possibility that the diversity of the single-gene resistance could be very limited or even located at a single locus. Several mapping studies, employing bulk segregant analysis, in different genetic backgrounds have reported additional molecular markers linked to supposedly new resistance genes. However, it is not possible to tell if these are indeed new genes in the absence adequate genetic map framework or allelism tests. To address this important question, a high-density single nucleotide polymorphism (SNP) map of cassava was developed through genotyping-by-sequencing a bi-parental mapping population (N = 180) that segregates for the dominant monogenic resistance to CMD. Virus screening using PCR showed that CMD symptoms and presence of virus were strongly correlated (r = 0.98). Genome-wide scan and high-resolution composite interval mapping using 6756 SNPs uncovered a single locus with large effect (R2 = 0.74). Projection of the previously published resistance-linked microsatellite markers showed that they co-occurred in the same chromosomal location surrounding the presently mapped resistance locus. Moreover, their relative distance to the mapped resistance locus correlated with the reported degree of linkage with the resistance phenotype. Cluster analysis of the landraces first shown to have this type of resistance revealed that they are very closely related, if not identical. These findings suggest that there is a single source of monogenic resistance in the crop’s genepool tracing back to a common ancestral clone. In the absence of further resistance diversification, the long-term effectiveness of the single gene resistance is known to be precarious, given the potential to be overcome by CMGs due to their fast-paced evolutionary rate. However, combining the quantitative with the qualitative type of resistance may ensure that this resistance gene continues to offer protection to cassava, a crop that is depended upon by millions of people in Africa against the devastating onslaught of CMGs.