Genome-Wide Association Analyses Reveal Key Aspects of Genetic Architecture Cassava in Africa

Cassava is one of the world’s most important root crops, serving as a staple food for hundreds of millions, especially in sub-Saharan Africa. Research addressing the diversity, population structure and genetics of Cassava has been limited at least in part owing to a lack of molecular resources. Recently and in order to realize Cassava’s potential, we assembled a collection of 6128 genotyped accessions, including genomic selection training populations from three African breeding programs as well as two generations of genomic-selection progenies. The collection was genotyped at about 50,000 high quality SNPs using genotype-by-sequencing and phenotyped to varying degrees over a total of 13 years and 15 locations for key agronomic traits. Our analyses of population stratification reveal a highly admixed African germplasm with complex patterns of relatedness. We tested several strategies for controlling population structure and implemented GWAS for the first time in Cassava. We examined the genetic architecture of nine agronomic traits relating to disease (CMD and CBB), root yield and dry matter content. Finally, we make a case study of cassava mosaic disease resistance to demonstrate the potential of genome-wide analyses to address the genetics of critical traits in Cassava. We identify several candidate genes for future study in a region of chromosome 8 corresponding to the dominant CMD2 locus, which explains up to 20% of the phenotypic variance. This study provides a description of the genetic resources available in African cassavas and demonstrates the potential for modern genomics to improve upon this critical crop.