SNP-based genetic linkage mapping and whole-genome diversity assessment in cassava (Manihot esculenta Crantz) accessions from Africa and Latin America

Abstract

Cassava is a staple crop grown in the tropics and supplies food to over half a billion people. It is recognised as a valuable crop for food security in the face of climate change, since it grows in resource poor areas and displays tolerance to drought conditions. Furthermore, the high starch content of the storage roots makes cassava a suitable feedstock for biofuel production. Considerable advancements have been made towards the development of cassava genomic resources, such as the release of the first draft genome sequence in 2012, leading to the identification of new DNA markers and the use of genotyping-by-sequencing technology. The aim of this MSc was to i) construct a genetic linkage map using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers implemented in a drought-tolerant mapping population (MCOL1734 x VEN77), ii) assess genetic diversity and genetic structure within African and Latin American cassava landraces and breeding varieties using SNP markers, iii) to assess genome-wide patterns of diversity, and iv) to select 128 SNP markers for routine genotyping of cassava germplasm. Genetic diversity and structure was assessed within genetic material from African and Latin American germplasm collections, research institutes and breeding programmes. Three potentially heterotic genetic groupings were identified predominantly representing: a) Latin American germplasm, b) West and East African improved varieties, and c) East African landraces. Interestingly, one West African landrace displayed higher than average relatedness to landraces from East Africa, suggesting that it was widely distributed as a favourable variety and hybridised to local landraces in East Africa. Furthermore, evidence of mislabelling and redundancy was observed, highlighting the need for improved management of germplasm collections through the use of molecular markers. A genetic linkage map, representing 23 linkage groups, was constructed using 443 SNP and 73 SSR markers. Alignment to the Manihot esculenta v6.1 genome assembly revealed regions of the genome with poor marker coverage, resulting in some chromosomes being split into several small linkage groups. Minor allele frequency for all mapped SNP markers was plotted to assess the genome-wide distribution of diversity for each genetic group. This revealed one region of the genome with low heterozygosity across all three groups and one region displaying divergence in the East African landraces, likely as a result of local adaptation and selection by farmers. Using this data, 128 highly informative SNP markers, distributed throughout the genome, were selected as candidates for routine genotyping in cassava. This study contributes to our understanding of genetic diversity and structure in African and Latin American cassava landraces and improved varieties. Furthermore, two new molecular breeding tools were developed: a) a genetic linkage map, constructed using a drought-tolerant mapping population, will provide future opportunities to identify markers associated with this important trait for marker-assisted breeding, and b) a set of informative SNP markers that will provide a costeffective tool for routine genotyping for improved management of germplasm collections and breeding applications, such as the identification of genetically distant accessions for controlled crosses, pedigree reconstruction and maintenance of identity of accessions.