Abstract
Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower's genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.
Highlights
Cassava (Manihot esculenta Crantz) is the third most important source of calories in the tropics after rice and maize with millions of people depending on it in the world [1, 2]
These ranged from 910 markers on chromosome18 to 2158 on chromosome1 (Fig 1) for the dominant SilicoDArT markers
Around 20.65% of the single nucleotide polymorphisms (SNPs) were in the lowest polymorphic information content (PIC) value range of 0
Summary
Cassava (Manihot esculenta Crantz) is the third most important source of calories in the tropics after rice and maize with millions of people depending on it in the world [1, 2]. Grown in marginal ecologies, the crop is usually cultivated by smallholder farmers due to its ability to grow and yield in unfavourable conditions with poor soil fertility and low rainfall [1, 3]. The cultivation of the crop continues to spread in Ghana and around the globe due to its storage roots which serve as the main raw material for industrial starch and alcohol production [5, 6]. Marginal yields continue to be realised at the farm level which is partly due to the lack of improved varieties and the use of low yielding and environmentally sensitive lines by farmers [7]. There are new emerging and diversified markets demand for cassava in Ghana which further suggests breeding for improved cultivars to meet specific domestic and industrial needs [8]
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