SNP-based genetic linkage mapping and whole-genome diversity assessment in cassava (Manihot esculenta Crantz) accessions from Africa and Latin America
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 cont...
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University of Pretoria
2017
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Online Access: | http://hdl.handle.net/2263/63354 Reynolds, SM 2017, SNP-based genetic linkage mapping and whole-genome diversity assessment in cassava (Manihot esculenta Crantz) accessions from Africa and Latin America, MSc Dissertation, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/63354> |
Summary: | 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. === Dissertation (MSc)--University of Pretoria, 2017. === Genetics === MSc === Unrestricted |
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