Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses

Abstract

In Burundi most small-scale farmers still grow traditional cassava landraces that are adapted to local conditions and have been selected for consumer preferred attributes. They tend to be susceptible, in varying degrees, to devastating cassava viral diseases such as Cassava Brown Streak Disease (CBSD) and Cassava Mosaic Disease (CMD) with annual production losses of US$1 billion. For long term resistance to the disease, several breeding strategies have been proposed. A sound basis for a breeding program is to understand the genetic diversity of both landraces and elite introduced breeding cultivars. This will also assist in efforts to conserve landraces ahead of the broad distribution of improved varieties which have the possibility of replacing landraces. Our study aimed at determining the genetic diversity and relationships within and between local landraces and introduced elite germplasm using morphological and single nucleotide polymorphism (SNP) markers. A total of 118 cultivars were characterized for morphological trait variation based on leaf, stem and root traits, and genetic variation using SNP markers. Results of morphological characterization based on Ward’s Method revealed three main clusters and five accessions sharing similar characteristics. Molecular characterization identified over 18,000 SNPs and six main clusters and three pairs of duplicates which should be pooled together as one cultivar to avoid redundancy. Results of population genetic analysis showed low genetic distance between populations and between local landraces and elite germplasm. Accessions that shared similar morphological traits were divergent at the molecular level indicating that clustering using morphological traits was inconsistent. Despite the variabilities found within the collection, it was observed that cassava germplasm in Burundi have a narrow genetic base.

Estimation of Genetic Diversity and Number of Unique Multilocus Genotypes (MLGs) of Cassava Germplasm from Burkina Faso Using Simple Sequence Repeat (SSR) Markers

“…Understanding genetic diversity of species is the basis of the success of any breeding program and to develop strategies for germplasm management, conservation, and improvement [28]. Assessment of genetic variability of a given population in order to provide breeding programs with interesting parental lines is a very important pre-breeding operation and must take into account the morphological and molecular variabilities in an existing population.…”

“…According to Collard et al (2005) the use of molecular markers can permit the detection of genetic differences among closely related genotypes. In addition, assessment of the agro-morphological diversity of cassava requires a great deal of space, depending on the number of accessions, and is spread over several months (9 to 12 months) [15,28]. It is therefore advisable to assess molecular diversity within the germplasm and to identify the unique multilocus genotypes first, before assessing agromorphological diversity.…”

“…On the other hand, the molecular markers are stable, easily detectable and not influenced by the environment [19,20]. Various molecular tools can be used to assess the genetic diversity of crops, including Random Amplified Polymorphic DNA (RAPD) [21], Restriction Fragment Length Polymorphism (RFLP) [21], Amplified Fragment Length Polymorphism (AFLP) [22], Simple Sequence Repeat (SSR) [1,19,23], Single Nucleotide Polymorphism (SNP) [13,18,[24][25][26], and Diversity Arrays Technology (DArT) [27,28]. The locus specific markers such as SSR markers have found its preferential application in genetic diversity and population structure assessment in many crops [1,[29][30][31].…”

Risk factors associated with cassava brown streak disease dissemination through seed pathways in Eastern D.R. Congo

“…The use of local agronomists was privileged in this study in the frame of a simple differentiation between local and improved varieties grown on field. The use of molecular markers to perform morphological identification, using for example SNP markers (Karim et al, 2020;Pierre et al, 2022), would have brought more precise information for confirming identities of cassava genotypes. This strategy would provide further evidence on the possible linkages between CBSD symptomology and cassava genotypes but we did not definitely envisage it in this study considering the resources and time available.…”

Estimation of Genetic Diversity and Number of Unique Genotypes of Cassava Germplasm from Burkina Faso Using Microsatellite Markers

“…On the other hand, the molecular markers are stable, easily detectable, and not influenced by the environment [19,20]. Various molecular tools can be used to assess the genetic diversity of crops, including Random Amplified Polymorphic DNA (RAPD) [21], Restriction Fragment Length Polymorphism (RFLP) [21], Amplified Fragment Length Polymorphism (AFLP) [22], simple sequence repeat (SSR) [1,19,23], single nucleotide polymorphism (SNP) [13,18,[24][25][26] and Diversity Arrays Technology (DArT) [27,28]. The locus-specific markers such as SSR markers have found their preferential application in genetic diversity and population structure assessment in many crops [1,[29][30][31].…”