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Attempts are being made to domesticate the grasscutter (Thryonomys swinderianus) for commercial production in Sub-Saharan Africa to cater for the protein needs of the people and to satisfy the craving for bushmeat, thereby reducing habitat destruction through hunting. The objective of this study was to determine the genetic diversity of grasscutter populations in Ghana. DNA was extracted from roots of hair samples collected from 84 grasscutters from three agro-ecological zones in Ghana, namely Guinea Savanna (n = 17), Forest (n = 22), and Coastal Savanna (n = 45). Mitochondrial D-loop was sequenced and the diversity was determined across the zones. Out of 26 haplotypes found, 15 were obtained from Guinea Savanna, 7 from Forest and 13 from Coastal Savanna. Haplotype diversities were 0.978, 0.853 and 0.875 respectively for Guinea Savanna, Forest and Coastal Savanna zones. Analysis of molecular variance (AMOVA) revealed significant differentiation between Forest and Savanna populations (F ST = 0.14, p < 0.05). Network analysis indicated two clusters, one of which consisted of only Savanna haplotypes. Population neutrality tests showed that Forest and Coastal Savanna populations had been stable while the Guinea Savanna zone population had undergone an expansion (Fu's F S = −7.132, p < 0.05). The results of this study demonstrated that the Ghanaian populations of grasscutters are highly diverse but are less distinctive.

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Domestication and commercial production of the grasscutter, Thryonomys swinderianus, a large rodent, represents an important opportunity to secure sustainable animal protein for local communities in West Africa. To support production, DNA markers are required for population diversity assessment, pedigree analysis and marker-assisted selection. This study reports the application of double-digest RAD sequencing to simultaneously discover and genotype SNP markers in 24 wild and recently domesticated grasscutters. An initial panel of 1209 SNP loci was characterised from a total of more than 21 000 candidate loci containing single SNPs. This genome-wide resource represents the first application of its type to commercial production of a large rodent for food and advances the use of agricultural genomics in Ghana.

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