Ecological Genetics and Genomics 17 (2020) 100068 Available online 17 September 2020 2405-9854/© 2020 Elsevier Inc. All rights reserved. Whole genome SNPs and phenotypic characterization of cassava (Manihot esculenta Crantz) germplasm in the semi-deciduous forest ecology of Ghana Bright G. Adu a, * , Alex Yeboah b , Richard Akromah c , Emmanuel Bobobee d , Stephen Amoah e , Alexander W. Kena c , Richard A. Amoah a a CSIR-Plant Genetic Resource Research Institute (CSIR-PGRRI), P. O. Box 7, Bunso, Ghana b CSIR-Savanna Agricultural Research Institute (CSIR-SARI), P. O. Box TL 52, Tamale, Ghana c Department of Crops and Soil Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana d Department of Agricultural and Biosystems Engineering, College of Engineering, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana e CSIR-Crops Research Institute (CSIR-CRI), P. Box, 3785, Fumesua-Kumasi, Ghana A R T I C L E INFO Keywords: Landraces Agro-morphological Genetic diversity Broad-sense heritability Diversity array technology SNP markers ABSTRACT Diversity assessment in crop germplasm is an essential component towards its improvement and conservation. This study was undertaken to determine the genetic diversity within 87 cassava accessions using agro- morphological traits and Diversity Array Technology by sequencing based SNP (DArTseq). Results indicated that, the accessions significantly vary for most traits. Principal component analysis further showed the extent to which height and levels of branching, petiole length and colour, yield, cassava mosaic severity and above ground biomass contribute to the variability among the genotypes. Cassava mosaic disease was also significantly negatively correlated with most of growth and yield traits including shoot biomass and tuber yield. High heri- tability estimates and genetic advance was obtained for most of the traits indicating a positive response to se- lection. The uniqueness of each genotype and enormous variability in accessions based on agro-morphological data were debunked by the DArT-based SNP markers as redundant accessions were obtained which goes to confirm the environmental sensitivity of genetically identical genotypes. SNP markers identified fifteen acces- sions as being redundant based on Gower’s distance matrix with nine of these being landraces which shows the continuous exchange of planting materials among cassava growers hence their removal from the collection will enhance the management of the cassava germplasm. This has implication for cassava breeders to make informed choices in the selection of parental accessions for use in breeding programs. The narrow genetic base of the accessions as established by the SNPs necessitate the need to broaden the genetic base. 1. Introduction Cassava (Manihot esculenta Crantz) serves as food source for millions of people in Africa, Asia, and Latin America [1]. The main nutritional component of cassava is carbohydrate, which is derived from the starch accumulated in its tuberous storage roots and used by industries for starch-based products and ethanol [2]. Despite its importance, cassava was listed as one of the least studied plant species [3]. The average cassava yield in Ghana hovers around 18.78 Mt ha- 1 which equals 41.73% of its potential yield on research fields [4]. The low yield of the crop is attributable to many factors. Chief among them is the use of unimproved and poor planting materials. Farmers also use outdated agronomic practices, such as late planting and weed control at the wrong time [5]. Other constraints are the upsurge of global climate change and a number of biotic challenges including pests and diseases, leading to low yields. Furthermore, there is also little or lack of knowledge of the genetic diversity among the various accessions available for improve- ment of the crop [6]. Knowledge about the amount of variability that exists in the germplasm collections of any crop is of utmost importance towards breeding for better varieties [7]. Moreover, cassava is mainly propagated vegetatively, hence they are mostly maintained on the field at the genetic resource centres which is expensive in terms of space and cost. Also, collections of cassava held on farms or the major ex-situ gene banks in Ghana are however not based on optimized collection strategies and genetic redundancy may be expected. Although, farmers’ management influences the genetic diversity of * Corresponding author. E-mail address: bg.adu@csir.org.gh (B.G. Adu). Contents lists available at ScienceDirect Ecological Genetics and Genomics journal homepage: http://www.elsevier.com/locate/egg https://doi.org/10.1016/j.egg.2020.100068 Received 13 April 2020; Received in revised form 29 August 2020; Accepted 13 September 2020