Development of next-generation sequencing (NGS)-based SSRs in African nightshades: Tools for analyzing genetic diversity for conservation and breeding

Abstract

Abstract African nightshade is an indigenous leafy vegetable in Eastern and Western Africa that is valued for its high nutrient content and potential to generate income. Efforts to improve this crop have been hampered by limited information available on intra- and interspecific genetic diversity. Here, we present data on the development and application of polymorphic simple sequence repeat (SSR) markers in a broad collection of entries (gene bank accessions, landraces from farmers, breeding lines and commercial cultivars) from two species of African nightshades, Solanum scabrum (Mill.) and S. villosum (Mill.). Next generation sequencing information was used to develop 16 polymorphic SSR markers that revealed genetic diversity within and between the 54 entries collected from various geographic locations in Sub-Saharan Africa. High levels of polymorphism were detected within entries, indicating gene flow between entries and/or a low intensity of selection during development of breeding lines and improved cultivars. As a consequence, they have retained sufficient variation for further selection within the improved germplasm. The two species were clearly distinct, and S. scabrum was found to be less diverse compared to S. villosum. Furthermore, some entries were identified as probably misclassified based on morphological markers as they can clearly be placed within the gene pool of either S. scabrum or S. villosum using the SSR data. In addition to the diversity studies, we determined the genome size and ploidy of a selection of 29 entries helpful for the design of future NGS-based marker projects. All entries of S. scabrum were found to be hexaploid, whereas entries of S. villosum were tetraploid with a haploid genome size of all samples slightly varying by approximately 1 pg. Finally, we also determined pollen viability parameters, which differed significantly between the two species but did not correlate to any of the other parameters measured.