Development of SSR Markers and Genetic Variability in Physiological Traits in Bambara Groundnut (Vigna subterranea L. Verdc)

Abstract

Bambara groundnut (Vigna subterranea L. Verdc) is a widely grown crop in marginal lands mainly in sub-Saharan Africa. Improvement of this crop has tremendous potential for its extension to other places including India. Though bambara groundnut is a drought-tolerant crop, from the agronomic point of view, drought tolerance should be linked with superior growth rates and productivity under water-limited conditions. Before attempting to improve these traits, it would be necessary to assess the genetic variability in the response of these traits to water-limited conditions. We assessed the genetic variability in WUE and the physiological traits associated with these traits. It was observed that on the average, there was a significant increase in WUE when the plants experienced water stress. This increase in WUE was primarily due to a significant reduction in total transpiration. This reduction in total transpiration (CWT) coupled with a reduction in total leaf area leads to a significant reduction in total biomass among these accessions under stress. There was significant reduction in oxygen evolution, potential photosynthesis and the chlorophyll content, all of which decreased significantly under stress. A strong correlation was noticed between oxygen evolution and potential photosynthesis, indicating that the chloroplast mechanism is severely affected by stress among bambara accessions. Marker-assisted breeding is expected to enhance the speed and accuracy of achieving such improvements. However, lack of locus-specific codominant marker systems in this crop is the major constraint for molecular breeding. Therefore, development of SSRs (simple sequence repeats) markers in bambara groundnut that can be subsequently employed in identification of QTL (quantitative trait locus) for specific physiological traits relevant for drought tolerance is the need of hour. A pre-cloning enrichment (selective hybridisation) strategy was adopted to fish out the SSRs from bambara groundnut genome to develop a microsatellite-enriched library. This strategy involves the hybridisation of digested genomic DNA with repeat oligomers, leading to selective enrichment. Based on this technique, we obtained 2,239 microsatellite-enriched clones, of which 734 clones were sequenced and analysed for the presence of microsatellite repeat regions. Among these, clones revealed microsatellite regions with more than 15 bp. Initially, primers were designed and synthesised for 143 SSR regions. These primers have been validated for their amplification using the genomic DNA of different land races. Of these, locus-specific amplification was observed in 99 primer pairs. These validated SSR markers are being used for molecular characterisation of different bambara groundnut landraces.