Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs

Abstract

In order to get an overview on the genetic relatedness of sorghum (Sorghum bicolor) landraces and cultivars grown in low-input conditions of small-scale farming systems, 46 sorghum accessions derived from Southern Africa were evaluated on the basis of amplified fragment length polymorphism (AFLPs), random amplified polymorphic DNAs (RAPDs) and simple sequence repeats (SSRs). By this approach all sorghum accessions were uniquely fingerprinted by all marker systems. Mean genetic similarity was estimated at 0.88 based on RAPDs, 0.85 using AFLPs and 0.31 based on SSRs. In addition to this, genetic distance based on SSR data was estimated at 57 according to a stepwise mutation model (Deltamu-SSR). All UPGMA-clusters showed a good fit to the similarity estimates (AFLPs: r = 0.92; RAPDs: r = 0.88; SSRs: r = 0.87; Deltamu-SSRs: r = 0.85). By UPGMA-clustering two main clusters were built on all marker systems comprising landraces on the one hand and newly developed varieties on the other hand. Further sub-groupings were not unequivocal. Genetic diversity (H, DI) was estimated on a similar level within landraces and breeding varieties. Comparing the three approaches to each other, RAPD and AFLP similarity indices were highly correlated (r = 0.81), while the Spearman's rank correlation coefficient between SSRs and AFLPs was r = 0.57 and r = 0.51 between RAPDs and SSRs. Applying a stepwise mutation model on the SSR data resulted in an intermediate correlation coefficient between Deltamu-SSRs and AFLPs (r = 0.66) and RAPDs ( r = 0.67), respectively, while SSRs and Deltamu-SSRs showed a lower correlation coefficient (r = 0.52). The highest bootstrap probabilities were found using AFLPs (56% on average) while SSR, Deltamu-SSR and RAPD-based similarity estimates had low mean bootstrap probabilities (24%, 27%, 30%, respectively). The coefficient of variation (CV) of the estimated genetic similarity decreased with an increasing number of bands and was lowest using AFLPs.

Common garden experiments in the genomic era: new perspectives and opportunities

“…Better relatedness estimates are useful because they will improve the precision of the estimates of h 2 and Q ST . Note however that many markers are typically needed to obtain precise molecular estimates of relatedness (Uptmoor et al, 2003). Dense markers provided by high-throughput genotyping naturally fulfill this requirement.…”

“…Microsatellites, on the other hand, are very different: they usually provide very sparse panels (up to a few dozens of markers), but highly mutable and with a large allelic diversity. Although it has been argued that microsatellites are better markers to infer relatedness (Ritland, 2000), they typically yield smaller relatedness estimates than SNP or AFLP markers because of higher mutation rates (Uptmoor et al, 2003;El Rabey et al, 2013). They also yield smaller F ST estimates (Edelaar and Björklund, 2011) for the same reason.…”

“…They also yield smaller F ST estimates (Edelaar and Björklund, 2011) for the same reason. Finally, although in theory more accurate than SNPs for the same number of loci, they typically yield one to two orders of magnitude less loci, and hence they are less accurate in practice (Uptmoor et al, 2003).…”

Genetic Diversity among Japanese Cultivated Sorghum Assessed with Simple Sequence Repeats Markers

“…Simple sequence repeats (SSR) markers are useful indices for studying the genetic diversity of the world sorghum germplasm lines, and were used for the study of Eritrean sorghum landraces, the elite sorghum inbred lines and the sorghum from Southern Africa (Dje et al, 2000;Ghebru et al, 2002;Smith, et al, 2000;Uptmoor et al, 2003); genetic redundancy in the 'Orange' sorghum (Dean et al, 1999); and mapping of sorghum genome (Bowers et al, 2003;Menz et al, 2002). SSR fi ngerprints are generally highly discriminative and are often used to distinguish varieties, or even individuals, and reveal parentage and identity (Karp et al, 1996) and grouping the maize germplasm based on heterotic groups (Reif et al, 2003).…”

DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces

“…Polymerase chain reaction (PCR) based assays for plant DNA fingerprinting such as AFLP (Vos et al, 1995), SSR (Tautz and Renz, 1984) and ISSR (Zietkiewicz et al, 1994) have become widely used. These markers have been widely used for reliable and robust characterization of crop genetic resources (Godwin et al, 1997;Pejic et al, 1998;Smith et al, 2000;Wen et al, 2002;Uptmoor et al, 2003;Medraoui et al, 2007;Weerasooriya et al, 2016). With the development of high-throughput sequencing (or next-generation sequencing-NGS) technologies in recent years, marker techniques such as single nucleotide polymorphism (SNPs) and genotyping by sequencing (GBS) have become very useful for exploring the diversity within plant species, constructing haplotype maps and performing genome-wide association studies as well as genomicsassisted breeding (He et al, 2014).…”