Genetic structure and diversity of European flint maize populations determined with SSR analyses of individuals and bulks

Abstract

Landraces of maize represent a valuable genetic resource for breeding and genetic studies. Using simple sequence repeat (SSR) markers, we analysed five flint maize populations from Central Europe that had played an important role in the pre-hybrid era in Germany. Our objectives were to (1) investigate the molecular genetic diversity within and among the populations based on the SSR analysis of individuals, (2) compare these results of the SSR analysis based on individuals with those based on bulks, (3) examine genotype frequencies for deviations from Hardy-Weinberg equilibrium (HWE) at individual loci, and (4) test for linkage disequilibrium (LD) between pairs of loci within populations. Thirty individuals and their bulked DNA per population were fingerprinted with 55 SSR markers. Across all populations, 46.7% of the SSR markers deviated significantly from HWE, with an excess of homozygosity in 97% of the cases. This excess of homozygosity can largely be explained by experimental errors during the amplification of SSRs apart from genuine genetic causes. Allele frequencies of the SSR analyses of individuals and bulks were significantly correlated (r=0.85, P< 0.01), suggesting that SSR analysis of bulks is very cost-effective for large-scale molecular characterisation of germ plasm collections. No evidence for genome-wide LD among pairs of loci was observed, indicating that the populations are well suited for high resolution association mapping studies.

Genetic diversity of the floury race of maize Avati Morotî from the Guaraní tribe in Paraguay

“…Altogether we found 13.13 alleles per locus, which is higher than the value reported by Aci et al (2013) among Algerian populations or Romay et al (2012) among Spanish germplasm with the same SSR set of loci. The number of alleles per locus was also higher than that reported in other American origins with different SSRs (Reif et al, 2003b(Reif et al, , 2004(Reif et al, , 2005(Reif et al, , 2006Wiethotler et al, 2008;Bracco et al, 2012).…”

High grain quality accessions within a maize drought tolerant core collection

“…This could be explained by the fact that alleles present in small percent can be missed in bulk analysis (Reif et al, 2005). In IP1 and IP2 accessions an unknown band (allele) was detected, positioned between the o2 and O2 bands.…”

Genetic Diversity of Maize Landraces as Sources of Favorable Traits

“…Better agreement with expected results was accomplished with AFLP analysis (Figure 3). In the work of Reif et al (2005) it was suggested that SSR analysis of bulked populations cannot detect alleles with a frequency below 0.2, so that a large number of alleles with low frequencies remains undetected. They also concluded that differences between populations are emphasized due to a concentration on alleles with high frequencies.…”

“…The results in our work which indicate that SSRs are not a good choice for bulk analysis of populations could be explained by several reasons, besides the low sensitivity of bulk approach in detecting low frequency alleles. Use of di-nucleotide repeat SSR (excluded in the work of Reif et al, 2005) which tend to be more polymorphic than SSR with longer repeat motifs (Smith et al, 1997) could have caused higher scoring errors. The silver staining of the gels is probably not the right choice for bulk analysis due to its low sensitivity.…”

“…The silver staining of the gels is probably not the right choice for bulk analysis due to its low sensitivity. It would be much better to use fluorescence as was done in the work of Reif et al (2005), in which it was shown that the allele frequencies of a population could be estimated with high accuracy from the band intensities of SSR profiles of bulks. Populations cannot detect alleles with a frequency below 0.2, so that a large number of alleles with low frequencies remain undetected.…”