Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers

Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger’s distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity

From RFLP to DArT: molecular tools for wheat (Triticum spp.) diversity analysis

Wheat (Triticum spp.) is a universally lucrative agricultural crop. An increase in wheat production has been shown through selection by the farmers which can increase the grain profitability. The determination of genetic associations among domestic cultivars is facilitated by molecular markers. Data on genetic polymorphism is valuable for the germplasm association and regarding the developing management strategies. The information would be supportive for potential genome mapping programs and for the relevance of intellectual property rights of wheat breeders. Present review is an effort for providing support information to wheat breeders to develop varieties with varied genetic environment to attain continuity in large-scale wheat production. In this review, we have tried to provide a collective depiction of relevant information about the usage of some commonly used markers in wheat. It may help researchers to find out the frequentness and application of different markers and compare their results. The manuscript may serve as a platform helping the intellectuals for the selection and modification of their marker system in wheat diversity analysis. The heart of this review is the emphasis on the performance of various molecular genetic markers in diversity studies in relation to definite approaches that are in practice since several years allied with the multifaceted wheat molecular breeding and its polyploid nature