Investigating the genetic diversity of grain maize lines using microsatellite markers

IntroductionMaize is one of the most important sources of energy supply to feed poultry, livestock, as well as humans, and the primary and raw material for industrial and food products. This valuable crop plant in terms of world production ranks third after wheat and rice. Since knowing the genetic diversity in germplasm collections and determining the genetic relationships between breeding materials is the first and most important step in breeding researches, so identifying high diversity and suitable genetic potential lines is one of the goals of plant breeders to product and introduce new varieties. The objective of this study is to investigate the genetic diversity of 18 maize inbred lines using microsatellite (SSR) markers, to evaluate the efficiency of the studied markers, and to introduce the most appropriate ones in determining the genetic diversity of maize lines.Materials and methodsThe plant materials of this research included 18 inbred lines of maize prepared from the Agriculture and Natural Resources Research Center of Khorasan-Razavi province, Iran. DNA extraction was carried out by CTAB method from fresh and young leaf samples after the three-leaf stage of seedlings. Polymerase chain reaction (PCR) was performed in a final volume of 10 μl, and horizontal electrophoresis on 3% agarose gels as well as vertical electrophoresis on 6% polyacrylamide gels were used to observe the amplified fragments. For data analysis, first the amplified fragments (bands) on the gels were valued and quantified, so that the numbers 1 and 0 were considered for the presence and absence of each band in each maize line, respectively. To evaluate the genetic diversity, different diversity indices including number of effective alleles, polymorphic information content (PIC) and Nei’s gene diversity were estimated using POPGEN software, and the most suitable markers were introduced. To group the studied maize lines, cluster analysis and principal coordinates analysis were performed and the corresponding graphs were drawn using NTSYSpc 2.0 software.Research findingsAssessing the genetic diversity of maize lines based on microsatellite markers showed that 20 SSR markers used in this research amplified a total of 81 scorable loci, whose size ranged from 65 to 200 bp. The average number effective alleles, polymorphism information content and Nei’s gene diversity were calculated as 2.05, 0.71 and 0.62, respectively, indicating that there was a considerable genetic diversity among the studied maize lines. Evaluating the polymorphic information content (PIC) index showed that the markers used in this study had highly variable PIC from 0.28 (for Phi024) to 0.91 (for Phi038) with an average of 0.71. Cluster analysis by UPGMA method using Jaccard similarity coefficient grouped 18 maize inbred lines into three distinct clusters with 1, 6 and 11 lines, respectively. Molecular analysis of variance based on three groups derived from cluster analysis showed that 11% and 89% of the total variance was between and within population, respectively. The results of principal coordinate analysis and grouping if maize lines based on the bi-plot of the first and second vectors confirmed the grouping of the cluster analysis.ConclusionThe results of the current study showed that there was a significant genetic diversity among the studied maize lines, which can be used in breeding programs. Also, microsatellite markers (SSRs) had the ability to assess the genetic diversity and separation of maize genotypes from each other. Evaluating the different diversity indices for the studied markers in this research showed that the markers Phi034, Phi038, Phi076, Phi084, and Phi092 were more suitable markers for determining genetic diversity. Therefore, it is recommended to use these informative markers to determine genetic diversity as well as to identify heterotic pattern in maize breeding programs.