Study of genetic diversity among maize hybrids using SSR markers and morphological traits under two different irrigation conditions

Genetic diversity of 38 maize hybrids was studied using 12 SSR primers and morphological traits under two different irrigation conditions. The 38 hybrids were evaluated in two trials, one under well-watered (WW) conditions and one under drought-stress (DS) conditions, using an RBCD design with three replications for two years (2008-09) in Moghan, Iran. The total number of PCR-amplified products was 40 bands, all of them polymorphic. Primer Phi031 generated the highest number of bands (6). Among the studied primers, UMC2359, PHI031 and UMC1862 showed the maximum polymorphism information content (PIC) and the greatest diversity. These were the most informative primers and thus could be used to assess the diversity of maize hybrids. To determine the genetic relationship among maize hybrids, cluster analysis was performed based on both morphological traits (using the Ward method) and SSR markers (using the CLINK method). Maize hybrids were divided into three main groups based on SSR markers. Principal coordinate analysis (PCoA) of a similarity matrix of hybrids showed that the first 13 coordinates explained 84.73% of the total variance, whereas the first two coordinates explained only 28.14% of total variance. Cluster analysis of morphological traits divided the maize hybrids into two groups under both WW and DS conditions. Grouping hybrids based on morphological data under WW and DS conditions yielded different groups. Generally, results indicated that SSR markers are able to more efficiently classify closely related maize hybrids than morphological traits.