Simple Sequence Repeats (SSRs) have been used to identify maize inbreds into heterotic groups related to the determining of parents hybrid. A total of 73 lines, collected from Maros, Bogor, Malang, Thailand and Mexico (CIMMYT), were analized with 30 SSRs primers (3-6 nucleotide repeats) that are distributed over the ten chromosomes of maize genome. Percent heterozygosity revealed 36 inbreds, mostly Indonesian, that are less than 80% pure and having two to four alleles at certain loci. This high percentage of heterozygous lines points to the need for use of the elite inbred lines in hybrid seed production as well as for future breeding purposes. The remaining of 37 inbreds was further analyzed along with 6 CIMMYT maize standard lines. The alleles were scored in reference to the sequencered-based, molecular sized standard alleles develop at the Asian Maize Biotechnology Network (AMBIONET) service laboratory. From 43 inbreds, identified 145 alleles ranged from 2 to 8 alleles per locus and average 4.8alleles. The polymorphism information content ranged from 0.21 (umcl 161) to 0.87 (umcl 196), and average at 0.62. According to PCA, there are three SSRs locus were not have contribution to the constructing of the dendrogram as the resulted of low PIC value i.e. phi050 (0.31%), phi420701 (0.40%), and umcl 161 (0.21%). Cluster analysis placed the inbred lines in nine groups and six inbreds were not belonging to the nine groups. Cophenetic correlation (r) was 0.874, showing a good fit of the dendrogram with the similarity matrix generated using SSRs data. Results showed that heterotic groups is not always derived from genotype which collected from the same institution or region. High value of genetic distance is closely related to the information of specific combining ability. SSRs technique can be used for assigning inbreds into heterotic groups and quantifying genetic similarity, but it seems that a large number of SSRs primers combination are required to obtain reliable estimates of genetic diversity analysis.
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