As multiple microsatellites were tested and the selective chromosome linkage data were limited, the positive results generated from J/qtl were analyzed again using two-tailed, nonparametric tests for independent variables (Mann-Whitney U Tests).
Because evaluating the full likelihood of multiple microsatellites may be computationally infeasible at present to the best of our knowledge, we summarized the data by two statistics, the average heterozygosity in wild (HR) and the average heterozygosity in cultivated rice (HC), which could be either HI or HJ for the analysis of subsp. indica and subsp. japonica, respectively.
This pattern is consistent with the 'general effect' hypothesis (David 1998), where heterozygosity across multiple microsatellite markers is an indirect measurement of a population's average fitness.
Microsatellites are multiple tandem repeats of a small number of nucleotides that are very prone to these errors; therefore MMR system activity is critical for their maintenance (Kunkel, 2004; Jiricny, 2006).
Multiple microsatellite markers were therefore designed within a 5-centiMorgan locus, thus reducing the odds of a deletion breakpoint between markers within a locus.
On the basis of the amplification results, the nucleotide sequences of three representative homoeologous microsatellites were amplified from multiple accessions of T. urartu and T. monococcum and compared.
The frequency of microsatellites was 23.7% considering multiple occurrence in a same unigene element, which was close to that calculated by Durand et al. [ 29] for 28,024 Sanger unigene elements in oak (18.6%).
While multiple repeat motifs were evident and represented as single copy sequences, tri-nucleotide microsatellites were the most common, and with tetra-nucleotide microsatellites, the most applicable to development as genetic loci.
Microsatellites are truly dynamic sequences, since their molecular structures change over time, driven by multiple evolutionary processes.
This showed that most microsatellites were polymorphic.
