1. Synteny - many distantly related species have co- linear maps for portions of their genomes; co-linearity between maize and sorghum, between maize and rice. - Once careful interspecific comparisons have been made, predictions for gene locations mapped in one species can be made in the second - regions that are sparsely mapped in one species might be filled by markers from the molecular map of the second species.

2. RAPD(randomly amplified pholymorphic DNA) 1) single short oligonucleotides primer (10mer-12mer) can recognize similar sequences(complementary sequences) that are opposed to each other at distances close enough for the intervening sequence to be amplified in the PCR 2) because of the availability of random oligonucleotides and easy assay, RAPD is simple matter to screen many loci rather rapidly. 3) limit of RAPD; priming polymorphism appears to be based on mismatches with target sequences so that alleles are either present or absent; no guarantee that the dominant allele will be present in a second population, not always possible to mapin a new population

4. Microsatellite(SSR;simple sequence repeat) - assay is PCR based; electrophoresis is sufficient to observe the results; reduce the time to obtain a result compared with methods based on Southern blotting - the use of radioisotopes can be avoided because the size of polymorphism between alleles is large enough to be seen in agarose gel or PAGE gel. - co-dominant marker, prevalent in soybean, a species with limited polymorphic markers in the past - method is well-established in phage library by screen with oligonucleotide probes - quicker approach is to examine sequence databank for their presence. - AC repeats, most frequent class in human and mouse, AT repeats, most prevalent in higher plants.

5. restriction fragment length polymorphism (RFLP) The occurrence of variation in the length of DNA fragments that are produced after cleavage with a type II restriction endonuclease. The differences in DNA lengths are due to the presence or absence of recognition site(s) for that particular restriction enzyme. RFLPs were initially detected using hybridization with DNA probes after separation of digested genomic DNA by gel electrophoresis (Southern analysis). Now they are typically detected by electrophoresis of digested PCR product.

7. A single-nucleotide polymorphism A single-nucleotide polymorphism (SNP, pronounced snip) is a DNA sequence variation occurring when a single nucleotide — A, T, C, or G — in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual) which was discovered by Dr. Steve Ligget. For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case we say that there are two alleles : C and T. Almost all common SNPs have only two alleles.DNA sequencenucleotide ATCGgenome alleles Within a population, SNPs can be assigned a minor allele frequency — the lowest allele frequency at a locus that is observed in a particular population. This is simply the lesser of the two allele frequencies for single-nucleotide polymorphisms. There are variations between human populations, so a SNP allele that is common in one geographical or ethnic group may be much rarer in another.minor allele frequencylocus