SSR: the most powerful marker

Emerson Hall, Cornell University
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SSR (microsatellite) is the most powerful marker because this marker is highly polymorphic, highly reproducible and codominant.

In 1997 a group of Susan McCouch at Cornell University developed 600 SSR markers in rice based on screening of genomic library. Then, 2000 SSR markers were developed based on the Monsanto's draft sequence of japonica rice published in 2002. With completion of map-based sequence of rice genome by IRGSP in 2005, at this moment there are 18,828 SSR markers publicly available.

In uncovering the function of a gene, forward genetics approaches (from phenotype to the responsible sequence) is more succesful than reverse genetics approaches (from known sequence to phenotype).

The success of forward genetics approaches relies on its openness on wherever the investigation process bring the researcher on the responsible sequence in the genome (instead of a priori approach in the case of reverse genetics). This also expresses the respect of the researcher to the complexity and dynamic interaction of the genome. In this way, the researcher is ready for any unpredictable result of her/his investigation, just like a plant breeder who crossed two different lines and got an unexpected superior progeny.

Before the xa5 gene had been cloned, nobody thought that a gene encoding general transcription factor was involved in susceptibility to certain strain of bacterial blight. Neither someone thought that a gene involved in the pollen development (Xa13) was also involved in susceptibility to certain strain of bacterial blight before this gene had been cloned.

Using this logic, I believe that in the field of genetic mapping, random approach using SSR marker is still superior than a priori approach using candidate gene-based markers.

The importance of phenotyping

In any molecular genetics study, having a reliable phenotyping is a basic requirement to get a true conclusion. Without reliable phenotype data, all expensive molecular works are useless, because all conclusion will be false.

Mapping of grain yield under pre-flowering drought stress is especially prone to mistake. Fukai et al. (1999) reported that flowering time is a major determinant of grain yield under late season drought conditions. It is very important to control the variable flowering time among the tested lines to avoid escape. Garrity and O'Toole (1994) reported that staggered planting date was effective in synchronizing the flowering of test entries during the stress treatment period. Abandoning this major factor in a genetic mapping work will bring to a false conclusion, and this fallacy will be more obvious if the identified drought QTL is in the same region with QTL for flowering time.

The same thing will be happened for genetic mapping for any other trait, including disease resistance.