DNA marker-based assay

DNA marker-based assay for rapid and reliable estimation of genetic purity of seeds of Rice Hybrids and Parental lines 

Technology Profile 

Seed quality control in terms of maintenance of genetic purity is a vital component of any hybrid crop seed industry. Traditionally, seed purity is ascertained through a morphological assay called ‘Grow-out Test (GOT)’, which has several limitations 

ICAR-IIRR, Hyderabad has developed a DNA marker-based assay for rapid and reliable estimation of purity of seeds of rice hybrids and parental lines. 

Hybrid seed purity is assessed on single seed/seedling basis using a parental polymorphic SSR marker, which is specific for a particular rice hybrid or using a functional marker, named RMS-PPR9-2, which targets the candidate gene for Rf4, the major fertility restoring gene. 

For assessing genetic purity of seeds of WA-CMS lines (i.e. the female parent used for hybrid seed production), a functional marker, named RMS-5-WA352, which is specific for the candidate gene associated with cytoplasmic male sterility is deployed to accurately discriminate WA-CMS lines from the maintainer lines. 


Most of the private hybrid rice seed industry is based in and around Hyderabad and seed production is generally done during Rabi season. Even a 1% contamination in seeds of rice hybrids can reduce the crop yields by 100 kg/ha. Similarly, 1% impurity in seeds of WA-CMS line can result in significantly higher level of impurities in hybrid seed production (i.e. > 5%).  Due to this, seed genetic purity and seed quality control are vital for success of hybrid rice seed industry. 

As GOT takes one full growing season and the private companies cannot wait for the results of GOT, a rapid and reliable assay for assessing seed purity is imperative. In this context, the DNA marker based assay developed by ICAR-IIRR can help the hybrid seed industry to accurately identify impure seed- lots quickly. 

The DNA marker based assay for hybrids and WA-CMS lines can be deployed immediately after the harvest of the seeds in Rabi season and the analysis is based on single seed/seedling. Results can be made available within a fortnight of submission and decision for marketing the pure seeds can be taken before the commencement of the Kharif season.

Empirical Evidences 

Blind tests and commercial analysis of seed-lots 

Through Blind tests carried out in collaboration with Hybrid rice section and also with samples provide by private seed companies, the assay was able to accurately identify contaminants in seed-lots of rice hybrids and WA-CMS lines. 

From 2007, ICAR-IIRR is providing the DNA-marker based assay for assessment of impurities in seed- lots of rice hybrids and parental lines on a commercial scale to several public and private sector seed companies. So far, we have successfully completed analysis for more than 1200 seed-lots and the results were deemed to be accurate by the clients. We are also working on using some of the high-throughput tools for analysis of bulked samples, thus saving cost and time.

Practical Utility/ Scalability 

The assay is presently offered on a single seed/seedling basis and results can be made available within 10-15 days of submission of samples. We are presently working towards utilizing some of the high throughput tools for estimation of purity on bulked sample basis. Once the assay is standardized, results can be provided within 3-4 days of submission of samples.