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Evaluation of molecular diversity of rice varieties in Central West Asia using microsatellite markers



Rice is one of the most important products in the world food chain, so that supplies the main food for more than half of the world's population, and especially the poorest people in the world. Rice is one of the most important crops, and more than 90 percent of it is produced and consumed in Asia. In each country, depending on the consumer's taste, the type of varieties that are cultivated are different. Hybridization method is very commonly used in crop breeding in order to obtain segregate populations portraying interesting agronomical traits and broad genetic variability. This method combines available genes from two or more different genitors in a unique individual. The choice of genitors is very important in this process because it assures the obtaining of promising segregate populations. This procedure is based on genetic dissimilarity of the subject under study. In plants, genetic diversity may be inferred through quantitative (phenotypic or genotypic traits) and predictive characteristics. Molecular markers are powerful tools for analyzing genome diversity within a species, and to evaluate genetic relationships between individuals and populations. They have been used for mapping of genomic regions containing genes of agricultural interest. In recent years, genetic divergence studies in different crops have often used microsatellite as the main tool for genetic diversity analysis. Microsatellites or SSRs are one of the most indicated techniques to study polymorphism between DNA sequences. These molecular markers are based on PCR reaction that detects loci variations of repetitive sequences. They present high levels of polymorphism, codominant inheritance, multi-alleles, mendelian pattern and good genome coverage. Microsatellites require low amount of DNA, can be easily automated for high throughput screening, may be exchanged between laboratories, and are highly transferable between populations.


Challenges and necessity

One of plant breeding approaches for increasing yield and quality is the use of natural genetic variation. The use of newly imported lines and targeted crosses with each other and regional cultivars can help to increase the diversity of germplasm. To understand genetic variation in populations, genetic diversity is often evaluated at the genome level. Since there has been no study on the molecular diversity of rice cultivars in Central and West Asian countries, the need to study on it is felt, the purpose of this research is to determine the diversity of varieties using SSR markers.



  1. Evaluating molecular diversity and classification of rice cultivars in central and west Asian countries.
  2. Measurement of morphological traits and determinants of baking quality in rice cultivars of central and west Asian countries. Comparison and classification of cultivars based on available variation.
  3. Provide the ground for achieving targeted crossing in case of sufficient diversity.


Materials and methods

Genotypes will be collected from Azerbaijan, Kazakhstan, Afghanistan, Turkey, Kyrgyzstan, Iraq and Tajikistan, and will be cultivated at Rice Research Institute of Iran. Then, their molecular diversity will be evaluated by 21 microsatellite markers after DNA extraction from leaf samples by CTAB method. In this study, characteristics including plant height, number of tillers, day to maturity, panicle length, number of filled grain per panicle, yield, 100 seed weight, grain length, grain width, grain shape, amylose content gel consistency and gelatinization temperature will be evaluated.


Final report

In this study, 60 microsatellite markers were used in 63 rice genotypes of Central and West Asia to group rice cultivars. Based on data from 60 markers, it was observed that a total of 252 polymorphic alleles were amplified with an average of 4.2 alleles per primer. The lowest number of alleles belonged to the RM490 marker with 2 alleles and the highest number was belonged to the RM424 and RM246 markers with 7 alleles, respectively. The mean number of effective alleles was 3.78 which RM490 and RM5423 markers had the lowest and the RM225 and RM246 markers had the highest value for this index. Gene diversity and amount of polymorphic information content showed that RM23 and RM212 markers had the highest value and RM3 marker had the lowest value for these two indices. Classification of genotypes was performed by cluster analysis using PAST software. Genotypes were classified into 5 clusters using Dice similarity coefficient and UPGMA method. Based on the results of cluster analysis and genetic distances, genotypes of Iran, Afghanistan and Azerbaijan can be used for hybrid production in order to increase grain yield and quality.