Substantial enhancement of high polymorphic SSR marker development using in silico method from 18 available rice blast fungus genome sequences and its application in genetic diversity assessment

Rice blast fungus, Magnaporthe oryzae, causes rice blast disease leading to the reduction of rice yield. Utilization of rice blast resistant cultivar is one of efficient ways to cope with this disease. The genetic diversity of rice blast is of great importance as it indicates the genotype of rice blast isolates in a population of epidemic area and reveals the dynamics of genotype change over time. Simple sequence repeat (SSR) marker is frequently used for indicating the genetic diversity of several organisms including rice blast fungus. The in silico SSR development method provides the enhancement of polymorphic rate and requires less time and labour. This study aimed to develop in silico SSR marker and study genetic diversity of rice blast isolates collected from Thailand. The 11,072 SSR loci were examined in rice blast reference genome 70–15. The most abundant SSR type and pattern were mono-nucleotide repeat and AGC/CTG motif respectively. Fourteen highly polymorphic SSR loci, identified by in silico from 18 rice blast genome sequences, were selected and specific primer were developed. Ten SSR loci were novel and detected the polymorphism in Thai rice blast isolates, which showed 2–7 alleles per locus and PIC values ranged from 0.07 to 0.56. The genetic relationship analysis showed that rice blast isolates were clustered by collection time and site. Our result indicated that in silico SSR development is a powerful technique to enhance the production of highly polymorphic SSR markers and these newly developed SSR markers were useful for genetic diversity assessment.

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