Unravelling genetic diversity and population structure of Sarocladium oryzae causing sheath rot disease in rice using hyper-variable SSR markers

Abstract

Rice sheath rot, caused by the fungus Sarocladium oryzae, poses a major threat to rice crops. This pathogen exhibits substantial variability in the field, yet limited information on its genetic diversity and population structure hampers the development of effective disease management strategies. In this study, hyper-variable Simple Sequence Repeats (HV-SSR) markers were employed for the first time to assess the genetic diversity of Sarocladium oryzae, collected from various rice cultivating regions in Odisha, Eastern India. The isolates were identified using both morphological and molecular criteria. A pathogenicity test was performed for all the isolates. A total of 2558 HV-SSRs with more than 10 repeat units were identified in the genome of S. oryzae. The most prevalent types of repeats were dinucleotides (26.8%), followed by trinucleotides (22.8%), tetranucleotides (8.67%), pentanucleotides (2.83%), and hexanucleotides (1.83%). A total of 150 HV-SSR primers were designed and 24 were randomly selected and validated, of which ten of them demonstrating polymorphism in the 87 isolates. These ten polymorphic hyper-variable SSR markers were subsequently used to assess the genetic diversity and population structure of Sarocladium oryzae isolates. The markers revealed a total of 32 alleles, with the number of alleles per locus varying from 2 to 4. Gene diversity ranged from 0.409 to 0.641, while the major allele frequency varied from 0.448 to 0.736. The Polymorphic Information Content (PIC) values ranged from 0.325 to 0.569, with an average of 0.457. Cluster analysis categorized the sheath rot isolates into three distinct major clusters. Principal coordinate analysis and structure analysis identified two genetic clusters within S. oryzae isolates. Analysis of molecular variance indicated that there was more genetic variation within populations (55%) and less variation among populations (45%). The findings of this study provide insights into the genetic diversity of S. oryzae in the rice-cultivating regions of Odisha, which can be used to develop more effective disease management strategies.