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<p><i>Bipolaris sorokiniana</i> (BS), causing spot blotch (SB) disease in wheat, represents a major constraint to global wheat production. Despite its agronomic significance, genome-wide investigations of microsatellites (SSRs) in BS remain scarce, particularly in relation to genetic diversity and diagnostic applications. This study presents the first genome wide comparative analysis of microsatellites in nine publicly available whole-genome sequence of BS (BS112, BRIP10943a, BRIP27492a, WAI2411, WAI2406, ND90Pr, ND93-1, Sacc. Shoemaker, and Yt-6<i>)</i> for diversity analysis and spot blotch disease diagnosis in wheat. Among these, the WAI2406 genome exhibited the highest SSR abundance (5617) followed by WAI2411 (5290), and BRIP27492a (3878). No significant correlation was observed between SSR distribution and genome size or GC content. Of the 50 SSR markers evaluated, 13 polymorphic markers generated 39 alleles and successfully grouped 30 <i>B. sorokiniana</i> isolates into two distinct clusters, as further supported by population structure analysis. Interestingly, one SSR locus, BS1011, was identified as monomorphic and specific to <i>B. sorokiniana</i>. A primer pair viz. BS1011F/BS1011R, designed for this locus consistently amplified a 150&#xa0;bp fragment across all tested fungal isolates. This locus was subsequently employed to develop a highly sensitive qPCR assay capable of detecting as little as 0.001 ng µl⁻¹ of <i>B. sorokiniana</i> DNA in wheat samples. The assay was validated across nine wheat genotypes and four distinct growth stages, and was also able to quantify fungal biomass in naturally infected wheat samples, demonstrating its robustness for early detection. Overall, the present study offers new information pertaining to the microsatellite landscape of <i>B. sorokiniana</i> and introduces a reliable molecular diagnostic assay, offering valuable tools for the early detection and effective control of SB disease in wheat.</p>

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Genome wide comparative analysis of microsatellites in Bipolaris sorokiniana for diversity analysis and spot blotch disease diagnosis in wheat

  • 期刊论文

  • 发表日期：

    2026年4月18日

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  • Prem Lal Kashyap,
  • Sudheer Kumar,
  • Annie Khanna,
  • Anju Sharma,
  • Sunita Mahapatra,
  • Pradeep Sharma,
  • Ratan Tiwari

摘要

Bipolaris sorokiniana (BS), causing spot blotch (SB) disease in wheat, represents a major constraint to global wheat production. Despite its agronomic significance, genome-wide investigations of microsatellites (SSRs) in BS remain scarce, particularly in relation to genetic diversity and diagnostic applications. This study presents the first genome wide comparative analysis of microsatellites in nine publicly available whole-genome sequence of BS (BS112, BRIP10943a, BRIP27492a, WAI2411, WAI2406, ND90Pr, ND93-1, Sacc. Shoemaker, and Yt-6) for diversity analysis and spot blotch disease diagnosis in wheat. Among these, the WAI2406 genome exhibited the highest SSR abundance (5617) followed by WAI2411 (5290), and BRIP27492a (3878). No significant correlation was observed between SSR distribution and genome size or GC content. Of the 50 SSR markers evaluated, 13 polymorphic markers generated 39 alleles and successfully grouped 30 B. sorokiniana isolates into two distinct clusters, as further supported by population structure analysis. Interestingly, one SSR locus, BS1011, was identified as monomorphic and specific to B. sorokiniana. A primer pair viz. BS1011F/BS1011R, designed for this locus consistently amplified a 150 bp fragment across all tested fungal isolates. This locus was subsequently employed to develop a highly sensitive qPCR assay capable of detecting as little as 0.001 ng µl⁻¹ of B. sorokiniana DNA in wheat samples. The assay was validated across nine wheat genotypes and four distinct growth stages, and was also able to quantify fungal biomass in naturally infected wheat samples, demonstrating its robustness for early detection. Overall, the present study offers new information pertaining to the microsatellite landscape of B. sorokiniana and introduces a reliable molecular diagnostic assay, offering valuable tools for the early detection and effective control of SB disease in wheat.