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Volume 9, Issue 3

Heritability and gene functions associated with sclerotia formation of AG-7 using whole genome sequencing and genome-wide association study Open Access

Abstract

Sclerotia are specialized fungal structures formed by pigmented and aggregated hyphae, which can survive under unfavourable environmental conditions and serve as the primary inocula for several phytopathogenic fungi including . Among 154 . anastomosis group 7 (AG-7) isolates collected in fields, the sclerotia-forming capability regarding sclerotia number and sclerotia size varied in the fungal population, but the genetic makeup of these phenotypes remained unclear. As limited studies have focused on the genomics of AG-7 and the population genetics of sclerotia formation, this study completed the whole genome sequencing and gene prediction of AG-7 using the Oxford NanoPore and Illumina RNA sequencing. Meanwhile, a high-throughput image-based method was established to quantify the sclerotia-forming capability, and the phenotypic correlation between sclerotia number and sclerotia size was low. A genome-wide association study identified three and five significant SNPs associated with sclerotia number and size in distinct genomic regions, respectively. Of these significant SNPs, two and four showed significant differences in the phenotypic mean separation for sclerotia number and sclerotia size, respectively. Gene ontology enrichment analysis focusing on the linkage disequilibrium blocks of significant SNPs identified more categories related to oxidative stress for sclerotia number, and more categories related to cell development, signalling and metabolism for sclerotia size. These results indicated that different genetic mechanisms may underlie these two phenotypes. Moreover, the heritability of sclerotia number and sclerotia size were estimated for the first time to be 0.92 and 0.31, respectively. This study provides new insights into the heritability and gene functions related to the development of sclerotia number and sclerotia size, which could provide additional knowledge to reduce fungal residues in fields and achieve sustainable disease management.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome-wide association study (GWAS) , genotyping-by-sequencing (GBS) , population structure , Rhizoctonia solani AG-7 , sclerotia , single nucleotide polymorphisms (SNPs) and whole genome sequencing (WGS)
Funding
This study was supported by the:
  • Council of Agriculture (Award 111AS-1.3.2-ST-aQ)
    • Principle Award Recipient: Hao-XunChang
  • Ministry of Science and Technology (Award MOST-110-2313-B-002-032-MY3)
    • Principle Award Recipient: Hao-XunChang
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000948
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Heritability and gene functions associated with sclerotia formation of Rhizoctonia solani AG-7 using whole genome sequencing and genome-wide association study
M Gen 9, 000948 (2023); https://doi.org/10.1099/mgen.0.000948
/content/journal/mgen/10.1099/mgen.0.000948
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