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Rapid Genotyping by Low-Coverage Resequencing to Construct Genetic Linkage Maps of Fungi: A Case Study in Lentinula edodes

Summary

This research developed a new method to create detailed genetic maps of fungi using modern DNA sequencing technology, focusing on the shiitake mushroom as a test case. The technique allows scientists to better understand how different genetic traits are inherited in fungi. Impacts on everyday life: • Improved breeding of commercial mushroom strains for better quality and yield • More efficient production of edible and medicinal mushrooms • Better understanding of how to optimize mushroom growing conditions • Potential development of new mushroom varieties with enhanced nutritional or medicinal properties • More sustainable and cost-effective mushroom farming methods

Background

Genetic linkage maps are important tools in breeding programmes and quantitative trait analyses. Traditional molecular markers used for genotyping are limited in throughput and efficiency. While next-generation sequencing technologies have facilitated progeny genotyping and genetic linkage map construction in major grains, the applicability of this approach remains untested in fungal systems.

Objective

To develop a rapid genotyping method based on low-coverage whole-genome resequencing and use it to construct the first high-density sequence-based genetic linkage map of Lentinula edodes (shiitake mushroom).

Results

The linkage map spanned a total genetic distance of 637.1 cM and contained 13 linkage groups. Two hundred sequence-based markers were placed on the map, with an average marker spacing of 3.4 cM. The accuracy of the map was confirmed by comparing the locations of known genes such as matA and matB with previous maps. The overall accuracy of the proposed genotyping approach was over 98%.

Conclusion

The study demonstrated that low-coverage resequencing could enable rapid genotyping of basidiospore-derived progenies, which could facilitate the construction of high-density genetic linkage maps of basidiomycetous fungi for quantitative trait analyses and improvement of genome assembly.
  • Published in:BMC Research Notes,
  • Study Type:Genomic Analysis,
  • Source: 10.1186/1756-0500-6-307
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