Rapid genotyping by low-coverage resequencing to construct genetic linkage maps of fungi: a case study in Lentinula edodes

BMC Research Notes

Hoi Shan Kwan¹  Patrick Tik Wan Law²  Astley Kin Kan Chu¹  Man Chun Wong¹  Man Kit Cheung¹  Chun Hang Au¹ 

[1] School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong;Core Facilities, Genome Sequencing Laboratory, The Chinese University of Hong Kong, Shatin, Hong Kong

关键词: Shiitake;    QTL;    Pyrosequencing;    NGS;    Mushroom;    Mapping;    Basidiomycota;    Assembly;   

Others  :  1142003
DOI  :  10.1186/1756-0500-6-307

 received in 2013-04-09, accepted in 2013-08-01,  发布年份 2013

【 摘 要 】

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. The advent of next-generation sequencing technologies has facilitated progeny genotyping and genetic linkage map construction in the major grains. However, the applicability of the approach remains untested in the fungal system.

Findings

Shiitake mushroom, Lentinula edodes, is a basidiomycetous fungus that represents one of the most popular cultivated edible mushrooms. Here, we developed a rapid genotyping method based on low-coverage (~0.5 to 1.5-fold) whole-genome resequencing. We used the approach to genotype 20 single-spore isolates derived from L. edodes strain L54 and constructed the first high-density sequence-based genetic linkage map of L. edodes. The accuracy of the proposed genotyping method was verified experimentally with results from mating compatibility tests and PCR-single-strand conformation polymorphism on a few known genes. 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 with previous maps the locations of known genes such as matA and matB.

Conclusions

We used the shiitake mushroom as an example to provide a proof-of-principle that low-coverage resequencing could allow rapid genotyping of basidiospore-derived progenies, which could in turn facilitate the construction of high-density genetic linkage maps of basidiomycetous fungi for quantitative trait analyses and improvement of genome assembly.

【 授权许可】

   
2013 Au et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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