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

Au CH, Cheung MK, Wong MC, Chu AK, Law PT, Kwan HS - BMC Res Notes (2013)

Bottom Line: Here, we developed a rapid genotyping method based on low-coverage (~0.5 to 1.5-fold) whole-genome resequencing.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.Two hundred sequence-based markers were placed on the map, with an average marker spacing of 3.4 cM.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.

ABSTRACT

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.

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Related in: MedlinePlus

Genetic linkage map of L. edodes. The map was constructed using 20 SSIs. Linkage group numbers were indicated on the top, distances between markers (in cM) were shown on the left and the markers named according to the scaffolds were shown on the right. Genes discussed in the text were marked in red and placed next to the scaffold markers on which they resided.
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Figure 1: Genetic linkage map of L. edodes. The map was constructed using 20 SSIs. Linkage group numbers were indicated on the top, distances between markers (in cM) were shown on the left and the markers named according to the scaffolds were shown on the right. Genes discussed in the text were marked in red and placed next to the scaffold markers on which they resided.

Mentions: The genetic linkage map spanned a genetic distance of 637.1 cM, and was composed of 13 linkage groups >20 cM in length (Figure 1, Table 1). The average size of the linkage groups was 49.0 cM. Two hundred sequence-based markers were placed on the linkage map. There were at least five and at most 40 sequence-based markers on the linkage groups, with an average of 15.4 markers per group. The distribution of the markers on the linkage groups was uneven. There were, for instance, 16 markers on the 25.1 cM long LG11, and only five markers were located on the 36.1 cM long LG7. The average spacing between markers varied from 1.7 cM to 9.0 cM, and the mean value was 3.4 cM. The total length of scaffolds on the linkage map was 18.8 Mb, covering 46.8% of the L54 genome. The average physical distance per linkage group was 1.4 Mb and the average physical to genetic distance ratio was 30.7 kbp/cM.


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

Au CH, Cheung MK, Wong MC, Chu AK, Law PT, Kwan HS - BMC Res Notes (2013)

Genetic linkage map of L. edodes. The map was constructed using 20 SSIs. Linkage group numbers were indicated on the top, distances between markers (in cM) were shown on the left and the markers named according to the scaffolds were shown on the right. Genes discussed in the text were marked in red and placed next to the scaffold markers on which they resided.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750829&req=5

Figure 1: Genetic linkage map of L. edodes. The map was constructed using 20 SSIs. Linkage group numbers were indicated on the top, distances between markers (in cM) were shown on the left and the markers named according to the scaffolds were shown on the right. Genes discussed in the text were marked in red and placed next to the scaffold markers on which they resided.
Mentions: The genetic linkage map spanned a genetic distance of 637.1 cM, and was composed of 13 linkage groups >20 cM in length (Figure 1, Table 1). The average size of the linkage groups was 49.0 cM. Two hundred sequence-based markers were placed on the linkage map. There were at least five and at most 40 sequence-based markers on the linkage groups, with an average of 15.4 markers per group. The distribution of the markers on the linkage groups was uneven. There were, for instance, 16 markers on the 25.1 cM long LG11, and only five markers were located on the 36.1 cM long LG7. The average spacing between markers varied from 1.7 cM to 9.0 cM, and the mean value was 3.4 cM. The total length of scaffolds on the linkage map was 18.8 Mb, covering 46.8% of the L54 genome. The average physical distance per linkage group was 1.4 Mb and the average physical to genetic distance ratio was 30.7 kbp/cM.

Bottom Line: Here, we developed a rapid genotyping method based on low-coverage (~0.5 to 1.5-fold) whole-genome resequencing.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.Two hundred sequence-based markers were placed on the map, with an average marker spacing of 3.4 cM.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus