A High-Density Single Nucleotide Polymorphism Map for <i>Neurospora crassa</i>

Lambreghts, Randy; Shi, Mi; Belden, William J.; DeCaprio, David; Park, Danny; Henn, Matthew R.; Galagan, James E.; Baştürkmen, Meray; Birren, Bruce W.; Sachs, Matthew S.; Dunlap, Jay C.; Loros, Jennifer J.

doi:10.1534/genetics.108.089292

Cited by 53 publications

(48 citation statements)

References 47 publications

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“…This indicates that 300-to 1000-fold higher light intensity was required to achieve the same period-shortening effect in csp-1 as in the csp 1 strain. This accounts for the difference in period length seen for the csp-1 vs. csp 1 strains under low light conditions (Table 1A) and is consistent with the finding that csp-1 codes for a light-inducible transcription factor (Lambreghts et al 2009). Figure 4 shows the effect of temperature on the period of the csp-1; bd; vvd P strain at several light intensities.…”

Section: Effects Of Growth Conditions On Rhythmicity Of Vvd Mutants Isupporting

confidence: 86%

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Rhythmic Conidiation in Constant Light inVividMutants ofNeurospora crassa

et al. 2009

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Section: Effects Of Growth Conditions On Rhythmicity Of Vvd Mutants Isupporting

confidence: 86%

“…The period-lengthening effect in LL therefore appears to segregate with csp-1. The csp-1 gene has been identified as a light-induced transcription factor (Lambreghts et al 2009) and this may explain why there is a difference between csp 1 and csp-1 in LL but not in DD.…”

Section: Effects Of Growth Conditions On Rhythmicity Of Vvd Mutants Imentioning

confidence: 99%

Rhythmic Conidiation in Constant Light inVividMutants ofNeurospora crassa

et al. 2009

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“…SNP-based BSA of maize mutants in a mixed B73-and Mo17-derived genetic background: The quantitative nature of the Sequenom platform provides the potential to map mutants via BSA (Michelmore et al 1991;Korol et al 2007;Lambreghts et al 2009). A series of 40 recessive mutants (Table S7 and Figure S3) generated via EMS mutagenesis (Till et al 2004) of B73 was used to demonstrate the utility of combining Sequenom-based quantitative SNP detection with BSA.…”

Section: Snp Validation and Map Constructionmentioning

confidence: 99%

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

Liu

Chen²,

Makarevitch

et al. 2010

Genetics

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Advances in next-generation sequencing technology have facilitated the discovery of single nucleotide polymorphisms (SNPs). Sequenom-based SNP-typing assays were developed for 1359 maize SNPs identified via comparative next-generation transcriptomic sequencing. Approximately 75% of these SNPs were successfully converted into genetic markers that can be scored reliably and used to generate a SNPbased genetic map by genotyping recombinant inbred lines from the intermated B73 3 Mo17 population. The quantitative nature of Sequenom-based SNP assays led to the development of a time-and costefficient strategy to genetically map mutants via quantitative bulked segregant analysis. This strategy was used to rapidly map the loci associated with several dozen recessive mutants. Because a mutant can be mapped using as few as eight multiplexed sets of SNP assays on a bulk of as few as 20 mutant F 2 individuals, this strategy is expected to be widely adopted for mapping in many species. W ITH the availability of a sequenced genome it is feasibletoundertakechromosomewalking projects to clone genes responsible for mutant phenotypes (Alleman et al. 2006;Briggs et al. 2007;Menzel et al. 2007;Song et al. 2007) and quantitative trait loci (QTL) (Glazier et al. 2002;Korstanje and Paigen 2002;Salvi et al. 2007). However, it can be logistically difficult and time-consuming to map mutants with current technologies. A high-throughput system to map phenotypic mutants would be very useful in converting the wealth of phenotypic mutants into an understanding of the molecular basis.Single nucleotide polymorphisms (SNPs) can be converted into genetic markers that are scored in mapping populations using various high-throughput SNP-typing technologies ( Maize (Zea mays L.) is an important model organism with substantial economic value. In this species, SNPs occur at a rate of one per 28-214 bp (Tenaillon et al. 2001;Barbazuk et al. 2007). Using our 454-based SNP discovery pipeline, we identified .7000 putative SNPs, .85% (94/ 110) of which could be validated via Sanger sequencing (Barbazuk et al. 2007). Here, we report the analysis of 1359 of these putative SNPs. Approximately 75% of the tested SNPs could be converted into genetic markers, and only 3% were deemed to be false positives. These SNP-based markers were used to construct a genetic map that can be used to address diverse biological questions. Finally, we apply the combination of quantitative SNP typing and bulked segregant analysis (BSA) (Michelmore et al. 1991) to efficiently map phenotypic mutants. MATERIALS AND METHODSGenetic materials: Using a high-throughput protocol (Dietrich et al. 2002) (Table S1, supporting information), the 25 non-B73 parents of the nested association mapping (NAM) population , and mutant and non-mutant pools of DNAs for BSA. For BSA, tissues from all mutant (or non-mutant) individuals from within the same F 2 family were pooled, and a single DNA isolation was performed or DNA was isolated from each individual and then equal amounts from each individ...

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“…Mutations in two conidial separation genes (csp-1 and csp-2) prevent the separation of cross walls to release free conidia (Springer 1993). Two developmental genes, fl (NCU08726) and csp-1 (NCU02713), have been identified, and the corresponding proteins are putative zinc-finger transcription factors (Bailey and Ebbole 1998;Lambreghts et al 2009). …”

mentioning

confidence: 99%

Regulation by Blue Light of the fluffy Gene Encoding a Major Regulator of Conidiation in Neurospora crassa

Olmedo¹,

Ruger-Herreros

Corrochano

2010

Genetics

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The development of asexual spores, that is, the process of conidiation, in the fungus Neurospora crassa is increased by light. The fluffy (fl) gene, encoding a major regulator of conidiation, is activated by light. We describe here a detailed characterization of the regulation by blue light of fl in vegetative hyphae. This induction requires the white collar complex (WCC) while the FLD protein acts as a dark repressor of fl transcription. We show that the WCC directly regulates fl transcription in response to blue light after transiently binding the promoter. We propose that fl is repressed by FLD in vegetative mycelia and that the repression is lost after light exposure and WCC activation. The increase in fl mRNA in vegetative mycelia after light exposure, and the corresponding increase in the amount of the regulatory FL protein, should promote the activation of the conidiation pathway. The activation by light of fl provides a simple mechanism for the activation of conidiation by blue light in Neurospora that may be at work in other fungi.

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A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa

Cited by 53 publications

References 47 publications

Rhythmic Conidiation in Constant Light inVividMutants ofNeurospora crassa

Rhythmic Conidiation in Constant Light inVividMutants ofNeurospora crassa

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

Regulation by Blue Light of the fluffy Gene Encoding a Major Regulator of Conidiation in Neurospora crassa

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