Genomic analysis of QTLs and genes altering natural variation in stochastic noise.
Quantitative genetic analysis has long been used to study how natural variation of genotype can influence an organism's phenotype. While most studies have focused on genetic determinants of phenotypic average, it is rapidly becoming understood that stochastic noise is genetically determined. Ho...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2011-09-01
|
| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3183082?pdf=render |
| _version_ | 1811225937345249280 |
|---|---|
| author | Jose M Jimenez-Gomez Jason A Corwin Bindu Joseph Julin N Maloof Daniel J Kliebenstein |
| author_facet | Jose M Jimenez-Gomez Jason A Corwin Bindu Joseph Julin N Maloof Daniel J Kliebenstein |
| author_sort | Jose M Jimenez-Gomez |
| collection | DOAJ |
| description | Quantitative genetic analysis has long been used to study how natural variation of genotype can influence an organism's phenotype. While most studies have focused on genetic determinants of phenotypic average, it is rapidly becoming understood that stochastic noise is genetically determined. However, it is not known how many traits display genetic control of stochastic noise nor how broadly these stochastic loci are distributed within the genome. Understanding these questions is critical to our understanding of quantitative traits and how they relate to the underlying causal loci, especially since stochastic noise may be directly influenced by underlying changes in the wiring of regulatory networks. We identified QTLs controlling natural variation in stochastic noise of glucosinolates, plant defense metabolites, as well as QTLs for stochastic noise of related transcripts. These loci included stochastic noise QTLs unique for either transcript or metabolite variation. Validation of these loci showed that genetic polymorphism within the regulatory network alters stochastic noise independent of effects on corresponding average levels. We examined this phenomenon more globally, using transcriptomic datasets, and found that the Arabidopsis transcriptome exhibits significant, heritable differences in stochastic noise. Further analysis allowed us to identify QTLs that control genomic stochastic noise. Some genomic QTL were in common with those altering average transcript abundance, while others were unique to stochastic noise. Using a single isogenic population, we confirmed that natural variation at ELF3 alters stochastic noise in the circadian clock and metabolism. Since polymorphisms controlling stochastic noise in genomic phenotypes exist within wild germplasm for naturally selected phenotypes, this suggests that analysis of Arabidopsis evolution should account for genetic control of stochastic variance and average phenotypes. It remains to be determined if natural genetic variation controlling stochasticity is equally distributed across the genomes of other multi-cellular eukaryotes. |
| first_indexed | 2024-04-12T09:16:33Z |
| format | Article |
| id | doaj.art-df00e07015c04e9690ef384894411d8f |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-12T09:16:33Z |
| publishDate | 2011-09-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-df00e07015c04e9690ef384894411d8f2022-12-22T03:38:50ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042011-09-0179e100229510.1371/journal.pgen.1002295Genomic analysis of QTLs and genes altering natural variation in stochastic noise.Jose M Jimenez-GomezJason A CorwinBindu JosephJulin N MaloofDaniel J KliebensteinQuantitative genetic analysis has long been used to study how natural variation of genotype can influence an organism's phenotype. While most studies have focused on genetic determinants of phenotypic average, it is rapidly becoming understood that stochastic noise is genetically determined. However, it is not known how many traits display genetic control of stochastic noise nor how broadly these stochastic loci are distributed within the genome. Understanding these questions is critical to our understanding of quantitative traits and how they relate to the underlying causal loci, especially since stochastic noise may be directly influenced by underlying changes in the wiring of regulatory networks. We identified QTLs controlling natural variation in stochastic noise of glucosinolates, plant defense metabolites, as well as QTLs for stochastic noise of related transcripts. These loci included stochastic noise QTLs unique for either transcript or metabolite variation. Validation of these loci showed that genetic polymorphism within the regulatory network alters stochastic noise independent of effects on corresponding average levels. We examined this phenomenon more globally, using transcriptomic datasets, and found that the Arabidopsis transcriptome exhibits significant, heritable differences in stochastic noise. Further analysis allowed us to identify QTLs that control genomic stochastic noise. Some genomic QTL were in common with those altering average transcript abundance, while others were unique to stochastic noise. Using a single isogenic population, we confirmed that natural variation at ELF3 alters stochastic noise in the circadian clock and metabolism. Since polymorphisms controlling stochastic noise in genomic phenotypes exist within wild germplasm for naturally selected phenotypes, this suggests that analysis of Arabidopsis evolution should account for genetic control of stochastic variance and average phenotypes. It remains to be determined if natural genetic variation controlling stochasticity is equally distributed across the genomes of other multi-cellular eukaryotes.http://europepmc.org/articles/PMC3183082?pdf=render |
| spellingShingle | Jose M Jimenez-Gomez Jason A Corwin Bindu Joseph Julin N Maloof Daniel J Kliebenstein Genomic analysis of QTLs and genes altering natural variation in stochastic noise. PLoS Genetics |
| title | Genomic analysis of QTLs and genes altering natural variation in stochastic noise. |
| title_full | Genomic analysis of QTLs and genes altering natural variation in stochastic noise. |
| title_fullStr | Genomic analysis of QTLs and genes altering natural variation in stochastic noise. |
| title_full_unstemmed | Genomic analysis of QTLs and genes altering natural variation in stochastic noise. |
| title_short | Genomic analysis of QTLs and genes altering natural variation in stochastic noise. |
| title_sort | genomic analysis of qtls and genes altering natural variation in stochastic noise |
| url | http://europepmc.org/articles/PMC3183082?pdf=render |
| work_keys_str_mv | AT josemjimenezgomez genomicanalysisofqtlsandgenesalteringnaturalvariationinstochasticnoise AT jasonacorwin genomicanalysisofqtlsandgenesalteringnaturalvariationinstochasticnoise AT bindujoseph genomicanalysisofqtlsandgenesalteringnaturalvariationinstochasticnoise AT julinnmaloof genomicanalysisofqtlsandgenesalteringnaturalvariationinstochasticnoise AT danieljkliebenstein genomicanalysisofqtlsandgenesalteringnaturalvariationinstochasticnoise |