Source 1primary paper2004Genetics
Toolkit/linkage disequilibrium mapping
linkage disequilibrium mapping
Also known as: LD mapping
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Linkage disequilibrium mapping is a computational genetic association method used here in Arabidopsis thaliana to connect natural CRY2 sequence variation with flowering-time phenotypes. In the cited study, it identified strong haplotype-phenotype associations under short-day photoperiod and implicated a candidate serine substitution linked to early flowering.
Usefulness & Problems
Why this is useful
This method is useful for extracting genotype-phenotype associations from natural variation without requiring a biparental mapping population. In this example, it leveraged strong linkage disequilibrium across CRY2 to distinguish haplogroups and associate them with early flowering in Arabidopsis ecotypes.
Problem solved
It addresses the problem of localizing naturally occurring allelic effects underlying phenotypic variation in flowering time. Specifically, it was applied to determine whether CRY2 haplotypes and linked polymorphisms are associated with early flowering under short-day conditions.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
genomic localization by disequilibrium structurehaplotype-phenotype associationlinkage disequilibrium-based association mappingTechniques
Computational DesignTarget processes
No target processes tagged yet.
Implementation Constraints
The reported application used natural variation in Arabidopsis thaliana CRY2 sequences and phenotypic measurements of flowering time under short-day photoperiod. The evidence indicates analysis of an unstratified population of 95 ecotypes and interpretation of haplogroup structure and linkage disequilibrium across the gene, but it does not provide further computational workflow details in the supplied text.
The evidence provided comes from a single Arabidopsis CRY2 case study and does not establish general performance across traits, loci, or species. The serine substitution was inferred to be directly responsible, but the supplied evidence does not describe direct functional validation or replication in independent cohorts.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
CRY2 DNA sequences show strong linkage disequilibrium and two highly differentiated haplogroups, A and B, across the gene.
CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene
CRY2 DNA sequences show strong linkage disequilibrium and two highly differentiated haplogroups, A and B, across the gene.
CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene
CRY2 DNA sequences show strong linkage disequilibrium and two highly differentiated haplogroups, A and B, across the gene.
CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene
CRY2 DNA sequences show strong linkage disequilibrium and two highly differentiated haplogroups, A and B, across the gene.
CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene
CRY2 DNA sequences show strong linkage disequilibrium and two highly differentiated haplogroups, A and B, across the gene.
CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene
CRY2 DNA sequences show strong linkage disequilibrium and two highly differentiated haplogroups, A and B, across the gene.
CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene
CRY2 DNA sequences show strong linkage disequilibrium and two highly differentiated haplogroups, A and B, across the gene.
CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene
Under short-day photoperiod, the AS and B CRY2 haplogroups are highly significantly associated with early flowering in an unstratified population of 95 Arabidopsis ecotypes.
Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering
population size 95
Under short-day photoperiod, the AS and B CRY2 haplogroups are highly significantly associated with early flowering in an unstratified population of 95 Arabidopsis ecotypes.
Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering
population size 95
Under short-day photoperiod, the AS and B CRY2 haplogroups are highly significantly associated with early flowering in an unstratified population of 95 Arabidopsis ecotypes.
Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering
population size 95
Under short-day photoperiod, the AS and B CRY2 haplogroups are highly significantly associated with early flowering in an unstratified population of 95 Arabidopsis ecotypes.
Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering
population size 95
Under short-day photoperiod, the AS and B CRY2 haplogroups are highly significantly associated with early flowering in an unstratified population of 95 Arabidopsis ecotypes.
Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering
population size 95
Under short-day photoperiod, the AS and B CRY2 haplogroups are highly significantly associated with early flowering in an unstratified population of 95 Arabidopsis ecotypes.
Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering
population size 95
Under short-day photoperiod, the AS and B CRY2 haplogroups are highly significantly associated with early flowering in an unstratified population of 95 Arabidopsis ecotypes.
Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering
population size 95
The serine substitution in CRY2 is strongly suggested to be directly responsible for the AS early flowering phenotype.
the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype
The serine substitution in CRY2 is strongly suggested to be directly responsible for the AS early flowering phenotype.
the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype
The serine substitution in CRY2 is strongly suggested to be directly responsible for the AS early flowering phenotype.
the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype
The serine substitution in CRY2 is strongly suggested to be directly responsible for the AS early flowering phenotype.
the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype
The serine substitution in CRY2 is strongly suggested to be directly responsible for the AS early flowering phenotype.
the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype
The serine substitution in CRY2 is strongly suggested to be directly responsible for the AS early flowering phenotype.
the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype
The serine substitution in CRY2 is strongly suggested to be directly responsible for the AS early flowering phenotype.
the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype
The CRY2-associated haplogroups are limited to an approximately 65-kb genomic region around CRY2.
Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2
genomic region size 65 kb
The CRY2-associated haplogroups are limited to an approximately 65-kb genomic region around CRY2.
Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2
genomic region size 65 kb
The CRY2-associated haplogroups are limited to an approximately 65-kb genomic region around CRY2.
Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2
genomic region size 65 kb
The CRY2-associated haplogroups are limited to an approximately 65-kb genomic region around CRY2.
Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2
genomic region size 65 kb
The CRY2-associated haplogroups are limited to an approximately 65-kb genomic region around CRY2.
Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2
genomic region size 65 kb
The CRY2-associated haplogroups are limited to an approximately 65-kb genomic region around CRY2.
Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2
genomic region size 65 kb
The CRY2-associated haplogroups are limited to an approximately 65-kb genomic region around CRY2.
Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2
genomic region size 65 kb
Linkage disequilibrium mapping is useful for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis
Linkage disequilibrium mapping is useful for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis
Linkage disequilibrium mapping is useful for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis
Linkage disequilibrium mapping is useful for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis
Linkage disequilibrium mapping is useful for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis
Linkage disequilibrium mapping is useful for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis
Linkage disequilibrium mapping is useful for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis
Approval Evidence
1 source1 linked approval claimfirst-pass slug linkage-disequilibrium-mapping
Here we apply LD mapping
Source:
method utilitysupports
Linkage disequilibrium mapping is useful for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis
Source:
Comparisons
Source-backed strengths
The study reported strong linkage disequilibrium across CRY2 and two highly differentiated haplogroups, A and B, providing a structured basis for association analysis. In an unstratified panel of 95 Arabidopsis ecotypes, the AS and B CRY2 haplogroups were highly significantly associated with early flowering under short-day photoperiod, and a serine substitution was strongly suggested as the causal variant for the AS phenotype.
Ranked Citations
- 1.