Table 2

Identification of known genes with expected variation in expression among accessions

Gene identified?c
ClassaGene nameGene IDPolymorphismbHolm'sFDR
GlucosinolateESPAT1G54040ExpressionYesYes
AOP2AT4G03060ExpressionYesYes
AOP3AT4G03050ExpressionYesYes
GS-OHAT2G25450ExpressionYesYes
MAM1AT5G23010ExpressionYesYes
MAMLAT5G23020ExpressionYesYes
Flowering timeFLCAT5G10140ExpressionYesYes
FRIAT4G00650ExpressionNoYes
FLMAT1G77080ExpressionNoNo
HUA2AT5G23150NonsenseNoNo
Light responsePHYAAT1G09570MissenseNoNo
CRY2AT1G04400MissenseNoNo
DefenseRPM1AT3G07040ExpressionYesYes
RPS2AT4G26090MissenseNoNo
RPS4AT5G45250ExpressionYesYes
RPS5AT1G12220ExpressionYesYes
RPP5AT4G16860ExpressionYesYes
• Shown are genes previously reported to be naturally variable among Arabidopsis accessions in foliar tissue and that generate a known phenotype.

• a Denotes the phenotype altered by the variation.

• b Lists whether the variation is expression based or not, as described in the literature (see text for references). Polymorphisms labeled as nonsense or missense have the corresponding sequence polymorphism and are not known to alter expression in plants.

• c Indicates if the gene was identified as being naturally variable (satisfying H02) by either Holm's procedure or FDR in our analyses.