Sequence Polymorphisms at the REDUCED DORMANCY5 Pseudophosphatase Underlie Natural Variation in Arabidopsis Dormancy

Abstract

Seed dormancy controls the timing of germination, which regulates the adaptation of plants to their environment and influences agricultural production. The time of germination is under strong natural selection and shows variation within species due to local adaptation. The identification of genes underlying dormancy quantitative trait loci is a major scientific challenge, which is relevant for agricultural and ecological goals. In this study, we describe the identification of the DELAY OF GERMINATION18 (DOG18) quantitative trait locus, which was identified as a factor in natural variation for seed dormancy in Arabidopsis (Arabidopsis thaliana). DOG18 encodes a member of the clade A of the type 2C protein phosphatases family, which we previously identified as the REDUCED DORMANCY5 (RDO5) gene. DOG18/RDO5 shows a relatively high frequency of loss-offunction alleles in natural accessions restricted to northwestern Europe. The loss of dormancy in these loss-of-function alleles can be compensated for by genetic factors like DOG1 and DOG6, and by environmental factors such as low temperature. RDO5 does not have detectable phosphatase activity. Analysis of the phosphoproteome in dry and imbibed seeds revealed a general decrease in protein phosphorylation during seed imbibition that is enhanced in the rdo5 mutant. We conclude that RDO5 acts as a pseudophosphatase that inhibits dephosphorylation during seed imbibition.

A Multi‐Omics Analysis of Glycine max Leaves Reveals Alteration in Flavonoid and Isoflavonoid Metabolism Upon Ethylene and Abscisic Acid Treatment

“…Peptides were analyzed with a QExactive Plus mass spectrometer (Thermo Fisher Scientific Inc., MA, USA) with a Top15 method with exactly the same parameters as described in ref. .…”

DELAY OF GERMINATION1 requires PP2C phosphatases of the ABA signalling pathway to control seed dormancy

“…RDO5 is a member of the PP2C family of protein phosphatases that does not show phosphatase activity 13–15 . The molecular function of DOG1 has not been solved and its protein lacks domains with a known function.…”

Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis

“…Moreover, field experiments using a diallel cross between accessions from Sweden and Italy identified a major QTL associated with total fitness that spanned the DOG1 region, and also demonstrated that genetic differences in seedling establishment—and most particularly in seed dormancy—are one of the main components of local adaptation (Postma and Ågren, 2016; Postma et al, 2016; Huang et al, 2010a). Finally, extensive natural variation for seed dormancy is not unique to the DOG1 locus and many other QTLs have been mapped in various populations (Alonso-Blanco et al, 2003; Bentsink et al, 2006, 2010; Amiguet-Vercher et al, 2015; Xiang et al, 2016). The recent cloning of the DELAY OF GERMINATION18 ( DOG18 )/ IBO QTLs in two independent diallel crosses revealed the existence of numerous loss-of-function alleles—mainly caused by nonsense mutations and structural variants—at the REDUCED DORMANCY5 ( RDO5 ) locus in wild A. thaliana populations (Xiang et al, 2016; Amiguet-Vercher et al, 2015; Xiang et al, 2014).…”

“…Finally, extensive natural variation for seed dormancy is not unique to the DOG1 locus and many other QTLs have been mapped in various populations (Alonso-Blanco et al, 2003; Bentsink et al, 2006, 2010; Amiguet-Vercher et al, 2015; Xiang et al, 2016). The recent cloning of the DELAY OF GERMINATION18 ( DOG18 )/ IBO QTLs in two independent diallel crosses revealed the existence of numerous loss-of-function alleles—mainly caused by nonsense mutations and structural variants—at the REDUCED DORMANCY5 ( RDO5 ) locus in wild A. thaliana populations (Xiang et al, 2016; Amiguet-Vercher et al, 2015; Xiang et al, 2014). …”