Functional Analysis of FRIGIDA Using Naturally Occurring Variation inArabidopsis thaliana

Abstract

The FRIGIDA locus (FRI, AT4G00650) has been extensively studied in Arabidopsis thaliana because of its role creating flowering time diversity. The FRI protein regulates flowering induction by binding partner proteins on its N-and C-terminus domains and creating a supercomplex that promotes transcription of the floral repressor FLC. Despite the knowledge accumulated on FRI, the function of the highly conserved central domain of the protein is still unknown. Functional characterization of naturally occurring DNA polymorphisms can provide useful information about the role of a protein and the localization of its operative domains. In the case of FRI, deleterious mutations are positively selected and widespread in nature, making them a powerful tool to study the function of the different domains of the protein. Here we explore natural sequence variation in the FRI locus in more than 1000 Arabidopsis accessions. We identify new mutations predicted to compromise the function of the protein and confirm our predictions by cloning 22 different alleles of FRI and expressing them in a common null genetic background. Our analysis allows us to pinpoint two single amino acid changes in the central domain that render the protein non-functional. We show that these two mutations determine the stability and cellular localization of the FRI protein. In summary, our work makes use of natural variants at the FRI locus to help understanding the function of the central domain of the FRI protein.

Testing for fitness epistasis in a transplant experiment identifies a candidate adaptive locus inTimemastick insects

“…With recent advances in sequencing technologies, genes associated with selected traits have been identified in many systems, with causal mutations even being identified in some systems. Examples include genes and mutations affecting coat colour in the deer mouse Peromyscus maniculatus ( Agouti ; ΔSer mutation) [8], defensive body armour and pelvic apparatus in the three-spined stickleback Gasterosteus aculeatus ( Eda and Pitx1 , respectively; recurrent deletion of the Pel -501 bp enhancer in Pitx1 ) [9,10] and flowering time in the mouse-ear cress Arabidopsis thaliana ( Frigida ; multiple mutations) [11,12]. Despite these discoveries, identifying genes and mutations underlying adaptation remains challenging in most systems.…”

TWAS coupled with eQTL analysis reveals the genetic connection between gene expression and flowering time in Arabidopsis

“…FRI -L er allele carries a 376-bp deletion combined with a 31-bp insertion in the promoter region that removes its translational start and dramatically reduces its expression (Schmalenbach et al ., 2014). Accordingly, we integrated the information about the FRI function (Zhang and Jiménez-Gómez, 2020) into our analysis (Fig. 6B).…”

“…Zhang and Jiménez-Gómez, (2020) recently defined 103 distinct FRI alleles based on nonsynonymous changes in 1,016 Arabidopsis accessions. Most accessions that do not require vernalization to induce flowering carry non-functional alleles of FRI. Two of the most common cases are the laboratory strains Col-0 and Landsberg erecta (Ler).…”

The genomic and bioclimatic characterization of Ethiopian barley (Hordeum vulgare L.) unveils challenges and opportunities to adapt to a changing climate

“…This signal is located 185 Kb upstream of the gene model HORVU.MOREX.r3.4HG0348870 , homolog to FRIGIDA . This gene has been extensively studied in Arabidopsis because of its role in flowering time variation (Noh & Amasino, 2003; Zhang & Jiménez-Gómez, 2020), having direct implications in floral transition. Latitudinal variation in flowering times in Arabidopsis is modulated by FRIGIDA (Stinchcombe et al, 2004), suggesting its key role in adaptation.…”