Eva Madrid, Edouard Severing, Elisa de Ansorena, Christiane Kiefer, Luise Brand, Rafael Martinez-Gallegos, Stefan Woetzel, Ulla Kemi, Wen-Biao Jiao, Korbinian Schneeberger, and George Coupland

PNAS September 28, 2021 118 (39) e2109204118

Significance

Annual and perennial species differ in their timing and intensity of flowering, but the underlying mechanisms are poorly understood. We hybridized closely related annual and perennial plants and used genetics, transgenesis, and genomics to characterize differences in the activity and function of their flowering-time genes. We identify a gene encoding a transcription factor that moved between chromosomes and is retained in the annual but absent from the perennial. This gene strongly delays flowering, and we propose that it has been retained in the annual to compensate for reduced activity of closely related genes. This study highlights the value of using direct hybridization between closely related plant species to characterize functional differences in fast-evolving reproductive traits.

Abstract

The timing of reproduction is an adaptive trait in many organisms. In plants, the timing, duration, and intensity of flowering differ between annual and perennial species. To identify interspecies variation in these traits, we studied introgression lines derived from hybridization of annual and perennial species, Arabis montbretiana and Arabis alpina, respectively. Recombination mapping identified two tandem A. montbretiana genes encoding MADS-domain transcription factors that confer extreme late flowering on A. alpina. These genes are related to the MADS AFFECTING FLOWERING (MAF) cluster of floral repressors of other Brassicaceae species and were named A. montbretiana (Am) MAF-RELATED (MAR) genes. AmMAR1 but not AmMAR2 prevented floral induction at the shoot apex of A. alpina, strongly enhancing the effect of the MAF cluster, and MAR1 is absent from the genomes of all A. alpina accessions analyzed. Exposure of plants to cold (vernalization) represses AmMAR1 transcription and overcomes its inhibition of flowering. Assembly of the tandem arrays of MAR and MAF genes of six A. alpina accessions and three related species using PacBio long-sequence reads demonstrated that the MARs arose within the Arabis genus by interchromosomal transposition of a MAF1-like gene followed by tandem duplication. Time-resolved comparative RNA-sequencing (RNA-seq) suggested that AmMAR1 may be retained in A. montbretiana to enhance the effect of the AmMAF cluster and extend the duration of vernalization required for flowering. Our results demonstrate that MAF genes transposed independently in different Brassicaceae lineages and suggest that they were retained to modulate adaptive flowering responses that differ even among closely related species.

See: https://www.pnas.org/content/118/39/e2109204118

Fig. 1. Phenotypic characterization of late-flowering plants identified from introgressing A. montbretiana genomic segments into A. alpina pep1. (A) Plants grown for 10 wk after germination. Days to flowering (DTF) after gemination are indicated on the Bottom. IL31 was later flowering than A. montbretiana (Am) and A. alpina pep-1-1. (B) Schematic representation of the genotypes of the IL used for association analysis. Different lines segregating for different fragments of chromosome 2 were chosen. Only chromosomes with introgressions from A. montbretiana are represented. (C) DTF for the ILs represented in B. n = 10 in parental lines, 70 in ILs. Only IL41 segregated for the flowering-time phenotype. The total phenotypic variation and P value are indicated for IL41. Individual plants are represented and color coded by the genotype of the most-associated molecular marker. (D) Physical map of the candidate region, showing markers (faint font) and flowering-time genes (bold font), as well as their physical positions on A. montbretiana chromosome 2 in megabases. The genotype of informative recombinants on chromosome 2 and the flowering time of each line is indicated on the Right. The candidate region that confers late flowering is located between markers E252 and E255, comprising ∼196 kb. (E) DTF of transgenic plants containing the genomic locus of each candidate gene in pep1-1. Only plants containing AmMAR1 showed a late-flowering phenotype. n = 10 to 12 plants. NF, non flowering plants at the end of the experiment. Flowering phenotype is measured in days from germination to the first open flower. Letters indicate statistically significant differences determined by multiple pairwise comparisons using Tukey’s least significant difference (LSD) test (P ≤ 0.05). In all panels, alleles from the recurrent parent (A. alpina pep1-1) are colored green, alleles from the donor (A. montbretiana) are in blue, and heterozygous regions are marked in red.