Genetic and physical mapping of the earliness per se locus Eps-A (m) 1 in Triticum monococcum identifies EARLY FLOWERING 3 (ELF3) as a candidate gene

Abstract

Wheat cultivars exposed to optimal photoperiod and vernalization treatments still exhibit differences in flowering time, referred to as earliness per se (Eps). We previously identified the Eps-A (m) 1 locus from Triticum monococcum and showed that the allele from cultivated accession DV92 significantly delays heading time and increases the number of spikelets per spike relative to the allele from wild accession G3116. Here, we expanded a high-density genetic and physical map of the Eps-A (m) 1 region and identified the wheat ortholog of circadian clock regulator EARLY FLOWERING 3 (ELF3) as a candidate gene. No differences in ELF3 transcript levels were found between near-isogenic lines carrying the DV92 and G3116 Eps-A (m) 1 alleles, but the encoded ELF3 proteins differed in four amino acids. These differences were associated with altered transcription profiles of PIF-like, PPD1, and FT1, which are known downstream targets of ELF3. Tetraploid wheat lines with combined truncation mutations in the A- and B-genome copies of ELF3 flowered earlier and had less spikelets per spike than the wild-type control under short- and long-day conditions. Both effects were stronger in a photoperiod-sensitive than in a reduced photoperiod-sensitive background, indicating a significant epistatic interaction between PPD1 and ELF3 (P < 0.0001). By contrast, the introgression of the T. monococcum chromosome segment carrying the Eps-A (m) 1 allele from DV92 into durum wheat delayed flowering and increased the number of spikelets per spike. Taken together, the above results support the hypothesis that ELF3 is Eps-A (m) 1. The ELF3 alleles identified here provide additional tools to modulate reproductive development in wheat.

Keywords: ELF3; Earliness per se; Flowering time; Spikelet number; Triticum monococcum; Wheat.

Fig. 1

a T. monococcum high-density genetic map based on the analysis of 10,000 gametes, showing the previous candidate region for Eps-A ^m 1 in light gray (Faricelli et al. 2010). The reevaluation of critical NIL 502 resulted in a new candidate region for Eps-A ^m 1, indicated in darker gray. b Graphical genotypes and heading times of a progeny test of critical NIL 502. Different colors indicate chromosome regions homozygous for the DV92 allele (dark gray), homozygous for the G3116 allele (light gray), or heterozygous (diagonal gray lines). Heading time for each line is shown as the mean of at least five plants ± standard error of the mean. Values followed by different letters are significantly different from each other (P < 0.01). This progeny test confirmed that the Eps-A ^m 1 locus in NIL 502 was distal to the MOT1/FTSH4 locus

Fig. 2

a Triticum monococcum high-density genetic map. Genetic distances are based on the analysis of 5800 gametes. Putative genes are color-coded and indicated as circles. b Triticum monococcum physical map. Sequenced BACs are indicated as blue bars and assembly gaps as striped bars. c Triticum aestivum 1AL IWGSC contigs colinear to the Eps-A ^m 1 region. Contig names were shortened, and only the contig number is shown. d Brachypodium distachyon region colinear to Eps-A ^m 1

Fig. 3

Expression analysis of candidate genes (a–c), flowering genes (d–f), and circadian clock genes (g–l). T. monococcum NILs carrying the Eps-A ^m 1 allele from DV92 (Eps-A ^m 1-l, blue dashed lines) or G3116 (Eps-A ^m 1-e, red lines) were grown under controlled conditions (16 °C; 16 h light). Each point represents means ± standard error of the mean of six individual plants (*P < 0.05, **P < 0.01, ***P < 0.001)

Fig. 4

Effect of the introgression of the T. monococcum chromosome segment carrying the Eps-A ^m 1-l allele from DV92 into tetraploid wheat on heading time (a) and spikelet number (b). Bars represent the mean of at least 15 plants ± standard error of the mean. Asterisks indicate significant differences (**P < 0.01, ***P < 0.001)

Fig. 5

a Schematic representation of the ELF3 gene. Positions of the selected mutations introducing premature stop codons on the A- and B-genome copies of the gene are indicated with red triangles. Exons are shown as gray rectangles and introns as black lines. b–e Heading time and spikelet number of tetraploid BC₂F₃ lines carrying four possible homozygous combinations of ELF3 and PPD1 alleles. Plants were grown either under LD (b, c) or SD conditions (d, e). ELF3 alleles: ELF3-WT (blue dashed lines), elf3-null (red lines). PPD1 alleles: PPD-A1a (allele with reduced photoperiodic response); PPD-A1b (photoperiod sensitive allele). Asterisks between lines indicate significant differences between ELF3 alleles; asterisks on top and below lines indicate significant differences between PPD1 alleles (*P < 0.05, **P < 0.01, ***P < 0.001, ns nonsignificant)