Wheat EARLY FLOWERING 3 affects heading date without disrupting circadian oscillations

Abstract

Plant breeders have indirectly selected for variation at circadian-associated loci in many of the world’s major crops when breeding to increase yield and improve crop performance. Using an eight-parent Multiparent Advanced Generation Inter-Cross (MAGIC) population, we investigated how variation in circadian-clock-associated genes contributes to the regulation of heading date in UK and European winter wheat (Triticum aestivum) varieties. We identified homoeologues of EARLY FLOWERING 3 (ELF3) as candidates for the Earliness per se (Eps) D1 and B1 loci under field conditions. We then confirmed a single-nucleotide polymorphism within the coding region of TaELF3-B1 as a candidate polymorphism underlying the Eps-B1 locus. We found that a reported deletion at the Eps-D1 locus encompassing TaELF3-D1 is instead an allele that lies within an introgression region containing an inversion relative to the Chinese Spring D genome. Using Triticum turgidum cv. Kronos carrying loss-of-function alleles of TtELF3 we showed that ELF3 regulates heading, with loss of a single ELF3 homoeologue sufficient to alter heading date. These studies demonstrated that ELF3 forms part of the circadian oscillator; however, loss of all homoeologues was required to affect circadian rhythms. Similarly, loss of functional LUX ARRHYTHMO (LUX) in T. aestivum, an orthologue of a protein partner of Arabidopsis (Arabidopsis thaliana) ELF3, severely disrupted circadian rhythms. ELF3 and LUX transcripts are not co-expressed at dusk, suggesting the structure of the wheat circadian oscillator might differ from that of Arabidopsis. Our demonstration that alterations to ELF3 homoeologues can affect heading date separately from effects on the circadian oscillator suggests a role for ELF3 in cereal photoperiodic responses that could be selected for without pleiotropic deleterious alterations to circadian rhythms.

EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time

“…In barley and wheat, loss-of-function mutations in ELF3 [ 26 , 27 , 30 ] or LUX [ 31 – 33 ] result in very early heading under both LD and SD conditions, suggesting that in these species the EC is critical for the photoperiodic response. Natural allelic variation at ELF3 has also been associated with differences in heading time in diploid Triticum monococcum and in hexaploid wheat [ 26 , 34 , 35 ].…”

GIGANTEAis required for circadian rhythms in wheat

“…The architecture of the circadian clock is broadly conserved across the plant kingdom, with alleles of circadian clock genes selected for domestication and in breeding programs to enhance agriculturally important crop traits, such as flowering time (McClung, 2021;Steed et al, 2021). However, we have found in wheat that transcripts of ELF3, which encodes a putative scaffold protein, peak at dawn, rather than dusk as in Arabidopsis (Wittern et al, 2023). Furthermore, wheat ELF3 protein is unstable in the light (Alvarez et al, 2023).…”

“…Leaf temperature relative to background temperature was recorded as described in Wittern et al, (2023), using Type-K thermocouples attached to the leaf and unattached thermocouples to record background temperature. Plants were grown under long day photoperiods (16 h L: 8 h D; 200 µmol m −2 s −1 , 20°C Day: 14°C night) and after 3 weeks, leaf temperature from the fully expanded flag leaves was measured under continuous light and temperature (150 µmol m −2 s −1 , 20°C Day 20°C).…”

“…Three technical replicates of gene-specific products were amplified in 10 µl reactions using QuantiNova SYBR Green PCR Kit (Quiagen) on a CFX384 Touch Real-Time PCR detection system (Bio Rad). Transcript levels were determined relative to the expression of two housekeeping genes, RP15 and RPT5A as described in Wittern et al, (2023). Primer sequences are shown in Table 1.…”

Compartmentation of photosynthesis gene expression between mesophyll and bundle sheath cells of C4maize is dependent on time of day

“…images. At dawn of the next day this repeating light regime was run continuously for a further 72 hours to simulate constant light but with dark breaks to allow imaging as has been used previously (Wittern et al, 2023). Chlorophyll fluorescence parameters were calculated using the image scripts provided by the manufacturer.…”