Investigating the genetic control of plant development in spring barley under speed breeding conditions

Abstract

This study found that the genes, PPD-H1 and ELF3, control the acceleration of plant development under speed breeding, with important implications for optimizing the delivery of climate-resilient crops. Speed breeding is a tool to accelerate breeding and research programmes. Despite its success and growing popularity with breeders, the genetic basis of plant development under speed breeding remains unknown. This study explored the developmental advancements of barley genotypes under different photoperiod regimes. A subset of the HEB-25 Nested Association Mapping population was evaluated for days to heading and maturity under two contrasting photoperiod conditions: (1) Speed breeding (SB) consisting of 22 h of light and 2 h of darkness, and (2) normal breeding (NB) consisting of 16 h of light and 8 h of darkness. GWAS revealed that developmental responses under both conditions were largely controlled by two loci: PPDH-1 and ELF3. Allelic variants at these genes determine whether plants display early flowering and maturity under both conditions. At key QTL regions, domesticated alleles were associated with late flowering and maturity in NB and early flowering and maturity in SB, whereas wild alleles were associated with early flowering under both conditions. We hypothesize that this is related to the dark-dependent repression of PPD-H1 by ELF3 which might be more prominent in NB conditions. Furthermore, by comparing development under two photoperiod regimes, we derived an estimate of plasticity for the two traits. Interestingly, plasticity in development was largely attributed to allelic variation at ELF3. Our results have important implications for our understanding and optimization of speed breeding protocols particularly for introgression breeding and the design of breeding programmes to support the delivery of climate-resilient crops.

Fig. 1

Manhattan plots from the three traits (heading (HEA), maturity (MAT), and plasticity in two photoperiod conditions (normal breeding and speed breeding)). Seven barley chromosomes are shown (1H-7H) horizontally, and –log10(p-values) are displayed vertically on the y-axis. Significant FDR threshold grey dashed line set at 0.05 (− log10 p-value). Flowering-time candidate genes are shown in the rectangle boxes. Plots were created using the “CMplot” package (Yin et al. 2021) in Rstudio version 4.2.2. The details of the significant peaks and the markers underlying these peaks are provided in Data S2

Fig. 2

PPD-H1 and ELF3 alleles-based boxplots from HEA a and MAT b. Boxplots of the response of different genotype groups to MAT and HEA, arising from the combinatorial allelic analysis displayed on the X-axis (PPD-H1_Hv/ELF3_Hv, PPD-H1_Hv/ELF3_Hsp, PPD-H1_Hsp/ELF3_Hv, and PPD-H1_Hsp/ELF3_Hsp). The P-values shown above each allelic class are derived from permutation t-tests as shown in Data S3. For both traits (flowering and maturity), the presence of domesticated alleles tends to delay flowering and maturity under both speed breeding and normal breeding conditions

Fig. 3

PPD-H1 and ELF3 alleles-based boxplots from Plasticity.HEA a and Plasticity.MAT b. Boxplots of the response of different genotype groups to Plasticity.HEA and Plasticity.MAT, arising from the combinatorial allelic analysis. PPD-H1_Hv/ELF3_Hv, PPD-H1_Hv/ELF3_Hsp, PPD-H1_Hsp/ELF3_Hv, and PPD-H1_Hsp/ELF3_Hsp are shown on the X-axis. The significance values shown are derived from permutation t-tests as shown in Data S3. The presence of wild alleles at PPD-H1 and ELF3 tends to reduce the levels of plasticity for flowering and maturity times across both speed breeding and normal conditions