Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

Abstract

The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time. A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.

Figure 1.

Vernalization time course in B. distachyon accessions Bd21 and Bd1-1. A and C, Photographs of representative plants taken after 60 d of growth. Imbibed seeds of Bd21 and Bd1-1 were cold treated at 5°C in soil in an 8-h photoperiod for the indicated length of time (weeks), followed by outgrowth in a growth chamber set to 16-h light/8-h dark (A) or 20-h light/4-h dark (C). B and D, Flowering time measured as the number of days to spike emergence from the end of cold treatment. Arrows indicate treatments where plants did not flower within 120 d of the experiment.

Figure 2.

Graphical representation of the estimated linkage map for the Bd21 X Bd1-1 RIL mapping population. A, Physical position of selected markers along B. distachyon chromosomes. B, Pairwise recombination fraction (upper-left triangle) and LOD scores for all pairs of markers ordered according to their position on the genome shown in (A). Yellow indicates linked markers; dark blue indicate unlinked markers. Axes show marker numbers. C, Genetic map of selected markers. Distances are shown in centimorgans. Mb, megabase; cM, centimorgans.

Figure 3.

Flowering-time distribution within the RIL population under five environmental treatments: 16-h long d nonvernalized (16-h LD NV), 20-h long d nonvernalized (20-h LD NV), 16- and 20-h long d after 2-week vernalization (16- and 20-h LD 2W Vern), and 16-h long d after 3 weeks of vernalization (16-h LD 3W Vern). Days to heading (x axis) indicate the number of days to spike emergence once plants germinated. The number of lines within the RIL population that flowered within ranges of 10 d is indicated by the y axis. White arrows indicate the average days to heading for Bd21 plants (n = 12) and black arrows indicate the average days to for Bd1-1 plants (n = 12).

Figure 4.

Location of flowering-time QTLs under five different environmental conditions. QTLs based on days to heading are indicated by a solid line whereas the QTLs based on leaf count on the parent culm are indicated by a dotted line. The red horizontal line represents the threshold of significance (see Materials and Methods). The phenotyping of the mapping population was repeated, which resulted in similar segregation of flowering-time phenotypes and QTL peaks (data not shown). The name attributed to the different QTLs (QTL1 to QTL6) and the candidate flowering-time genes underlying each QTL (bold red line) are shown at the bottom of the diagram. Orange vertical lines indicate candidate flowering-time genes that are not correlated with QTLs.

Figure 5.

Phenotype by genotype influence on flowering for nonvernalized plants grown in 20-h-long d. Phenotype by genotype plot for the two major loci (QTL1, VRN1/PHYC candidate and QTL2, VRN2 candidate) influencing flowering time in the Bd21 X Bd1-1 RIL population grown in 20 h nonvernalized conditions in which both QTLs are simultaneously present. Days to heading results indicate that presence of the Bd21 genotype at both QTL1 and QTL2 results in rapid flowering whereas presence of the Bd1-1 genotype at both loci results in delayed flowering. Difference in letters above box plots (a, b, a,b, c) indicate statistical significance based on the mean days to heading values between the various genotypes at QTL1 and QTL2 computed with an ANOVA Tukey’s HSD test (P ≤ 0.01).