Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley

Abstract

Time to flowering has an important impact on yield and has been a key trait in the domestication of crop plants and the spread of agriculture. In 1961, the cultivar Mari (mat-a.8) was the very first induced early barley (Hordeum vulgare L.) mutant to be released into commercial production. Mari extended the range of two-row spring barley cultivation as a result of its photoperiod insensitivity. Since its release, Mari or its derivatives have been used extensively across the world to facilitate short-season adaptation and further geographic range extension. By exploiting an extended historical collection of early-flowering mutants of barley, we identified Praematurum-a (Mat-a), the gene responsible for this key adaptive phenotype, as a homolog of the Arabidopsis thaliana circadian clock regulator Early Flowering 3 (Elf3). We characterized 87 induced mat-a mutant lines and identified >20 different mat-a alleles that had clear mutations leading to a defective putative ELF3 protein. Expression analysis of HvElf3 and Gigantea in mutant and wild-type plants demonstrated that mat-a mutations disturb the flowering pathway, leading to the early phenotype. Alleles of Mat-a therefore have important and demonstrated breeding value in barley but probably also in many other day-length-sensitive crop plants, where they may tune adaptation to different geographic regions and climatic conditions, a critical issue in times of global warming.

Fig. 1.

Phenotyping of the heading date trait in barley based on appearance of the awns protruding from the flag leaf. (A) One-month-old barley plants carrying the wild-type Mat-a allele (Left) and the recessive mat-a allele (Right). Arrows indicate regions of the main stems around the flag leaf of these two genotypes, which are shown magnified in B and C. (B) The cultivar Bowman. (C) The Bowman backcross-derived line BW290 that carries the eam8.w allele on a 1.5-cM introgressed segment from Early Russian.

Fig. 2.

Mapping and synteny at the Mat-a locus. (A) Inference of HvElf3 as a candidate gene for Mat-a using genetic mapping data from wheat and barley and the Sorghum physical map. The wheat map shows a fragment of the Eps-A^m1 locus. The Sorghum physical map shows only those gene model names that have barley homologs mapped on the telomeric region of barley chromosome 1H (shown as connecting lines to barley consensus map loci). Markers colocating on the barley consensus map (21) are boxed. The mapping of the backcross-derived near-isogenic line BW289, carrying the Mat-a allele eam8.k, is indicated. (B) Barley-Sorghum synteny model-based prediction of the genetic position of the HvElf3 gene. Positions of barley genetic markers were regressed against physical map positions of homologous sequences in Sorghum. The scatter plot shows only those homologous pairs that map in the syntenic regions. R² is the coefficient of determination for the linear regression function. Physical distances (in kb) in Sorghum are shown on the x axis. Genetic map distances (21) on barley chromosome 1H are given on the y axis.

Fig. 3.

Correlation between phenotype and genotype in control plants (A) and two F₂ mapping populations (B and C). (A) The day of heading for BW289 carrying the eam8.k mutation in comparison with the barley cultivars Bowman and Barke. (B and C) F₂ mapping population from the cross BW289 × Bowman (B) and BW289 × Barke (C).

Fig. 4.

Structure of the barley Mat-a gene and the positions of the detected mutations. A 5,075-bp MluI–MunI DNA fragment from BAC clone HVVMRXALLhA0624F14 (34) was used as template for resequencing 87 mutant alleles. E1–E4 designate exons. The complex eam8.k allele with two deletions, one inversion, and two small insertions is shown separately in Lower.

Fig. 5.

Expression profiles of Gigantea (A) and Elf3 (B) in the near-isogenic mat-a mutant line BW289 (open circles) and Bowman (filled circles). Plants were harvested at 3-h intervals at the three-leaf stage. The open and filled bars at the bottom indicate the light and dark periods, respectively. (B Inset) The Elf3 expression in Bowman in more detail.