Rht23 (5Dq') likely encodes a Q homeologue with pleiotropic effects on plant height and spike compactness

The domesticated gene Q on wheat chromosome 5A (5AQ) encodes an AP2 transcription factor. The 5AQ was originated from a G to A mutation in exon 8 and/or C to T transition in exon 10 and resulted in free-threshing and subcompact spike characters of bread wheat. The Q homeoalleles on 5B and 5D are either a pseudogene or expressed at a low level. Our previous study identified a mutant, named NAUH164, by EMS treatment of wheat variety Sumai 3. The mutant exhibits compact spike and dwarfness, and the mutated locus Rht23 was mapped to the distal of the long arm of chromosome 5D, where 5Dq was located. To investigate the relationship of Rht23 and 5Dq, sequences and expression patterns of 5Dq from Sumai 3 and NAUH164 were compared. The two genotypes had a G3147A single nucleotide polymorphism (SNP), which was predicted to be located within the miR172 binding site of 5Dq. Based on this SNP, an SNP marker was developed and linkage analysis using a (NAUH164 x Alondra's) RIL population showed the marker was co-segregated with the Rht23 mutant traits. The qRT-PCR and Northern blot showed that in NAUH164, the expression of 5Dq was significantly up-regulated, and consistently, the expression of Ta-miR172 was down-regulated in leaves, stems and spikes. Our results demonstrated that point mutation in the miR172 binding site of the 5Dq likely increased its transcript level via a reduction in miRNA-dependent degradation, and this resulted in pleiotropic effects on spike compactness and plant dwarfness.