Features of Ppd-B1 expression regulation and their impact on the flowering time of wheat near-isogenic lines

Abstract

Background: Photoperiod insensitive Ppd-1a alleles determine early flowering of wheat. Increased expression of homoeologous Ppd-D1a and Ppd-A1a result from deletions in the promoter region, and elevated expression of Ppd-B1a is determined by an increased copy number.

Results: In this study, using bread wheat cultivars Sonora and PSL2, which contrast in flowering time, and near-isogenic lines resulting from their cross, "Ppd-m" and "Ppd-w" with Ppd-B1a introgressed from Sonora, we investigated the putative factors that influence Ppd-B1a expression. By analyzing the Ppd-B1a three distinct copies, we identified an indel and the two SNPs, which distinguished the investigated allele from other alleles with a copy number variation. We studied the expression of the Ppd-A1, Ppd-B1a, and Ppd-D1 genes along with genes that are involved in light perception (PhyA, PhyB, PhyC) and the flowering initiation (Vrn-1, TaFT1) and discussed their interactions. Expression of Ppd-B1a in the "Ppd-m" line, which flowered four days earlier than "Ppd-w", was significantly higher. We found PhyC to be up-regulated in lines with Ppd-B1a alleles. Expression of PhyC was higher in "Ppd-m". Microsatellite genotyping demonstrated that in the line "Ppd-m", there is an introgression in the pericentromeric region of chromosome 5B from the early flowering parental Sonora, while the "Ppd-w" does not have this introgression. FHY3/FAR1 is known to be located in this region. Expression of the transcription factor FHY3/FAR1 was higher in the "Ppd-m" line than in "Ppd-w", suggesting that FHY3/FAR1 is important for the wheat flowering time and may cause earlier flowering of "Ppd-m" as compared to "Ppd-w".

Conclusions: We propose that there is a positive bidirectional regulation of Ppd-B1a and PhyC with an FHY3/FAR1 contribution. The bidirectional regulation can be proposed for Ppd-A1a and Ppd-D1a. Using in silico analysis, we demonstrated that the specificity of the Ppd-B1 regulation compared to that of homoeologous genes involves not only a copy number variation but also distinct regulatory elements.

Keywords: Common wheat; Flowering time; Photoperiod sensitivity; Phytochrome; Ppd-B1.

Fig. 1

Scheme of the Ppd-B1 gene features. Distances are presented in base pairs from the TSS (transcription start site). Black rectangles indicate exons. CS means Chinese Spring cultivar. Numbers on the right side of some sequences indicate number of gene copies in actual alleles

Fig. 2

Patterns of the diurnal gene expression. Quantitative gene expression data from plants grown in short days (0–9 h light period) in а climatic chamber. Gray shadowing indicates the dark period (9–24 h). The graphs compare the expression between the photoperiod sensitive parental line PSL2 (red) and the photoperiod insensitive NILs (“Ppd-m” (green), “Ppd-w” (purple)) and parent Sonora (blue). Values are expressed as the relative levels normalized against 18S ribosomal RNA. Error bars indicate the SE of the means. Asterisks indicate significant (P < 0.05) differences in a one-way ANOVA with a post hoc Tukey test comparing the photoperiod insensitive NILs (“Ppd-m”, “Ppd-w”) and the parent Sonora with the photoperiod sensitive parental line PSL2 in each time point

Fig. 3

5B chromosome genotyping of NILs. Genotypes of the 5B chromosome of the near-isogenic “Ppd-m” and “Ppd-0^m”, “Ppd-w” and “Ppd-0^w” lines with introgressed chromosome regions of the Sonora variety (white color) into the genetic background of the recipient PSL2 parent (gray color). C indicates centromere region

Fig. 4

Patterns of the FHY3/FAR1 diurnal expression. Quantitative gene expression data from plants grown in short days (0–9 h light period) in а climatic chamber. Gray shadowing indicates the dark period (9–24 h). The graphs compare the expression between the photoperiod insensitive NILs “Ppd-m” (green), “Ppd-w” (purple). Values are expressed as the relative levels normalized against 18S ribosomal RNA. Error bars indicate the SE of the means. Asterisks indicate significant (P < 0.05) differences in a one-way ANOVA with a post hoc Tukey test comparing the “Ppd-m” and “Ppd-w” in each time point

Fig. 5

Groups of transcription factor binding sites that are common in the Ppd-1 genes. Vertical dotted lines indicate the borders of a 900-bp region that is commonly deleted in the Ppd-A1 and Ppd-D1 photoperiod insensitive alleles [4, 7]. TSS indicates Transcription Start Site; the distances are presented in base pairs

Fig. 6

Groups of transcription factor binding sites that are specific to Ppd-B1. TSS indicates Transcription Start Site; the distances are presented in base pairs. Different colors designate different TFBSs or TFBSs with unknown TF