The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity

Abstract

Background: Transcription factor (TF) GAMYB, belonging to MYB family (named after the gene of the avian myeloblastosis virus) is a master gibberellin (GA)-induced regulatory protein that is crucial for development and germination of cereal grain and involved in anther formation. It activates many genes including high-molecularweight glutenin and α-amylase gene families. This study presents the first attempt to characterize the rye gene encoding GAMYB in relation to its sequence, polymorphisms, and phenotypic effects. Results: ScGAMYB was mapped on rye chromosome 3R using high-density Diversity Arrays Technology (DArT)/ DArTseq-based maps developed in three mapping populations. The ScGAMYB sequences were identified in RNAseq libraries of four rye inbred lines. The transcriptome used for the search contained almost 151,000 transcripts with a median contig length of 500 nt. The average amount of total base raw data was approximately 9 GB. Comparative analysis of the ScGAMYB sequence revealed its high level of homology to wheat and barley orthologues. Single nucleotide polymorphisms (SNPs) detected among rye inbred lines allowed the development of allele specific-PCR (AS-PCR) markers for ScGAMYB that might be used to detect this gene in wide genetic stocks of rye and triticale. Segregation of the ScGAMYB alleles showed significant relationship with α-amylase activity (AMY). Conclusions: The research showed the strong similarity of rye GAMYB sequence to its orthologues in other Graminae and confirmed the position in the genome consistent with the collinearity rule of cereal genomes. Concurrently, the ScGAMYB coding sequence (cds) showed stronger variability (24 SNPs) compared to the analogous region of wheat (5 SNPs) and barley (7 SNPs). The moderate regulatory effect of ScGAMYB on AMY was confirmed, therefore, ScGAMYB was identified as a candidate gene for partial control of α-amylase production in rye grain. The predicted structural protein change in the aa region 362-372, caused by a single SNP (C/G) at the 1100 position in ScGAMYB cds and single aa sequence change (S/C) at the 367 position, is the likely cause of the differences in the effectiveness of ScGAMYB regulatory function associated with AMY. The development of sequence-based, allele-specific (AS) PCR markers could be useful in research and application.

The effects of heading time on yield performance and HvGAMYB expression in spring barley subjected to drought

“…The previous investigations (Gocal et al 2001 ; Tsuji et al 2006 ) suggest that GAMYB is a part of the central GA pathway, not only in the cereal aleurone layer but also in other plant tissues. This transcription factor (TF) encodes gibberellin-induced regulatory protein that is engaged in plant development and involved, among others, in anther formation (Bienias et al 2020 ). In these organs, HvGAMYB levels are approximately doubled in response to GA3 (Aya et al 2009 ).…”

Genotyping of polyploid plants using quantitative PCR: application in the breeding of white-fleshed triploid loquats (Eriobotrya japonica)

“…The qPCR genotyping primer design strategy focuses on large deletions, indel insertion/deletion sites or SNP sites of alleles. Meanwhile, mismatched bases can be introduced at the 3′ ends of the primers to improve their resolution [ 50 , 51 ].…”

High‐temperature stress in crops: male sterility, yield loss and potential remedy approaches

“…In Arabidopsis and rice, GA can regulate stamen and anther development via the transcriptional regulation of GAMYB. GAMYB is the specific transcriptional regulator of GA, involved in the development of the anther and produced by miRNA159 (Bienias et al ., 2020; Zhang et al ., 2014b).…”

“…The first study of GAMYB was in cereals (Barley) and was found in the aleurone cells, where it was found that GAMYB binds specifically to a GA‐response element in the 5′ regulatory regions of GA‐activated genes (Gubler et al ., 1995). In further study, it was found that GAMYB not only functions in the aleurone cells but also has a role in the cells of the anther (Bienias et al ., 2020). For instance, GAMYB‐4 produces an abnormal (enlarged) tapetum, due to which the normal process of meiosis is disturbed (Liu et al ., 2010).…”