PMID- 32831010
OWN - NLM
STAT- MEDLINE
DCOM- 20210514
LR  - 20220531
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 21
IP  - 1
DP  - 2020 Aug 24
TI  - The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific 
      markers, and relationship with alpha-amylase activity.
PG  - 578
LID - 10.1186/s12864-020-06991-3 [doi]
LID - 578
AB  - 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-molecular-weight glutenin and alpha-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 RNA-seq 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 alpha-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 alpha-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.
FAU - Bienias, Anna
AU  - Bienias A
AD  - Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian 
      University of Technology in Szczecin, Szczecin; ul, Slowackiego 17, 71-434, 
      Szczecin, Poland.
FAU - Goralska, Magdalena
AU  - Goralska M
AD  - Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian 
      University of Technology in Szczecin, Szczecin; ul, Slowackiego 17, 71-434, 
      Szczecin, Poland.
FAU - Masojc, Piotr
AU  - Masojc P
AD  - Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian 
      University of Technology in Szczecin, Szczecin; ul, Slowackiego 17, 71-434, 
      Szczecin, Poland.
FAU - Milczarski, Pawel
AU  - Milczarski P
AD  - Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian 
      University of Technology in Szczecin, Szczecin; ul, Slowackiego 17, 71-434, 
      Szczecin, Poland.
FAU - Myskow, Beata
AU  - Myskow B
AUID- ORCID: 0000-0001-5062-9841
AD  - Department of Plant Genetics, Breeding and Biotechnology, West Pomeranian 
      University of Technology in Szczecin, Szczecin; ul, Slowackiego 17, 71-434, 
      Szczecin, Poland. bmyskow@zut.edu.pl.
LA  - eng
GR  - 2015/17/B/NZ9/01694/National Science Centre, Poland/
PT  - Journal Article
DEP - 20200824
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
RN  - EC 3.2.1.1 (alpha-Amylases)
SB  - IM
MH  - Alleles
MH  - *Chromosomes, Plant/genetics
MH  - Genes, Plant/genetics
MH  - *Secale/genetics
MH  - alpha-Amylases/genetics
PMC - PMC7444254
OTO - NOTNLM
OT  - DArTseq
OT  - High-density genetic map
OT  - RNAseq
OT  - SNP
OT  - ScGAMYB
OT  - Secale cereale L.
OT  - transcription factor
COIS- The authors declare that they have no competing interests.
EDAT- 2020/08/25 06:00
MHDA- 2021/05/15 06:00
PMCR- 2020/08/24
CRDT- 2020/08/25 06:00
PHST- 2019/12/31 00:00 [received]
PHST- 2020/08/13 00:00 [accepted]
PHST- 2020/08/25 06:00 [entrez]
PHST- 2020/08/25 06:00 [pubmed]
PHST- 2021/05/15 06:00 [medline]
PHST- 2020/08/24 00:00 [pmc-release]
AID - 10.1186/s12864-020-06991-3 [pii]
AID - 6991 [pii]
AID - 10.1186/s12864-020-06991-3 [doi]
PST - epublish
SO  - BMC Genomics. 2020 Aug 24;21(1):578. doi: 10.1186/s12864-020-06991-3.