Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat (Avena sativa)
Tsardakas Renhuldt, Nikos LU
; Bentzer, Johan
LU
; Ahrén, Dag
LU
; Marmon, Sofia
LU
and Sirijovski, Nick
LU
(2024)
In Frontiers in Plant Science
15.
- Abstract
- In an ethyl methanesulfonate oat (Avena sativa) mutant population
we have found a mutant with striking differences to the wild-type (WT)
cv. Belinda. We phenotyped the mutant and compared it to the WT. The
mutant was crossed to the WT and mapping-by-sequencing was performed on a
pool of F2 individuals sharing the mutant phenotype, and variants were
called. The impacts of the variants on genes present in the reference
genome annotation were estimated. The mutant allele frequency
distribution was combined with expression data to identify which among
the affected genes was likely to cause the observed phenotype. A
brassinosteroid sensitivity assay was performed to validate one of the
... (More) - In an ethyl methanesulfonate oat (Avena sativa) mutant population
we have found a mutant with striking differences to the wild-type (WT)
cv. Belinda. We phenotyped the mutant and compared it to the WT. The
mutant was crossed to the WT and mapping-by-sequencing was performed on a
pool of F2 individuals sharing the mutant phenotype, and variants were
called. The impacts of the variants on genes present in the reference
genome annotation were estimated. The mutant allele frequency
distribution was combined with expression data to identify which among
the affected genes was likely to cause the observed phenotype. A
brassinosteroid sensitivity assay was performed to validate one of the
identified candidates. A literature search was performed to identify
homologs of genes known to be involved in seed shape from other species.
The mutant had short kernels, compact spikelets, altered plant
architecture, and was found to be insensitive to brassinosteroids when
compared to the WT. The segregation of WT and mutant phenotypes in the
F2 population was indicative of a recessive mutation of a single locus.
The causal mutation was found to be one of 123 single-nucleotide
polymorphisms (SNPs) spanning the entire chromosome 3A, with further
filtering narrowing this down to six candidate genes. In-depth analysis
of these candidate genes and the brassinosteroid sensitivity assay
suggest that a Pro303Leu substitution in AVESA.00010b.r2.3AG0419820.1
could be the causal mutation of the short kernel mutant phenotype. We
identified 298 oat proteins belonging to orthogroups of previously
published seed shape genes, with AVESA.00010b.r2.3AG0419820.1 being the
only of these affected by a SNP in the mutant. The
AVESA.00010b.r2.3AG0419820.1 candidate is functionally annotated as a
GSK3/SHAGGY-like kinase with homologs in Arabidopsis, wheat, barley,
rice, and maize, with several of these proteins having known mutants
giving rise to brassinosteroid insensitivity and shorter seeds. The
substitution in AVESA.00010b.r2.3AG0419820.1 affects a residue with a
known gain-of function substitution in Arabidopsis
BRASSINOSTEROID-INSENSITIVE2. We propose a gain-of-function mutation in AVESA.00010b.r2.3AG0419820.1 as the most likely cause of the observed phenotype, and name the gene AsGSK2.1.
The findings presented here provide potential targets for oat breeders,
and a step on the way towards understanding brassinosteroid signaling,
seed shape and nutrition in oats. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/3a5fd751-dde2-44b6-98dc-2b1e1236fe84
- author
- Tsardakas Renhuldt, Nikos
LU
; Bentzer, Johan
LU
; Ahrén, Dag
LU
; Marmon, Sofia
LU
and Sirijovski, Nick
LU
- organization
- publishing date
- 2024-04-26
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- seed shape, oats, Avena sativa, brassinosteroids, GSK3/SHAGGY-like kinase, mapping-by-sequencing, plant architecture, gene mapping
- in
- Frontiers in Plant Science
- volume
- 15
- article number
- 1358490
- pages
- 11 pages
- publisher
- Frontiers Media S. A.
- ISSN
- 1664-462X
- DOI
- 10.3389/fpls.2024.1358490
- language
- English
- LU publication?
- yes
- id
- 3a5fd751-dde2-44b6-98dc-2b1e1236fe84
- date added to LUP
- 2024-04-26 09:42:09
- date last changed
- 2024-04-30 03:02:51
@article{3a5fd751-dde2-44b6-98dc-2b1e1236fe84,
abstract = {{In an ethyl methanesulfonate oat (<i>Avena sativa</i>) mutant population<br>
we have found a mutant with striking differences to the wild-type (WT) <br>
cv. Belinda. We phenotyped the mutant and compared it to the WT. The <br>
mutant was crossed to the WT and mapping-by-sequencing was performed on a<br>
pool of F2 individuals sharing the mutant phenotype, and variants were <br>
called. The impacts of the variants on genes present in the reference <br>
genome annotation were estimated. The mutant allele frequency <br>
distribution was combined with expression data to identify which among <br>
the affected genes was likely to cause the observed phenotype. A <br>
brassinosteroid sensitivity assay was performed to validate one of the <br>
identified candidates. A literature search was performed to identify <br>
homologs of genes known to be involved in seed shape from other species.<br>
The mutant had short kernels, compact spikelets, altered plant <br>
architecture, and was found to be insensitive to brassinosteroids when <br>
compared to the WT. The segregation of WT and mutant phenotypes in the <br>
F2 population was indicative of a recessive mutation of a single locus. <br>
The causal mutation was found to be one of 123 single-nucleotide <br>
polymorphisms (SNPs) spanning the entire chromosome 3A, with further <br>
filtering narrowing this down to six candidate genes. In-depth analysis <br>
of these candidate genes and the brassinosteroid sensitivity assay <br>
suggest that a Pro303Leu substitution in AVESA.00010b.r2.3AG0419820.1 <br>
could be the causal mutation of the short kernel mutant phenotype. We <br>
identified 298 oat proteins belonging to orthogroups of previously <br>
published seed shape genes, with AVESA.00010b.r2.3AG0419820.1 being the <br>
only of these affected by a SNP in the mutant. The <br>
AVESA.00010b.r2.3AG0419820.1 candidate is functionally annotated as a <br>
GSK3/SHAGGY-like kinase with homologs in Arabidopsis, wheat, barley, <br>
rice, and maize, with several of these proteins having known mutants <br>
giving rise to brassinosteroid insensitivity and shorter seeds. The <br>
substitution in AVESA.00010b.r2.3AG0419820.1 affects a residue with a <br>
known gain-of function substitution in Arabidopsis <br>
BRASSINOSTEROID-INSENSITIVE2. We propose a gain-of-function mutation in <i>AVESA.00010b.r2.3AG0419820.1</i> as the most likely cause of the observed phenotype, and name the gene <i>AsGSK2.1</i>.<br>
The findings presented here provide potential targets for oat breeders,<br>
and a step on the way towards understanding brassinosteroid signaling, <br>
seed shape and nutrition in oats.}},
author = {{Tsardakas Renhuldt, Nikos and Bentzer, Johan and Ahrén, Dag and Marmon, Sofia and Sirijovski, Nick}},
issn = {{1664-462X}},
keywords = {{seed shape; oats; Avena sativa; brassinosteroids; GSK3/SHAGGY-like kinase; mapping-by-sequencing; plant architecture; gene mapping}},
language = {{eng}},
month = {{04}},
publisher = {{Frontiers Media S. A.}},
series = {{Frontiers in Plant Science}},
title = {{Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat (<i>Avena sativa</i>)}},
url = {{http://dx.doi.org/10.3389/fpls.2024.1358490}},
doi = {{10.3389/fpls.2024.1358490}},
volume = {{15}},
year = {{2024}},
}