scholarly journals DELAY OF GERMINATION 6, encoding the ANAC060 transcription factor, inhibits seed dormancy

2021 ◽  
Author(s):  
Shuang Song ◽  
Hanzi He ◽  
Kerstin Guhl ◽  
Marieke van Bolderen Veldkamp ◽  
Gonda Buijs ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Seed Dormancy ◽  
Quantitative Trait ◽  
Genomic Sequence ◽  
Class A ◽  
Natural Variants ◽  
Alternatively Spliced ◽  
Membrane Bound ◽  
Trait Locus ◽  
Pp2c Gene

The timing of seed germination is regulated by seed dormancy. There is ample natural variation for seed dormancy among as well as within plant species. In Arabidopsis several DELAY OF GERMINATION quantitative trait loci have been identified, of which DOG1 is best studied. Here we report the identification of DOG6, a quantitative trait locus with a similar strong effect on seed dormancy as DOG1. DOG6 affects the timing of germination both in laboratory as well as in field conditions. Complementation cloning revealed that DOG6 encodes the membrane bound transcription factor ANAC060. The absence of the ANAC060 protein or its sequestration outside the nucleus results in increased seed dormancy levels. The different natural variants of ANAC060 differ for the presence of the membrane binding domain, either due to the fact that this domain is absent in the genomic sequence or because the cDNA is alternatively spliced. Our data indicates that ANAC060 regulates seed dormancy by among others binding to and regulating the expression of protein phosphatases 2C class A proteins including PROTEIN PHOSPHATASE 2CA (PP2CA), ABI FIVE BINDING PROTEIN 3 (AFP3) and HIGHLY ABA-INDUCED PP2C GENE 3 (HAI3).

Changes in Regulation of a Transcription Factor Lead to Autogamy in Cultivated Tomatoes

Science ◽  
2007 ◽  
Vol 318 (5850) ◽  
pp. 643-645 ◽  
Author(s):  
Kai-Yi Chen ◽  
Bin Cong ◽  
Rod Wing ◽  
Julia Vrebalov ◽  
Steven D. Tanksley
Keyword(s):  
Quantitative Trait Locus ◽  
Transcription Factor ◽  
Quantitative Trait ◽  
Flower Development ◽  
Cell Elongation ◽  
Major Quantitative Trait Locus ◽  
Style Length ◽  
Self Pollination ◽  
Putative Transcription Factor ◽  
Trait Locus

We report the cloning ofStyle2.1, the major quantitative trait locus responsible for a key floral attribute (style length) associated with the evolution of self-pollination in cultivated tomatoes. The gene encodes a putative transcription factor that regulates cell elongation in developing styles. The transition from cross-pollination to self-pollination was accompanied, not by a change in the STYLE2.1 protein, but rather by a mutation in theStyle2.1promoter that results in a down-regulation ofStyle2.1expression during flower development.

Seed dormancy in barley: identifying superior genotypes through incorporating epistatic interactions

2008 ◽  
Vol 59 (6) ◽  
pp. 517 ◽  
Author(s):  
Y. Bonnardeaux ◽  
C. Li ◽  
R. Lance ◽  
X. Q. Zhang ◽  
K. Sivasithamparam ◽  
...  
Keyword(s):  
Seed Dormancy ◽  
Quantitative Trait ◽  
Major Quantitative Trait Locus ◽  
Specific Gene ◽  
Phenotypic Variance ◽  
Epistatic Interactions ◽  
Minor Qtls ◽  
Superior Genotypes ◽  
Gene Complexes ◽  
Trait Locus

A genetic linkage map of barley with 128 molecular markers was constructed using a doubled haploid (DH) mapping population derived from a cross between barley (Hordeum vulgare) cvv. Stirling and Harrington. Quantitative trait loci controlling seed dormancy were characterised in the population. A major quantitative trait locus (QTL) controlling seed dormancy and accounting for over half the phenotypic variation (52.17%) was identified on the distal end of the long arm of chromosome 5H. Minor QTLs were also detected near the centromeric region of 5H and on chromosomes 1H and 3H. These minor QTLs with additive effects accounted for 7.52% of the phenotypic variance measured. Examination of epistatic interactions further detected additional minor QTLs near the centromere of 2H and on the long arm and short arms of 4H. Combinations of parental alleles at the QTL locations in predictive analyses indicated dramatic differences in germination. These results emphasise the potential differences in dormancy that can be achieved through the use of specific gene combinations and highlights the importance of minor genes and the epistatic interactions that occur between them. This study found that the combination of Stirling alleles at the two QTL locations on the 5H chromosome and Harrington alleles at the 1H and 3H QTL locations significantly produced the greatest dormancy. Uncovering gene complexes controlling the trait may enable breeders to produce superior genotypes with the desirable allele combinations necessary for manipulating seed dormancy in barley.

Dynamic quantitative trait locus analysis of seed dormancy at three development stages in rice

2014 ◽  
Vol 34 (2) ◽  
pp. 501-510 ◽  
Author(s):  
Jinping Cheng ◽  
Ling Wang ◽  
Wenli Du ◽  
Yanyan Lai ◽  
Xi Huang ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait Locus Analysis ◽  
Seed Dormancy ◽  
Quantitative Trait ◽  
Development Stages ◽  
Trait Locus

scholarly journals Genetic variation in the promoter of an R2R3−MYB transcription factor determines fruit malate content in apple (Malus domestica Borkh.)

2021 ◽  
Author(s):  
Dongjie Jia ◽  
Peng Wu ◽  
Fei Shen ◽  
Wei Li ◽  
Xiaodong Zheng ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Malus Domestica ◽  
Quantitative Trait ◽  
Molecular Mechanisms ◽  
Chromosome 8 ◽  
Myb Transcription Factor ◽  
Nucleotide Polymorphisms ◽  
Malus Domestica Borkh ◽  
Trait Locus ◽  
R2r3 Myb

Abstract Deciphering the mechanism of malate accumulation in apple (Malus domestica Borkh.) fruits can help to improve their flavor quality and enhance their benefits for human health. Here, we analyzed malate content as a quantitative trait that is determined mainly by genetic effects. In a previous study, we identified an R2R3−MYB transcription factor named MdMYB44 that was a candidate gene in qtl08.1 (quantitative trait locus mapped to chromosome 8) of fruit malate content. In the present study, we established that MdMYB44 negatively regulates fruit malate accumulation by repressing the promoter activity of the malate-associated genes Ma1 (Al-Activated Malate Transporter 9), Ma10 (P-type ATPase 10), MdVHA-A3 (V-type ATPase A3), and MdVHA-D2 (V-type ATPase D2). Two single-nucleotide polymorphisms (SNPs) in the MdMYB44 promoter, SNP A/G and SNP T/−, were experimentally shown to associate with fruit malate content. The TATA-box in the MdMYB44 promoter in the presence of SNP A enhances the basal activity of the MdMYB44 promoter. The binding of a basic-helix–loop–helix transcription factor MdbHLH49 to the MdMYB44 promoter was enhanced by the presence of SNP T, leading to increased MdMYB44 transcript levels and reduced malate accumulation. Furthermore, MdbHLH49 interacts with MdMYB44 and enhances MdMYB44 activity. The two SNPs could be used in combination to select for sour or non-sour apples, providing a valuable tool for the selection of fruit acidity by the apple breeding industry. This research is important for understanding the complex molecular mechanisms of fruit malate accumulation and accelerating the development of germplasm innovation in apple species and cultivars.

scholarly journals Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis

2006 ◽  
Vol 103 (45) ◽  
pp. 17042-17047 ◽  
Author(s):  
L. Bentsink ◽  
J. Jowett ◽  
C. J. Hanhart ◽  
M. Koornneef
Keyword(s):  
Quantitative Trait Locus ◽  
Seed Dormancy ◽  
Quantitative Trait ◽  
Trait Locus

Identification of Quantitative Trait Locus for Seed Dormancy and Expression Analysis of Four Dormancy-Related Genes in Sorghum

2015 ◽  
Vol 8 (1-2) ◽  
pp. 9-18 ◽  
Author(s):  
Yan Guo ◽  
Pan Li ◽  
Nana Yuyama ◽  
Lubin Tan ◽  
Yongcai Fu ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Seed Dormancy ◽  
Expression Analysis ◽  
Quantitative Trait ◽  
Trait Locus

scholarly journals Natural Variants of ELF3 Affect Thermomorphogenesis by Transcriptionally Modulating PIF4-Dependent Auxin Response Genes

2015 ◽  
Author(s):  
Anja Raschke ◽  
Carla Ibañez ◽  
Kristian Karsten Ullrich ◽  
Muhammad Usman Anwer ◽  
Sebastian Becker ◽  
...  
Keyword(s):  
Ambient Temperature ◽  
Quantitative Trait ◽  
Natural Variation ◽  
Target Genes ◽  
Allelic Variation ◽  
Selective Advantage ◽  
Coding Region ◽  
Temperature Changes ◽  
Natural Variants ◽  
Trait Locus

Perception and transduction of temperature changes result in altered growth enabling plants to adapt to increased ambient temperature. While PHYTOCHROME-INTERACTING FACTOR4 (PIF4) has been identified as a major ambient temperature signaling hub, its upstream regulation seems complex and is poorly understood. Here, we exploited natural variation for thermo-responsive growth in Arabidopsis thaliana using quantitative trait locus (QTL) analysis. We identified GIRAFFE2.1, a major QTL explaining ~18% of the phenotypic variation for temperature-induced hypocotyl elongation in the Bay-0 x Sha recombinant inbred line population. Transgenic complementation demonstrated that allelic variation in the circadian clock regulator EARLY FLOWERING3 (ELF3) is underlying this QTL. The source of variation could be allocated to a single nucleotide polymorphism in the ELF3 coding region, resulting in differential expression of PIF4 and its target genes, likely causing the observed natural variation in thermo-responsive growth. In combination with other recent studies, this work establishes the role of ELF3 in the ambient temperature signaling network. Natural variation of ELF3-mediated gating of PIF4 expression during nightly growing periods seems to be affected by a coding sequence quantitative trait nucleotide that confers a selective advantage in certain environments. In addition, natural ELF3 alleles seem to differentially integrate temperature and photoperiod cues to induce architectural changes. Thus, ELF3 emerges as an essential coordinator of growth and development in response to diverse environmental cues and implicates ELF3 as an important target of adaptation.

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