Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here, we identified, with a high level of confidence, 208 imprinted gene candidates from rice (). Imprinted genes of rice showed limited association with the transposable elements, which contrasts with findings from Arabidopsis (). Generally, imprinting in rice is conserved within a species, but intraspecific variation also was detected. The imprinted rice genes do not show signatures of selection, which suggests that domestication has had a limited evolutionary consequence on genomic imprinting. Although conservation of imprinting in plants is limited, we show that some loci are imprinted in several different species. Moreover, our results suggest that different types of epigenetic regulation can be established either before or after fertilization. Imprinted 24-nucleotide small RNAs and their neighboring genes tend to express alleles from different parents. This association was not observed between 21-nucleotide small RNAs and their neighboring genes. Together, our findings suggest that the regulation of imprinting can be diverse, and genomic imprinting has evolutionary and biological significance.
Flavonoids are plant secondary metabolites that contribute to the adaptation of plants to environmental stresses, including resistance to abiotic and biotic stress. Flavonoids are also beneficial for human health and depress the progression of some chronic diseases. The biosynthesis of flavonoids, which belong to a large family of phenolic compounds, is a complex metabolic process with many pathways that produce different metabolites, controlled by key enzymes. There is limited knowledge about the composition, biosynthesis and regulation of flavonoids in cereals. Improved understanding of the accumulation of flavonoids in cereal grains would help to improve human nutrition through these staple foods. The biosynthesis of flavonoids, scope for altering the flavonoid composition in cereal crops and benefits for human nutrition are reviewed here.
Pre-harvest sprouting (PHS), the germination of grain before harvest, is a serious problem resulting in wheat yield and quality losses.Here, we mapped the PHS resistance gene PHS-3D from synthetic hexaploid wheat to a 2.4 Mb presence-absence variation (PAV) region and found that its resistance effect was attributed to the pleiotropic Myb10-D by integrated omics and functional analyses.Three haplotypes were detected in this PAV region among 262 worldwide wheat lines and 16 Aegilops tauschii, and the germination percentages of wheat lines containing Myb10-D was approximately 40% lower than that of the other lines. Transcriptome and metabolome profiling indicated that Myb10-D affected the transcription of genes in both the flavonoid and abscisic acid (ABA) biosynthesis pathways, which resulted in increases in flavonoids and ABA in transgenic wheat lines. Myb10-D activates 9-cis-epoxycarotenoid dioxygenase (NCED) by biding the secondary wall MYB-responsive element (SMRE) to promote ABA biosynthesis in early wheat seed development stages.We revealed that the newly discovered function of Myb10-D confers PHS resistance by enhancing ABA biosynthesis to delay germination in wheat. The PAV harboring Myb10-D associated with grain color and PHS will be useful for understanding and selecting white grained PHS resistant wheat cultivars.
A group of phylogenetically conserved nuclear factor Y transcription factors are preferentially expressed in the endosperm and probably play essential roles in endosperm development for rice and other monocots.
Background
Environmental toxicity from non-essential heavy metals such as cadmium (Cd), which is released from human activities and other environmental causes, is rapidly increasing. Wheat can accumulate high levels of Cd in edible tissues, which poses a major hazard to human health. It has been reported that heat shock transcription factor A 4a (
HsfA4a
) of wheat and rice conferred Cd tolerance by upregulating metallothionein gene expression. However, genome-wide identification, classification, and comparative analysis of the
Hsf
family in wheat is lacking. Further, because of the promising role of
Hsf
genes in Cd tolerance, there is need for an understanding of the expression of this family and their functions on wheat under Cd stress. Therefore, here we identify the wheat
TaHsf
family and to begin to understand the molecular mechanisms mediated by the
Hsf
family under Cd stress.
Results
We first identified 78 putative
Hsf
homologs using the latest available wheat genome information, of which 38 belonged to class A, 16 to class B and 24 to class C subfamily. Then, we determined chromosome localizations, gene structures, conserved protein motifs, and phylogenetic relationships of these
TaHsfs
. Using RNA sequencing data over the course of development, we surveyed expression profiles of these
TaHsfs
during development and under different abiotic stresses to characterise the regulatory network of this family. Finally, we selected 13
TaHsf
genes for expression level verification under Cd stress using qRT-PCR.
Conclusions
To our knowledge, this is the first report of the genome organization, evolutionary features and expression profiles of the wheat
Hsf
gene family. This work therefore lays the foundation for targeted functional analysis of wheat
Hsf
genes, and contributes to a better understanding of the roles and regulatory mechanism of wheat
Hsfs
under Cd stress.
Electronic supplementary material
The online version of this article (10.1186/s12864-019-5876-x) contains supplementary material, which is available to authorized users.
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