Conclusion
Secondary metabolites biosynthesis impulsed under the action of phytohormone in general and jasmonates in particular is crucial for the plant growth, development and defense in a stressed environment. So far, tremendous efforts drive to the elucidation of some key genes involved into the physiological mechanisms deployed by the plant to grow and survive. The jasmonate-elicited plant secondary metabolism machinery involved several transcription factors including APE2/ERFs VAN DER FITS AND MEMELINK, 2000, WRKYs Wang et al., 2007, bHLHs Zhang et al., 2011, and R2R3-MYBs Shan et al., 2009. The interaction networking with synthesis enzymes have been under elucidation in the plant model A. thaliana and some medicinal plant system including Catharanthus roseus, Nicotina tabacum and Artemisia annua for example De Geyter et al. 2012.
Owing the growing interest for the natural produced secondary metabolites in human health, plant protection and neutraceutical enriched foods, a better comprehension of the accumulation of the plant metabolites is gaining more attention. To extend the application field, we suggested here the inclusion of the medicinal orphan crops that also represent a secondary metabolites gold mine that deserve to be investigated. Among those orphan crop, the transcriptional comprehension of certain secondary metabolites synthesis have been initiated Kang et al. 2020 Hu et al., 2021, Wang et al. 2021, Wang et al. 2021 paving the way for not only effective JA triggered health oriented metabolic enginering, but also engineered crop protection against adverse biotic and abiotic stresses.
Altogether, under the ongoing environmental change status, JAs' mediated metabolites elicitation machinery needs further investigation in diverse plant systems.
New Ref for transcriptomics
-01 2020 | Imbibition of Seed Germination | RNA-Seq Study Reveals AP2-Domain-Containing Signalling Regulators Involved in Initial Imbibition of Seed Germination in Rice
-02 2017 | Coleoptile growth | RNA-Seq Analysis of Diverse Rice Genotypes to Identify the Genes Controlling Coleoptile Growth during Submerged Germination
-03 2016 | Seed germination | Transcriptome Analysis of Oryza sativa (Rice) Seed Germination at High Temperature Shows Dynamics of Genome Expression Associated with Hormones Signalling and Abiotic Stress Pathways
-04 2010 | Seed dormancy | Transcriptomics Analysis Identified Candidate Genes Colocalized with Seed Dormancy QTLs in Rice ( Oryza sativa L.)
-05 2021 | Integrating GWAS and Transcriptomics to Identify Genes Involved in Seed Dormancy in Rice
-06 2020| PHS | Analysis of Varietal Differences in Pre-harvest Sprouting of Rice using RNA-Sequencing
New ref for GWAS
-02 2021 | Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement
Excellent summary
In the case of rice, the map-based cloning of qSD7-1/qPC1 identified the Rc gene, encoding a basic helix-loop-helix family transcription factor, which upregulates genes involved in the biosynthesis of both flavonoid and ABA [12]. In the T-DNA/Tos17 insertional mutant populations, genes involved in the biosynthesis of carotenoids (i.e., OsPDS, OsZDS, OsCRTISO, and β-OsLCY), the important precursors of ABA, were identified [13]. A similar study using rice mutants with the PHS phenotype identified causal mutations in OsCNX1 and OsCNX6, the genes encoding molybdenum cofactors required for ABA biosynthesis [14]. Also, characterization of phs9-D revealed that this PHS mutant in rice carries a dominant mutation in PHS9, a gene encoding a CC-type glutaredoxin, which mediates ABA signaling through the interaction with ABA receptors [15]. In spite of these findings underlying clear biochemical mechanisms on PHS resistance, breeding efforts enhancing PHS resistance in rice varieties have been limited due to lack of genetic resources. Sdr4 and qSD7-1/qPC1, the major loci associated with PHS resistance were from a single genetic resource: Aus landrace Kasalath having red pericarp color and strong dormancy [12,16].
New for genome wide identification
New functional validation
-01 Control of rice pre-harvest sprouting by glutaredoxin-mediated abscisic acid signaling
Review
Genomics assisted breeding for PHS has retained the attention of the scientific community the last two decades. Tremendous advances were carried out with the identification of useful PHS resistance genes. A glance of the diverse strategies employed for PHS resistance detection is summarized in the figure 1. The first and foremost stage in this process relied on the characterization of germplasm for the identification of promising genetics resources.
Figure 1: Diagrammatic of the genomics-assisted breeding for PHS tolrance in rice.
QTL
Meanwhile several parental lines were released including IR24, Asominori, Jinsang, and Gopum. Besides the detection of contrasting materials regarding PHS resistance, the resistance gene pool from wild relatives including O. rufipogon (Phan et al., 2021) and O. nivara (Li et al., 2006) and weedy rice Gu et al 2004 was investigated. Several mapping populations were generated following RILs, BILs, CSSLs, Three-way cross hybrid, and double haploidy. The earlier detection of QTLs relied mostly on RFLP and SSRs markers. However, whole genome sequencing approach with a high resolution mapping at SNP level has been initiated. A total of xxxx QTLs have been detected within all chromosomes of the rice genome (Table 1).
Comparative genomics
At early stage of PHS gene detection, comparative genomics has been tested. Orthologous genes identification by comparing with well characterized PHS genes in barley and wheat exhibited the presence of the hormonal GA20-oxidase encoding gene Li et al. 2004.
Transcriptomics
In order to find out genes involved in PHS and subsequent related biological processes including seed dormancy and maturation, transcriptome studies (Huh et al., 2013,Xie et al., 2019, Park et al., 2021) using contrasting rice materials has been performed. Interestingly, candidate genes regulating hormones including ABA, GA and IAA have been highlighted including transcription factors such as DREB (dehydration-responsive element-binding protein), Basic Helix-Loop-Helix Transcription Factor (bHLH), late embryogenesis abundant protein (LEA), NAC transcription factor, and CCAAT-HAP3 transcription factor. This emphasizes the contributions of TFs as one of the key players mediating of the hormonal expression.
RNA splicing
Meanwhile microRNAs (miRNAs) are well known to be dependent of hormonal regulation in planta (Reyes et al., 2007)). Recently, Park et al. (2021) identified two candidate miRNAs (osa-miR5827 and osa-miR1862h) associated with two PHS-related genes OsFbox594 and OsbHLH084 respectively.
GWAS and Genome-wide identification
High quality genome resource enabled the detection of PHS related-genes via genome wide association analysis and genome-wide identification approaches. Zhu et al. (2021) pinpointed the role of a bZIP transcription factor OsbZIP09 which expression is induced by ABA. The mutation of this gene inhibited PHS in rice. By mining GWAS and transcriptome data, Shi et al. (2021) found a significant effect of the variation of SNPs in the promoter region of the Os9BGlu33 gene regarding germination index.
Functional validation
From those huge genetic and genomic resources, few genes have been functionally validated. (Sugimoto et al., 2010) identified the Sdr4 gene as responsible of seed dormancy control. Interestingly, OsVP1 exhibited a regulatory effect on Sdr4 gene via ABA signaling pathway. (Chen et al., 2021). Transcription factor also play a crucial role for regulating the hormonal expression in rice. Hobo et al. (1999), Wu et al. (2021) and Wang et al. 2020 demonstrated the interaction between VP1 and TRAP1 (bZIP transcription factor) and Rc (basic helix–loop–helix (bHLH) transcription factor) genes for ABA regulation.
Perspectives
Considering the importance of environmental effect on seed dormancy and germination, we suggest an investigation of the epigenome on rice. In fact, an increasing evidence has been in favor of DNA and histone methylation in regards with PHS resistance genetic mechanism (Singh et al. 2013), Lujan-Soto et al 2021. The role of the ARGONAUTE4_9, a DNA methylation RNA-dependent gene has been proved in wheat PHS. However, the epigenetic framework of PHS in rice is still elusive. Therefore, deciphering the epigenetic factors contributing to the PHS resistance regulation in rice will lay a foundation for a deep understanding of the full machinery in real climate impacted conditions. Moreover, an intensive validation of the existing candidate genes should be processed via Crispr-Cas9, RNAi, Agrobacterium tumefaciens mediated transformation for example. This will surely boost the design of PHS resistant rice. Altogether, post-transcriptional regulation encompassing, splicing RNA and epigenetics offer a new avenue for unravelling of the mechanism of resistance of PHS in rice. Ultimately, a deeper comprehension of the whole machinery will provide a gain for designing better rice with added value.
auxin_repressed_gene
Genome-Wide Identification and Comparative Analysis of ARF Family Genes in Three Apiaceae Species
transcriptome pre sprouting rice
Genetic map locations for orthologous Vp1 genes in wheat and rice
Generalities
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2021 very nice review 2021 Pre-harvest sprouting in cereals: genetic and biochemical mechanisms
Abscisic acid and the pre-harvest sprouting in cereals
Identification of valuable resource for pre-sprouting resistence
Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement
Genome wide identification area
Oriza sativa
Transcriptomics
Analysis of Varietal Differences in Pre-harvest Sprouting of Rice using RNA-Sequencing
The RNA-seq transcriptome analysis identified genes related to rice seed dormancy
Agronomy area
GWAS
Integrating GWAS and Transcriptomics to Identify Genes Involved in Seed Dormancy in Rice
QTL detection
Genetic dissection of pre-harvest sprouting resistance in an upland rice cultivar
Oriza japonica
Functionnal validation Oryza sativa
OsVP1 activates Sdr4 expression to control rice seed dormancy via the ABA signaling pathway Control of rice pre-harvest sprouting by glutaredoxin-mediated abscisic acid signaling
Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice
A bZIP factor, TRAB1, interacts with VP1 and mediates abscisic acid-induced transcription
Contribution of wild relative
ABA regulation
Recently, key regulators of ABA biosynthesis or signaling pathway have been characterized: LEC2, ABI3, and DOG1 in Arabidopsis [[11], [12], [13], [14]]; TaPHS1 and TaMFT in wheat [2,15]; VP1 in maize [16]; and OsFbx352, OsNCED3, OsPDS, OsCRTISO, β-OsLCY, OsZDS, OsVP1, Sdr4, OsDSG1, OsABI3, OsABI5, PHS8, PHS9, and OsMFT2 in rice [1,7,[17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30]]. All of these genes control seed dormancy, but their regulatory mechanisms remain elusive.
Wheat case
[Identification of QTLs and a Candidate Gene for Reducing Pre-Harvest Sprouting in Aegilops tauschii–Triticum aestivum Chromosome Segment Substitution Line](Identification of QTLs and a Candidate Gene for Reducing Pre-Harvest Sprouting in Aegilops tauschii–Triticum aestivum Chromosome Segment Substitution Lines)
Comaparative genomics for identification of candidate genes
Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison