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Profiling of Barley, Wheat, and Rye FPG and OGG1 Genes during Grain Germination

by Sylwia Kowalik and Jolanta Groszyk

Int. J. Mol. Sci. 2023, 24(15), 12354; https://doi.org/10.3390/ijms241512354 - 2 Aug 2023

Cited by 2 | Viewed by 1191

Abstract

This research is about the profiling of barley (Hordeum vulgare L.), wheat (Triticum aestivum L.), and rye (Secale cereale L.) FPG and OGG1 genes during grain germination. During seed germination, reactive oxygen species accumulate, which leads to DNA damage. In [...] Read more.

This research is about the profiling of barley (Hordeum vulgare L.), wheat (Triticum aestivum L.), and rye (Secale cereale L.) FPG and OGG1 genes during grain germination. During seed germination, reactive oxygen species accumulate, which leads to DNA damage. In the base excision repair (BER) system, the enzymes formamidopyrimidine DNA glycosylase (FPG) and 8-oxoguanine DNA glycosylase (OGG1), among others, are responsible for repairing such damage. We decided to check how the expression of genes encoding these two enzymes changes in germinating grains. Spring varieties of barley, wheat, and rye from the previous growing season were used in the study. Expression level changes were checked using Real-Time PCR. After analyzing the obtained results, the maximum expression levels of FPG and OGG1 genes during germination were determined for barley, wheat, and rye. The results of the study show differences in expression levels specific to each species. The highest expression was observed at different time points for each of them. There were no differences in the highest expression for FPG and OGG1 within one species. In conclusion, the research provides information on how the level of FPG and OGG1 gene expression changes during the germination process in cereals. This is the first study looking at the expression levels of these two genes in cereals. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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21 pages, 5497 KiB

Open AccessArticle

Transcriptomic Analysis of the Dehydration Rate of Mature Rice (Oryza sativa) Seeds

by Zhongqi Liu, Jinxin Gui, Yuntao Yan, Haiqing Zhang and Jiwai He

Int. J. Mol. Sci. 2023, 24(14), 11527; https://doi.org/10.3390/ijms241411527 - 16 Jul 2023

Viewed by 1580

Abstract

In this study, a transcriptomic analysis of the dehydration rate of mature rice seeds was conducted to explore candidate genes related to the dehydration rate and provide a theoretical basis for breeding and utilization. We selected two rice cultivars for testing (Baghlani Nangarhar, [...] Read more.

In this study, a transcriptomic analysis of the dehydration rate of mature rice seeds was conducted to explore candidate genes related to the dehydration rate and provide a theoretical basis for breeding and utilization. We selected two rice cultivars for testing (Baghlani Nangarhar, an extremely rapid dehydration genotype, and Saturn, a slow dehydration genotype) based on the results determined by previous studies conducted on the screening of 165 germplasm materials for dehydration rate phenotypes. A rapid dehydration experiment performed on these two types of seeds was conducted. Four comparative groups were set up under control and dehydration conditions. The differentially expressed genes (DEGs) were quantified via transcriptome sequencing and real-time quantitative PCR (RT-qPCR). GO (Gene ontology) and KEGG(Kyoto Encyclopedia of Genes and Genomes) analyses were also conducted. In Baghlani Nangarhar, 53 DEGs were screened, of which 33 were up-regulated and 20 were down-regulated. In Saturn, 25 DEGs were screened, of which 19 were up-regulated and 6 were down-regulated. The results of the GO analysis show that the sites of action of the differentially expressed genes enriched in the rapid dehydration modes are concentrated in the cytoplasm, internal components of the membrane, and nucleosomes. They play regulatory roles in the processes of catalysis, binding, translocation, transcription, protein folding, degradation, and replication. They are also involved in adaptive responses to adverse external environments, such as reactive oxygen species and high temperature. The KEGG analysis showed that protein processing in the endoplasmic reticulum, amino acid biosynthesis, and oxidative phosphorylation were the main metabolic pathways that were enriched. The key differentially expressed genes and the most important metabolic pathways identified in the rapidly and slowly dehydrated genotypes were protein processing in the endoplasmic reticulum and oxidative phosphorylation metabolism. They were presumed to have important regulatory roles in the mechanisms of stress/defense, energy metabolism, protein synthesis/folding, and signal transduction during the dehydration and drying of mature seeds. The results of this study can potentially provide valuable information for further research on the genes and metabolic pathways related to the dehydration rate of mature rice seeds, and provide theoretical guidance for the selection and breeding of new rice germplasm that can be rapidly dehydrated at the mature stage. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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13 pages, 5408 KiB

Open AccessArticle

Triphosphate Tunnel Metalloenzyme 2 Acts as a Downstream Factor of ABI4 in ABA-Mediated Seed Germination

by Yu-Rui Feng, Ting-Ting Li, Shi-Jia Wang, Ying-Tang Lu and Ting-Ting Yuan

Int. J. Mol. Sci. 2023, 24(10), 8994; https://doi.org/10.3390/ijms24108994 - 19 May 2023

Cited by 1 | Viewed by 1536

Abstract

Seed germination is a complex process that is regulated by various exogenous and endogenous factors, in which abscisic acid (ABA) plays a crucial role. The triphosphate tunnel metalloenzyme (TTM) superfamily exists in all living organisms, but research on its biological role is limited. [...] Read more.

Seed germination is a complex process that is regulated by various exogenous and endogenous factors, in which abscisic acid (ABA) plays a crucial role. The triphosphate tunnel metalloenzyme (TTM) superfamily exists in all living organisms, but research on its biological role is limited. Here, we reveal that TTM2 functions in ABA-mediated seed germination. Our study indicates that TTM2 expression is enhanced but repressed by ABA during seed germination. Promoted TTM2 expression in 35S::TTM2-FLAG rescues ABA-mediated inhibition of seed germination and early seedling development and ttm2 mutants exhibit lower seed germination rate and reduced cotyledon greening compared with the wild type, revealing that the repression of TTM2 expression is required for ABA-mediated inhibition of seed germination and early seedling development. Further, ABA inhibits TTM2 expression by ABA insensitive 4 (ABI4) binding of TTM2 promoter and the ABA-insensitive phenotype of abi4-1 with higher TTM2 expression can be rescued by mutation of TTM2 in abi4-1 ttm2-1 mutant, indicating that TTM2 acts downstream of ABI4. In addition, TTM1, a homolog of TTM2, is not involved in ABA-mediated regulation of seed germination. In summary, our findings reveal that TTM2 acts as a downstream factor of ABI4 in ABA-mediated seed germination and early seedling growth. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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15 pages, 5385 KiB

Open AccessArticle

Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination

by Heng Zhang, Guang Chen, Heng Xu, Sasa Jing, Yingying Jiang, Ziwen Liu, Hua Zhang, Fulin Wang, Xiangyang Hu and Ying Zhu

Int. J. Mol. Sci. 2023, 24(10), 8710; https://doi.org/10.3390/ijms24108710 - 13 May 2023

Cited by 7 | Viewed by 2712

Abstract

Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between [...] Read more.

Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dry seeds and the germinating seeds. Of these DEGs, 7109 were identified in both the embryo and endosperm, 3953 were embryo specific, and 3329 were endosperm specific. The embryo-specific DEGs were enriched in the plant-hormone signal-transduction pathway, while the endosperm-specific DEGs were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis. We categorized these DEGs into early-, intermediate-, and late-stage genes, as well as consistently responsive genes, which can be enriched in various pathways related to seed germination. Transcription-factor (TF) analysis showed that 643 TFs from 48 families were differentially expressed during seed germination. Moreover, 12 unfolded protein response (UPR) pathway genes were induced by seed germination, and the knockout of OsBiP2 resulted in reduced germination rates compared to the wild type. This study enhances our understanding of gene responses in the embryo and endosperm during seed germination and provides insight into the effects of UPR on seed germination in rice. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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25 pages, 4518 KiB

Open AccessArticle

Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice

by Dandan Chen, Wenli Zou, Mingpei Zhang, Jindong Liu, Liang Chen, Ting Peng and Guoyou Ye

Int. J. Mol. Sci. 2023, 24(7), 6117; https://doi.org/10.3390/ijms24076117 - 24 Mar 2023

Cited by 1 | Viewed by 2128

Abstract

Seed dormancy is a key factor used to determine seed germination in rice production. So far, only a few genes controlling seed dormancy have been reported, and the genetic mechanism of rice seed dormancy is still elusive. In this study, a population of [...] Read more.

Seed dormancy is a key factor used to determine seed germination in rice production. So far, only a few genes controlling seed dormancy have been reported, and the genetic mechanism of rice seed dormancy is still elusive. In this study, a population of 195 diverse re-sequenced accessions from 40 countries was evaluated for the seed germination rate (GR) without dormancy breaking (WDB) as a control and under dry heating (DH) and gibberellic acid (GA) treatments, as dormancy breaking agents to identify QTLs for seed dormancy. Phenotypic assessment revealed that these accessions had abundant variations in seed dormancy. GWAS using 1,120,223 high-quality single nucleotide polymorphisms (SNPs) and a mixed linear model (MLM) incorporating both principal components (PCs) and kinship (K) identified 30 QTLs on 10 chromosomes, accounting for 7.3–20.4% of the phenotypic variance in GR. Ten of the QTLs were located in the regions of previously reported QTLs, while the rest were novel ones. Thirteen high-confidence candidate genes were predicted for the four QTLs detected in two or three conditions (qGR4-4, qGR4-5, qGR8 and qGR11-4) and one QTL with a large effect (qGR3). These genes were highly expressed during seed development and were significantly regulated by various hormone treatments. This study provides new insights into the genetic and molecular basis of rice seed dormancy/germination. The accessions with moderate and strong dormancy and markers for the QTLs and candidate genes are useful for attaining a proper level of seed dormancy. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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14 pages, 4109 KiB

Open AccessArticle

Transcriptome and Proteome Analysis Revealed That Hormone and Reactive Oxygen Species Synergetically Regulate Dormancy of Introgression Line in Rice (Oryza sativa L.)

by Naihui Guo, Shengjia Tang, Jiayu Wang, Shikai Hu, Shaoqing Tang, Xiangjin Wei, Gaoneng Shao, Guiai Jiao, Zhonghua Sheng and Peisong Hu

Int. J. Mol. Sci. 2023, 24(7), 6088; https://doi.org/10.3390/ijms24076088 - 23 Mar 2023

Cited by 4 | Viewed by 1914

Abstract

Dormancy is a complex agronomy phenotype controlled by multiple signaling and a key trait repressing pre-harvest sprouting (PHS). However, the signaling network of dormancy remains unclear. In this study, we used Zhonghua11 (ZH11) with a weak dormancy, and Introgression line (IL) with a [...] Read more.

Dormancy is a complex agronomy phenotype controlled by multiple signaling and a key trait repressing pre-harvest sprouting (PHS). However, the signaling network of dormancy remains unclear. In this study, we used Zhonghua11 (ZH11) with a weak dormancy, and Introgression line (IL) with a strong dormancy to study the mechanism of hormones and reactive oxygen species (ROS) crosstalk regulating rice dormancy. The germination experiment showed that the germination rate of ZH11 was 76.86%, while that of IL was only 1.25%. Transcriptome analysis showed that there were 1658 differentially expressed genes (DEGs) between IL and ZH11, of which 577 were up-regulated and 1081 were down-regulated. Additionally, DEGs were mainly enriched in oxidoreductase activity, cell periphery, and plant hormone signal transduction pathways. Tandem mass tags (TMT) quantitative proteomics analysis showed 275 differentially expressed proteins (DEPs) between IL and ZH11, of which 176 proteins were up-regulated, 99 were down-regulated, and the DEPs were mainly enriched in the metabolic process and oxidation-reduction process. The comprehensive transcriptome and proteome analysis showed that their correlation was very low, and only 56 genes were co-expressed. Hormone content detection showed that IL had significantly lower abscisic acid (ABA) contents than the ZH11 while having significantly higher jasmonic acid (JA) contents than the ZH11. ROS content measurement showed that the hydrogen peroxide (H₂O₂) content of IL was significantly lower than the ZH11, while the production rate of superoxide anion (O₂^.−) was significantly higher than the ZH11. These results indicate that hormones and ROS crosstalk to regulate rice dormancy. In particular, this study has deepened our mechanism of ROS and JA crosstalk regulating rice dormancy and is conducive to our precise inhibition of PHS. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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16 pages, 4537 KiB

Open AccessArticle

Characterizing the Status of Energetic Metabolism of Dinoflagellate Resting Cysts under Mock Conditions of Marine Sediments via Physiological and Transcriptional Measurements

by Fengting Li, Caixia Yue, Yunyan Deng and Ying Zhong Tang

Int. J. Mol. Sci. 2022, 23(23), 15033; https://doi.org/10.3390/ijms232315033 - 30 Nov 2022

Cited by 3 | Viewed by 1573

Abstract

Similar to the seeds of higher plants, resting cysts, a non-motile, benthic, and dormant stage in the life history of many dinoflagellate species, play vital roles via germination in the seasonal dynamics and particularly the initiation of harmful algal blooms (HABs) of dinoflagellates. [...] Read more.

Similar to the seeds of higher plants, resting cysts, a non-motile, benthic, and dormant stage in the life history of many dinoflagellate species, play vital roles via germination in the seasonal dynamics and particularly the initiation of harmful algal blooms (HABs) of dinoflagellates. It is thus crucial for resting cysts to balance between the energetic catabolism for viability maintenance and the energy preservation for germination during their dormancy. Despite this importance, studies on how resting cysts of dinoflagellates accomplish energetic metabolism in marine sediment have been virtually absent. In this study, using the cosmopolitan HABs-causing species Scrippsiella acuminata as a representative, we measured the transcriptional activity of the most efficient pathway of the energy catabolism tricarboxylic acid (TCA) cycle, cell viability (via neutral red staining), and the cellular ATP content of resting cysts under a set of mock conditions in marine sediments (e.g., 4 °C, darkness, and anoxia) for a maximum period of one year. Based on the correlation analyses among the expression levels of genes, cyst viability, and ATP content, we revealed that the TCA cycle was still a crucial pathway of energetic catabolism for resting cysts under aerobic conditions, and its expression was elevated at higher temperatures, light irradiation, and the early stage of dormancy. Under anaerobic conditions, however, the TCA cycle pathway ceased expression in resting cysts, as also supported by ATP measurements. Our results have laid a cornerstone for the comprehensive revelation of the energetic metabolism and biochemical processes of dormancy of resting cysts in marine sediments. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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16 pages, 3283 KiB

Open AccessArticle

FtbZIP12 Positively Regulates Responses to Osmotic Stress in Tartary Buckwheat

by Wenfeng Weng, Xiang Lu, Meiliang Zhou, Anjing Gao, Xin Yao, Yong Tang, Weijiao Wu, Chao Ma, Qing Bai, Ruiqi Xiong and Jingjun Ruan

Int. J. Mol. Sci. 2022, 23(21), 13072; https://doi.org/10.3390/ijms232113072 - 28 Oct 2022

Cited by 3 | Viewed by 1582

Abstract

ABFs play a key role in regulating plant osmotic stress. However, in Tartary buckwheat, data on the role of ABF genes in osmotic stress remain limited and its associated mechanism in osmoregulation remain nebulous. Herein, a novel ABF family in Tartary buckwheat, FtbZIP12 [...] Read more.

ABFs play a key role in regulating plant osmotic stress. However, in Tartary buckwheat, data on the role of ABF genes in osmotic stress remain limited and its associated mechanism in osmoregulation remain nebulous. Herein, a novel ABF family in Tartary buckwheat, FtbZIP12, was cloned and characterized. FtbZIP12 is a transcriptional activator located in the nucleus; its expression is induced by NaCl, mannitol, and abscisic acid (ABA). Atopic expression of FtbZIP12 in Arabidopsis promoted seed germination, reduced damage to primary roots, and improved the tolerance of seedlings to osmotic stress. The quantitative realtime polymerase chain reaction (RT-qPCR) results showed that the expressions of the typical genes related to stress, the SOS pathway, and the proline synthesis pathway in Arabidopsis were significantly (p < 0.05) upregulated under osmotic stress. FtbZIP12 improved the osmotic pressure resistance by reducing the damage caused by reactive oxygen species to plants and maintained plant homeostasis by upregulating the expression of genes related to stress, osmotic regulation, and ion homeostasis. This study identified a key candidate gene for understanding the mechanism underlying osmotic-stress-regulated function in Tartary buckwheat, thereby providing a theoretical basis for improving its yield and quality. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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19 pages, 9635 KiB

Open AccessArticle

Identification and Investigation of the Genetic Variations and Candidate Genes Responsible for Seed Weight via GWAS in Paper Mulberry

by Yanmin Hu, Xianjun Peng and Shihua Shen

Int. J. Mol. Sci. 2022, 23(20), 12520; https://doi.org/10.3390/ijms232012520 - 19 Oct 2022

Cited by 2 | Viewed by 1688

Abstract

Seeds directly determine the survival and population size of woody plants, but the genetic basis of seed weight in woody plants remain poorly explored. To identify genetic variations and candidate genes responsible for seed weight in natural woody populations, we investigated the hundred-seed [...] Read more.

Seeds directly determine the survival and population size of woody plants, but the genetic basis of seed weight in woody plants remain poorly explored. To identify genetic variations and candidate genes responsible for seed weight in natural woody populations, we investigated the hundred-seed weight of 198 paper mulberry individuals from different areas. Our results showed that the hundred-seed weight of paper mulberry was significantly associated with the bioclimatic variables of sampling sites, which increased from south to north along the latitudinal-temperature gradient. Using 2,414,978 high-quality SNPs from re-sequencing data, the genome-wide association analysis of the hundred-seed weight was performed under three models, which identified 148, 19 and 12 associated genes, respectively. Among them, 25 candidate genes were directly hit by the significant SNPs, including the WRKY transcription factor, fatty acid desaturase, F-box protein, etc. Most importantly, we identified three crucial genetic variations in the coding regions of candidate genes (Bp02g2123, Bp01g3291 and Bp10g1642), and significant differences in the hundred-seed weight were detected among the individuals carrying different genotypes. Further analysis revealed that Bp02g2123 encoding a fatty acid desaturase (FAD) might be a key factor affecting the seed weight and local climate adaptation of woody plants. Furthermore, the genome-wide investigation and expression analysis of FAD genes were performed, and the results suggested that BpFADs widely expressed in various tissues and responded to multiple phytohormone and stress treatments. Overall, our study identifies valuable genetic variations and candidate genes, and provides a better understanding of the genetic basis of seed weight in woody plants. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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21 pages, 5229 KiB

Open AccessArticle

Identification of miRNAs Mediating Seed Storability of Maize during Germination Stage by High-Throughput Sequencing, Transcriptome and Degradome Sequencing

by Yongfeng Song, Zhichao Lv, Yue Wang, Chunxiang Li, Yue Jia, Yong Zhu, Mengna Cao, Yu Zhou, Xing Zeng, Zhenhua Wang, Lin Zhang and Hong Di

Int. J. Mol. Sci. 2022, 23(20), 12339; https://doi.org/10.3390/ijms232012339 - 15 Oct 2022

Cited by 3 | Viewed by 1982

Abstract

Seed storability is an important trait for improving grain quality and germplasm conservation, but little is known about the regulatory mechanisms and gene networks involved. MicroRNAs (miRNAs) are small non-coding RNAs regulating the translation and accumulation of their target mRNAs by means of [...] Read more.

Seed storability is an important trait for improving grain quality and germplasm conservation, but little is known about the regulatory mechanisms and gene networks involved. MicroRNAs (miRNAs) are small non-coding RNAs regulating the translation and accumulation of their target mRNAs by means of sequence complementarity and have recently emerged as critical regulators of seed germination. Here, we used the germinating embryos of two maize inbred lines with significant differences in seed storability to identify the miRNAs and target genes involved. We identified a total of 218 previously known and 448 novel miRNAs by miRNA sequencing and degradome analysis, of which 27 known and 11 newly predicted miRNAs are differentially expressed in two maize inbred lines, as measured by Gene Ontology (GO) enrichment analysis. We then combined transcriptome sequencing and real-time quantitative polymerase chain reaction (RT-PCR) to screen and confirm six pairs of differentially expressed miRNAs associated with seed storability, along with their negative regulatory target genes. The enrichment analysis suggested that the miRNAs/target gene mediation of seed storability occurs via the ethylene activation signaling pathway, hormone synthesis and signal transduction, as well as plant organ morphogenesis. Our results should help elucidate the mechanisms through which miRNAs are involved in seed storability in maize. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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21 pages, 4771 KiB

Open AccessArticle

A Long Noncoding RNA Derived from lncRNA–mRNA Networks Modulates Seed Vigor

by Qiaoli Gao, Jinzhao Liu, Huibin Weng, Xi Yuan, Wuming Xiao and Hui Wang

Int. J. Mol. Sci. 2022, 23(16), 9472; https://doi.org/10.3390/ijms23169472 - 22 Aug 2022

Cited by 7 | Viewed by 2713

Abstract

The discovery of long noncoding RNAs (lncRNAs) has filled a great gap in our understanding of posttranscriptional gene regulation in a variety of biological processes related to plant stress responses. However, systematic analyses of the lncRNAs expressed in rice seeds that germinate under [...] Read more.

The discovery of long noncoding RNAs (lncRNAs) has filled a great gap in our understanding of posttranscriptional gene regulation in a variety of biological processes related to plant stress responses. However, systematic analyses of the lncRNAs expressed in rice seeds that germinate under cold stress have been elusive. In this study, we performed strand-specific whole transcriptome sequencing in germinated rice seeds under cold stress and normal temperature. A total of 6258 putative lncRNAs were identified and expressed in a stage-specific manner compared to mRNA. By investigating the targets of differentially expressed (DE) lncRNAs of LT-I (phase I of low temperature)/NT-I (phase I of normal temperature), it was shown that the auxin-activated signaling pathway was significantly enriched, and twenty-three protein-coding genes with most of the members of the SAUR family located in chromosome 9 were identified as the candidate target genes that may interact with five lncRNAs. A seed vigor-related lncRNA, SVR, which interplays with the members of the SAUR gene family in cis was eventually identified. The CRISPR/Cas 9 engineered mutations in SVR cause delay of germination. The findings provided new insights into the connection between lncRNAs and the auxin-activated signaling pathway in the regulation of rice seed vigor. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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Review

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23 pages, 1738 KiB

Open AccessReview

Underlying Biochemical and Molecular Mechanisms for Seed Germination

by Muhammad Awais Farooq, Wei Ma, Shuxing Shen and Aixia Gu

Int. J. Mol. Sci. 2022, 23(15), 8502; https://doi.org/10.3390/ijms23158502 - 31 Jul 2022

Cited by 37 | Viewed by 8463

Abstract

With the burgeoning population of the world, the successful germination of seeds to achieve maximum crop production is very important. Seed germination is a precise balance of phytohormones, light, and temperature that induces endosperm decay. Abscisic acid and gibberellins—mainly with auxins, ethylene, and [...] Read more.

With the burgeoning population of the world, the successful germination of seeds to achieve maximum crop production is very important. Seed germination is a precise balance of phytohormones, light, and temperature that induces endosperm decay. Abscisic acid and gibberellins—mainly with auxins, ethylene, and jasmonic and salicylic acid through interdependent molecular pathways—lead to the rupture of the seed testa, after which the radicle protrudes out and the endosperm provides nutrients according to its growing energy demand. The incident light wavelength and low and supra-optimal temperature modulates phytohormone signaling pathways that induce the synthesis of ROS, which results in the maintenance of seed dormancy and germination. In this review, we have summarized in detail the biochemical and molecular processes occurring in the seed that lead to the germination of the seed. Moreover, an accurate explanation in chronological order of how phytohormones inside the seed act in accordance with the temperature and light signals from outside to degenerate the seed testa for the thriving seed’s germination has also been discussed. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Seed Dormancy and Germination)

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