OsGRETCHENHAGEN3-2 modulates rice seed storability via accumulation of abscisic acid and protective substances

The role of redox-active small molecules and oxidative protein post-translational modifications in seed aging

Seed vigor is a crucial indicator of seed quality. Variations in seed vigor are closely associated with seed properties and storage conditions. The vigor of mature seeds progressively declines during storage, which is called seed deterioration or aging. Seed aging induces a cascade of cellular damage, including impaired subcellular structures and macromolecules, such as lipids, proteins, and DNA. Reactive oxygen species (ROS) act as signaling molecules during seed aging causing oxidative damage and triggering programmed cell death (PCD). Mitochondria are the main site of ROS production and change morphology and function before other organelles during aging. The roles of other small redox-active molecules in regulating cell and seed vigor, such as nitric oxide (NO) and hydrogen sulfide (H2S), were identified later. ROS, NO, and H2S typically regulate protein function through post-translational modifications (PTMs), including carbonylation, S-glutathionylation, S-nitrosylation, and S-sulfhydration. These signaling molecules as well as the PTMs they induce interact to regulate cell fate and seed vigor. This review was conducted to describe the physiological changes and underlying molecular mechanisms that in seed aging and provides a comprehensive view of how ROS, NO, and H2S affect cell death and seed vigor.

A peroxisomal cinnamate:CoA ligase-dependent phytohormone metabolic cascade in submerged rice germination

The mechanism underlying the ability of rice to germinate underwater is a largely enigmatic but key research question highly relevant to rice cultivation. Moreover, although rice is known to accumulate salicylic acid (SA), SA biosynthesis is poorly defined, and its role in underwater germination is unknown. It is also unclear whether peroxisomes, organelles essential to oilseed germination and rice SA accumulation, play a role in rice germination. Here, we show that submerged imbibition of rice seeds induces SA accumulation to promote germination in submergence. Two submergence-induced peroxisomal Oryza sativa cinnamate:CoA ligases (OsCNLs) are required for this SA accumulation. SA exerts this germination-promoting function by inducing indole-acetic acid (IAA) catabolism through the IAA-amino acid conjugating enzyme GH3. The metabolic cascade we identified may potentially be adopted in agriculture to improve the underwater germination of submergence-intolerant rice varieties. SA pretreatment is also a promising strategy to improve submerged rice germination in the field.

Allantoate Amidohydrolase OsAAH is Essential for Preharvest Sprouting Resistance in Rice

Preharvest sprouting (PHS) is an undesirable trait that decreases yield and quality in rice production. Understanding the genes and regulatory mechanisms underlying PHS is of great significance for breeding PHS-resistant rice. In this study, we identified a mutant, preharvest sprouting 39 (phs39), that exhibited an obvious PHS phenotype in the field. MutMap+ analysis and transgenic experiments demonstrated that OsAAH, which encodes allantoate amidohydrolase, is the causal gene of phs39 and is essential for PHS resistance. OsAAH was highly expressed in roots and leaves at the heading stage and gradually increased and then weakly declined in the seed developmental stage. OsAAH protein was localized to the endoplasmic reticulum, with a function of hydrolyzing allantoate in vitro. Disruption of OsAAH increased the levels of ureides (allantoate and allantoin) and activated the tricarboxylic acid (TCA) cycle, and thus increased energy levels in developing seeds. Additionally, the disruption of OsAAH significantly increased asparagine, arginine, and lysine levels, decreased tryptophan levels, and decreased levels of indole-3-acetic acid (IAA) and abscisic acid (ABA). Our findings revealed that the OsAAH of ureide catabolism is involved in the regulation of rice PHS via energy and hormone metabolisms, which will help to facilitate the breeding of rice PHS-resistant varieties.

Chalkiness and premature controlled by energy homeostasis in OsNAC02 Ko-mutant during vegetative endosperm development

BACKGROUND

Chalkiness is a common phenotype induced by various reasons, such as abiotic stress or the imbalance of starch synthesis and metabolism during the development period. However, the reason mainly for one gene losing its function such as NAC (TFs has a large family in rice) which may cause premature is rarely known to us.

RESULTS

The Ko-Osnac02 mutant demonstrated an obviously early maturation stage compared to the wild type (WT) with 15 days earlier. The result showed that the mature endosperm of Ko-Osnac02 mutant exhibited chalkiness, characterized by white-core and white-belly in mature endosperm. As grain filling rate is a crucial factor in determining the yield and quality of rice (Oryza sativa, ssp. japonica), it's significant that mutant has a lower amylose content (AC) and higher soluble sugar content in the mature endosperm. Interestingly among the top DEGs in the RNA sequencing of N2 (3DAP) and WT seeds revealed that the OsBAM2 (LOC_Os10g32810) expressed significantly high in N2 mutant, which involved in Maltose up-regulated by the starch degradation. As Prediction of Protein interaction showed in the chalky endosperm formation in N2 seeds (3 DAP), seven genes were expressed at a lower-level which should be verified by a heatmap diagrams based on DEGs of N2 versus WT. The Tubulin genes controlling cell cycle are downregulated together with the MCM family genes MCM4 ( ↓), MCM7 ( ↑), which may cause white-core in the early endosperm development. In conclusion, the developing period drastically decreased in the Ko-Osnac02 mutants, which might cause the chalkiness in seeds during the early endosperm development.

CONCLUSIONS

The gene OsNAC02 which controls a great genetic co-network for cell cycle regulation in early development, and KO-Osnac02 mutant shows prematurity and white-core in endosperm.

ABA Inhibits Rice Seed Aging by Reducing H2O2 Accumulation in the Radicle of Seeds

The seed, a critical organ in higher plants, serves as a primary determinant of agricultural productivity, with its quality directly influencing crop yield. Improper storage conditions can diminish seed vigor, adversely affecting seed germination and seedling establishment. Therefore, understanding the seed-aging process and exploring strategies to enhance seed-aging resistance are paramount. In this study, we observed that seed aging during storage leads to a decline in seed vigor and can coincide with the accumulation of hydrogen peroxide (H2O2) in the radicle, resulting in compromised or uneven germination and asynchronous seedling emergence. We identified the abscisic acid (ABA) catabolism gene, abscisic acid 8'-hydroxylase 2 (OsABA8ox2), as significantly induced by aging treatment. Interestingly, transgenic seeds overexpressing OsABA8ox2 exhibited reduced seed vigor, while gene knockout enhanced seed vigor, suggesting its role as a negative regulator. Similarly, seeds pretreated with ABA or diphenyleneiodonium chloride (DPI, an H2O2 inhibitor) showed increased resistance to aging, with more robust early seedling establishment. Both OsABA8ox2 mutant seeds and seeds pretreated with ABA or DPI displayed lower H2O2 content during aging treatment. Overall, our findings indicate that ABA mitigates rice seed aging by reducing H2O2 accumulation in the radicle. This study offers valuable germplasm resources and presents a novel approach to enhancing seed resistance against aging.

OsCSD2 and OsCSD3 Enhance Seed Storability by Modulating Antioxidant Enzymes and Abscisic Acid in Rice

Seed deterioration during storage poses a significant challenge to rice production, leading to a drastic decline in both edible quality and viability, thereby impacting overall crop yield. This study aimed to address this issue by further investigating candidate genes associated with two previously identified QTLs for seed storability through genome association analysis. Among the screened genes, two superoxide dismutase (SOD) genes, OsCSD2 (Copper/zinc Superoxide Dismutase 2) and OsCSD3, were selected for further study. The generation of overexpression and CRISPR/Cas9 mutant transgenic lines revealed that OsCSD2 and OsCSD3 play a positive regulatory role in enhancing rice seed storability. Subsequent exploration of the physiological mechanisms demonstrated that overexpression lines exhibited lower relative electrical conductivity, indicative of reduced cell membrane damage, while knockout lines displayed the opposite trend. Furthermore, the overexpression lines of OsCSD2 and OsCSD3 showed significant increases not only in SOD but also in CAT and POD activities, highlighting an augmented antioxidant system in the transgenic seeds. Additionally, hormone profiling indicated that ABA contributed to the improved seed storability observed in these lines. In summary, these findings provide valuable insights into the regulatory mechanisms of OsCSDs in rice storability, with potential applications for mitigating grain loss and enhancing global food security.

Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study

The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only qPP2 was detected repeatedly two times. The candidate gene analysis showed that LOC_Os02g57530 (ETR3), LOC_Os01g57610 (GH3.1) and LOC_Os04g0425 (CTB2) were the candidate genes for qPP2, qPP1 and qPP4, respectively. The haplotype (Hap) analysis revealed that Hap1 of ETR3, Hap1 and 3 of GH3.1 and Hap2 and 5 of CTB2 are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of ETR3 is a favorable allele for the germination percentage; Hap3 of GH3.1 is an elite allele for seed germination; and Hap5 of CTB2 is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.

Seed Longevity and Ageing: A Review on Physiological and Genetic Factors with an Emphasis on Hormonal Regulation

Upon storage, seeds inevitably age and lose their viability over time, which determines their longevity. Longevity correlates with successful seed germination and enhancing this trait is of fundamental importance for long-term seed storage (germplasm conservation) and crop improvement. Seed longevity is governed by a complex interplay between genetic factors and environmental conditions experienced during seed development and after-ripening that will shape seed physiology. Several factors have been associated with seed ageing such as oxidative stress responses, DNA repair enzymes, and composition of seed layers. Phytohormones, mainly abscisic acid, auxins, and gibberellins, have also emerged as prominent endogenous regulators of seed longevity, and their study has provided new regulators of longevity. Gaining a thorough understanding of how hormonal signalling genes and pathways are integrated with downstream mechanisms related to seed longevity is essential for formulating strategies aimed at preserving seed quality and viability. A relevant aspect related to research in seed longevity is the existence of significant differences between results depending on the seed equilibrium relative humidity conditions used to study seed ageing. Hence, this review delves into the genetic, environmental and experimental factors affecting seed ageing and longevity, with a particular focus on their hormonal regulation. We also provide gene network models underlying hormone signalling aimed to help visualize their integration into seed longevity and ageing. We believe that the format used to present the information bolsters its value as a resource to support seed longevity research for seed conservation and crop improvement.

Full-Length Transcriptome Sequencing Reveals the Molecular Mechanism of Metasequoia glyptostroboides Seed Responding to Aging

Metasequoia glyptostroboides, Hu and W. C. Cheng, as the only surviving relict species of the Taxodiaceae Metasequoia genus, is a critically endangered and protected species in China. There is a risk of extinction due to the low vigor of M. glyptostroboides seeds, and the physiological mechanism of seed aging in M. glyptostroboides is not yet clear. In order to investigate the physiological and molecular mechanisms underlying the aging process of M. glyptostroboides seeds, we analyzed the antioxidant system and transcriptome at 0, 2, 4, 6, and 8 days after artificial accelerated aging treatment at 40 °C and 100% relative humidity. It was found that the germination percentage of fresh dried M. glyptostroboides seeds was 54 ± 5.29%, and significantly declined to 9.33 ± 1.88% after 6 days of aging, and then gradually decreased until the seed died on day 8. Superoxide dismutase (SOD) activity, ascorbic acid (AsA), glutathione (GSH) content and superoxide anion (O₂^·-) content and production rate significantly decreased, while malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) content and glutathione peroxidase (GPX) and catalase (CAT) activity gradually increased during the aging process. A total of 42,189 unigenes were identified in the whole transcriptome, and 40,446 (95.86%) unigenes were annotated in at least one protein database. A total of 15,376 differentially expressed genes (DEGs) were obtained; KEGG enrichment analysis results revealed that seed aging may be mainly involved in the protein-processing pathways in endoplasmic reticulum, oxidative phosphorylation, and ascorbate and aldarate metabolism. Weighted gene co-expression network analysis (WGCNA) revealed that the dark magenta, orange, and medium purple modules were highly correlated with physiological indicators such as SOD, CAT, and GSH and further identified 40 hub genes such as Rboh, ACO, HSF, and CML as playing important roles in the antioxidant network of M. glyptostroboides seeds. These findings provide a broader perspective for studying the regulatory mechanism of seed aging and a large number of potential target genes for the breeding of other endangered gymnosperms.

Seedling establishment: The neglected trait in the seed longevity field

Seed longevity is a central actor in plant germplasm resource conservation, species reproduction, geographical distribution, crop yield and quality and food processing and safety. Seed longevity and vigor decrease gradually during storage, which directly influences seed germination and post-germination seedling establishment. It is noted that seedling establishment is a key shift from heterotropism to autotropism and is fueled by the energy reserved in the seeds per se. Numerous studies have demonstrated that expedited catabolism of triacylglycerols, fatty acid and sugars during seed storage is closely related to seed longevity. Storage of farm-saved seeds of elite cultivars for use in subsequent years is a common practice and it is recognized that aged seed (especially those stored under less-than-ideal conditions) can lead to poor seed germination, but the significance of poor seedling establishment as a separate factor capable of influencing crop yield has been overlooked. This review article summarizes the relationship between seed germination and seedling establishment and the effect of different seed reserves on seed longevity. Based on this, we emphasize the importance of simultaneous scoring of seedling establishment and germination percentage from aged seeds and discuss the reasons.

Biotechnological interventions for improving the seed longevity in cereal crops: progress and prospects

Seed longevity is a measure of the viability of seeds during long-term storage and is crucial for germplasm conservation and crop improvement programs. Also, longevity is an important trait for ensuring food and nutritional security. Thus, a better understanding of various factors regulating seed longevity is requisite to improve this trait and to minimize the genetic drift during the regeneration of germplasm. In particular, seed deterioration of cereal crops during storage adversely affects agricultural productivity and food security. The irreversible process of seed deterioration involves a complex interplay between different genes and regulatory pathways leading to: loss of DNA integrity, membrane damage, inactivation of storage enzymes and mitochondrial dysfunction. Identifying the genetic determinants of seed longevity and manipulating them using biotechnological tools hold the key to ensuring prolonged seed storage. Genetics and genomics approaches had identified several genomic regions regulating the longevity trait in major cereals such as: rice, wheat, maize and barley. However, very few studies are available in other Poaceae members, including millets. Deploying omics tools, including genomics, proteomics, metabolomics, and phenomics, and integrating the datasets will pinpoint the precise molecular determinants affecting the survivability of seeds. Given this, the present review enumerates the genetic factors regulating longevity and demonstrates the importance of integrated omics strategies to dissect the molecular machinery underlying seed deterioration. Further, the review provides a roadmap for deploying biotechnological approaches to manipulate the genes and genomic regions to develop improved cultivars with prolonged storage potential.

Identification and Functional Analysis of Long Non-Coding RNA (lncRNA) in Response to Seed Aging in Rice

Many lncRNAs have been shown to play a vital role in aging processes. However, how lncRNAs regulate seed aging remains unknown. In this study, we performed whole transcriptome strand-specific RNA sequencing of samples from rice embryos, analyzed the differences in expression of rice seed lncRNAs before and after artificial aging treatment (AAT), and systematically screened 6002 rice lncRNAs. During the AAT period, the expression levels of most lncRNAs (454) were downregulated and only four were upregulated among the 458 differentially expressed lncRNAs (DELs). Cis- or trans-regulated target genes of the four upregulated lncRNAs were mainly related to base repair, while 454 downregulated lncRNAs were related to plant-pathogen interaction, plant hormones, energy metabolism, and secondary metabolism. The pathways of DEL target genes were similar with those of differentially expressed mRNAs (DEGs). A competing endogenous RNA (ceRNA) network composed of 34 lncRNAs, 24 microRNAs (miRNA), and 161 mRNAs was obtained. The cDNA sequence of lncRNA LNC_037529 was obtained by rapid amplification of cDNA ends (RACE) cloning with a total length of 1325 bp, a conserved 5' end, and a non-conserved 3' end. Together, our findings indicate that genome-wide selection for lncRNA downregulation was an important mechanism for rice seed aging. LncRNAs can be used as markers of seed aging in rice. These findings provide a future path to decipher the underlying mechanism associated with lncRNAs in seed aging.

Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice

Highly seed vigor (SV) is essential for rice direct seeding (DS). Understanding the genetic mechanism of SV-related traits could contribute to increasing the efficiency of DS. However, only a few genes responsible for SV have been determined in rice, and the regulatory network of SV remains obscure. In this study, the seed germination rate (GR), seedling shoot length (SL), and shoot fresh weight (FW) related to SV traits were measured, and a genome-wide association study (GWAS) was conducted to detect high-quality loci responsible for SV using a panel of 346 diverse accessions. A total of 51 significant SNPs were identified and arranged into six quantitative trait locus (QTL) regions, including one (qGR1-1), two (qSL1-1, qSL1-2), and three (qFW1-1, qFW4-1, and qFW7-1) QTLs associated with GR, SL, and FW respectively, which were further validated using chromosome segment substitution lines (CSSLs). Integrating gene expression, gene annotation, and haplotype analysis, we found 21 strong candidate genes significantly associated with SV. In addition, the SV-related functions of LOC_Os01g11270 and LOC_Os01g55240 were further verified by corresponding CRISPR/Cas9 gene-edited mutants. Thus, these results provide clues for elucidating the genetic basis of SV control. The candidate genes or QTLs would be helpful for improving DS by molecular marker-assisted selection (MAS) breeding in rice.

Genome-Wide Identification of Auxin-Responsive GH3 Gene Family in Saccharum and the Expression of ScGH3-1 in Stress Response

Gretchen Hagen3 (GH3), one of the three major auxin-responsive gene families, is involved in hormone homeostasis in vivo by amino acid splicing with the free forms of salicylic acid (SA), jasmonic acid (JA) or indole-3-acetic acid (IAA). Until now, the functions of sugarcane GH3 (SsGH3) family genes in response to biotic stresses have been largely unknown. In this study, we performed a systematic identification of the SsGH3 gene family at the genome level and identified 41 members on 19 chromosomes in the wild sugarcane species, Saccharum spontaneum. Many of these genes were segmentally duplicated and polyploidization was the main contributor to the increased number of SsGH3 members. SsGH3 proteins can be divided into three major categories (SsGH3-I, SsGH3-II, and SsGH3-III) and most SsGH3 genes have relatively conserved exon-intron arrangements and motif compositions. Diverse cis-elements in the promoters of SsGH3 genes were predicted to be essential players in regulating SsGH3 expression patterns. Multiple transcriptome datasets demonstrated that many SsGH3 genes were responsive to biotic and abiotic stresses and possibly had important functions in the stress response. RNA sequencing and RT-qPCR analysis revealed that SsGH3 genes were differentially expressed in sugarcane tissues and under Sporisorium scitamineum stress. In addition, the SsGH3 homolog ScGH3-1 gene (GenBank accession number: OP429459) was cloned from the sugarcane cultivar (Saccharum hybrid) ROC22 and verified to encode a nuclear- and membrane-localization protein. ScGH3-1 was constitutively expressed in all tissues of sugarcane and the highest amount was observed in the stem pith. Interestingly, it was down-regulated after smut pathogen infection but up-regulated after MeJA and SA treatments. Furthermore, transiently overexpressed Nicotiana benthamiana, transduced with the ScGH3-1 gene, showed negative regulation in response to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum. Finally, a potential model for ScGH3-1-mediated regulation of resistance to pathogen infection in transgenic N. benthamiana plants was proposed. This study lays the foundation for a comprehensive understanding of the sequence characteristics, structural properties, evolutionary relationships, and expression of the GH3 gene family and thus provides a potential genetic resource for sugarcane disease-resistance breeding.

Seed Dormancy and Longevity: A Mutual Dependence or a Trade-Off?

Seed dormancy is an important agronomic trait in cereals and leguminous crops as low levels of seed dormancy during harvest season, coupled with high humidity, can cause preharvest sprouting. Seed longevity is another critical trait for commercial crop propagation and production, directly influencing seed germination and early seedling establishment. Both traits are precisely regulated by the integration of genetic and environmental cues. Despite the significance of these two traits in crop production, the relationship between them at the molecular level is still elusive, even with contradictory conclusions being reported. Some studies have proposed a positive correlation between seed dormancy and longevity in association with differences in seed coat permeability or seed reserve accumulation, whereas an increasing number of studies have highlighted a negative relationship, largely with respect to phytohormone-dependent pathways. In this review paper, we try to provide some insights into the interactions between regulatory mechanisms of genetic and environmental cues, which result in positive or negative relationships between seed dormancy and longevity. Finally, we conclude that further dissection of the molecular mechanism responsible for this apparently contradictory relationship between them is needed.

Understanding of Hormonal Regulation in Rice Seed Germination

Seed germination is a critical stage during the life cycle of plants. It is well known that germination is regulated by a series of internal and external factors, especially plant hormones. In Arabidopsis, many germination-related factors have been identified, while in rice, the important crop and monocot model species and the further molecular mechanisms and regulatory networks controlling germination still need to be elucidated. Hormonal signals, especially those of abscisic acid (ABA) and gibberellin (GA), play a dominant role in determining whether a seed germinates or not. The balance between the content and sensitivity of these two hormones is the key to the regulation of germination. In this review, we present the foundational knowledge of ABA and GA pathways obtained from germination research in Arabidopsis. Then, we highlight the current advances in the identification of the regulatory genes involved in ABA- or GA-mediated germination in rice. Furthermore, other plant hormones regulate seed germination, most likely by participating in the ABA or GA pathways. Finally, the results from some regulatory layers, including transcription factors, post-transcriptional regulations, and reactive oxygen species, are also discussed. This review aims to summarize our current understanding of the complex molecular networks involving the key roles of plant hormones in regulating the seed germination of rice.

Insights into the Regulation of Rice Seed Storability by Seed Tissue-Specific Transcriptomic and Metabolic Profiling

Non-dormant seeds are continuously aging and deteriorating during storage, leading to declining seed vigor, which is a challenge for the rice seed industry. Improving the storability of seeds is of great significance to ensure the quality of rice and national food security. Through a set of chromosome segment substitution lines population constructed using japonica rice NIP as donor parent and indica rice ZS97 as recurrent parent, we performed seed storability QTL analysis and selected four non-storable NILs to further investigate the storability regulatory mechanisms underlying it. The seeds were divided into four tissues, which were the embryo, endosperm, aleurone layer, and hull, and tissue-specific transcriptome and metabolome analyses were performed on them. By exploring the common differentially expressed genes and differentially accumulated metabolites, as well as the KEGG pathway of the four non-storable NILs, we revealed that the phenylpropanoid biosynthesis pathway and diterpenoid biosynthesis pathway played a central role in regulating seed storability. Integrated analysis pinpointed 12 candidate genes that may take part in seed storability. The comprehensive analysis disclosed the divergent and synergistic effect of different seed tissues in the regulation of rice storability.

Transcriptome-Wide Characterization of Seed Aging in Rice: Identification of Specific Long-Lived mRNAs for Seed Longevity

Various long-lived mRNAs are stored in seeds, some of which are required for the initial phase of germination and are critical to seed longevity. However, the seed-specific long-lived mRNAs involved in seed longevity remain poorly understood in rice. To identify these mRNAs in seeds, we first performed aging experiment with 14 rice varieties, and categorized them as higher longevity (HL) and lower longevity (LL) rice varieties in conventional rice and hybrid rice, respectively. Second, RNA-seq analysis showed that most genes showed similar tendency of expression changes during natural and artificial aging, suggesting that the effects of these two aging methods on transcription are comparable. In addition, some differentially expressed genes (DEGs) in the HL and LL varieties differed after natural aging. Furthermore, several specific long-lived mRNAs were identified through a comparative analysis of HL and LL varieties after natural aging, and similar sequence features were also identified in the promoter of some specific long-lived mRNAs. Overall, we identified several specific long-lived mRNAs in rice, including gibberellin receptor gene GID1, which may be associated with seed longevity.

A multiomic study uncovers a bZIP23-PER1A-mediated detoxification pathway to enhance seed vigor in rice

Seed vigor is important to farmers, breeders, and industries, with critical implications for seed quality and germplasm preservation. We included RNA sequencing data, searching the differentially expressed genes, separately, in seeds of two rice varieties with huge differences in seed vigor. We then compared the transcriptome profiles between them. We compared the metabolic profiling of these two seeds. We uncovered the genetic architecture of two rice varieties with distinct seed vigor. We identified PER1A that acts as a positive regulator and bZIP23 that functions upstream and as a transcription activator of PER1A and is also a positive regulator of seed vigor. Finally, we demonstrated that the bZIP23-PER1A regulatory module for rice seed vigor operates via the abscisic acid signaling pathway.

Seed vigor in crops is important in terms of improving grain quality and germplasm conservation; however, little is known about its regulatory mechanisms through the encoded proteome and gene network. Comparative analyses of transcriptome (RNA sequencing [RNA-seq]) and broadly targeted metabolic profiling of two subspecific rice cultivars with distinct seed vigor during accelerated aging revealed various biological pathways and metabolic processes as key influences explaining trait differences. RNA-seq coexpression regulatory network analyses identified several transcription factors, including bZIP23 and bZIP42, that act as nodes in the gene network. Importantly, transgenic seeds of overexpression of bZIP23 enhanced seed vigor, whereas its gene knockout reduced seed vigor, suggesting that the protein it encodes functions as a positive regulator. Similarly, overexpression and knockout of PER1A that encodes a key player in the detoxification pathway enhanced and decreased seed vigor, respectively. We further demonstrated a direct interaction of the PER1A promoter with bZIP23 in seeds, which activates the expression of PER1A, and the genetic evidence suggested that bZIP23 most likely functions in a common pathway with and acts upstream of PER1A to modulate seed vigor. In addition, the control of seed vigor by the bZIP23-PER1A module was connected with that of the abscisic acid signaling pathway. Collectively, we revealed the genetic architecture of variation in seed vigor and uncovered the bZIP23-PER1A–mediated detoxification pathway that enhances the trait in rice.

Genome-Wide Association Study Reveals the QTLs for Seed Storability in World Rice Core Collections

Seed storability is a main agronomically important trait to assure storage safety of grain and seeds in rice. Although many quantitative trait loci (QTLs) and associated genes for rice seed storability have been identified, the detailed genetic mechanisms of seed storability remain unclear in rice. In this study, a genome-wide association study (GWAS) was performed in 456 diverse rice core collections from the 3K rice genome. We discovered the new nine QTLs designated as qSS1-1, qSS1-2, qSS2-1, qSS3-1, qSS5-1, qSS5-2, qSS7-1, qSS8-1, and qSS11-1. According to the analysis of the new nine QTLs, our results could well explain the reason why seed storability of indica subspecies was superior to japonica subspecies in rice. Among them, qSS1-2 and qSS8-1 were potentially co-localized with a known associated qSS1/OsGH3-2 and OsPIMT1, respectively. Our results also suggest that pyramiding breeding of superior alleles of these associated genes will lead to new varieties with improved seed storability in the future.

Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice

Seed vigor is a complex trait, including the seed germination, seedling emergence, and growth, as well as seed storability and stress tolerance, which is important for direct seeding in rice. Seed vigor is established during seed development, and its level is decreased during seed storage. Seed vigor is influenced by genetic and environmental factors during seed development, storage, and germination stages. A lot of factors, such as nutrient reserves, seed dying, seed dormancy, seed deterioration, stress conditions, and seed treatments, will influence seed vigor during seed development to germination stages. This review highlights the current advances on the identification of quantitative trait loci (QTLs) and regulatory genes involved in seed vigor at seed development, storage, and germination stages in rice. These identified QTLs and regulatory genes will contribute to the improvement of seed vigor by breeding, biotechnological, and treatment approaches.