Ethylene-Inhibited Jasmonic Acid Biosynthesis Promotes Mesocotyl/Coleoptile Elongation of Etiolated Rice Seedlings

Rapid Identification of QTL for Mesocotyl Length in Rice Through Combining QTL-seq and Genome-Wide Association Analysis

Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F₂ populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or G-value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3–14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, Indel-Chr1:18932318 and Indel-Chr7:15404166 for loci qML1.3 and qML7.2 respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding.

Primary Root and Mesocotyl Elongation in Maize Seedlings: Two Organs with Antagonistic Growth below the Soil Surface

Maize illustrates one of the most complex cases of embryogenesis in higher plants that results in the development of early embryo with distinctive organs such as the mesocotyl, seminal and primary roots, coleoptile, and plumule. After seed germination, the elongation of root and mesocotyl follows opposite directions in response to specific tropisms (positive and negative gravitropism and hydrotropism). Tropisms represent the differential growth of an organ directed toward several stimuli. Although the life cycle of roots and mesocotyl takes place in darkness, their growth and functions are controlled by different mechanisms. Roots ramify through the soil following the direction of the gravity vector, spreading their tips into new territories looking for water; when water availability is low, the root hydrotropic response is triggered toward the zone with higher moisture. Nonetheless, there is a high range of hydrotropic curvatures (angles) in maize. The processes that control root hydrotropism and mesocotyl elongation remain unclear; however, they are influenced by genetic and environmental cues to guide their growth for optimizing early seedling vigor. Roots and mesocotyls are crucial for the establishment, growth, and development of the plant since both help to forage water in the soil. Mesocotyl elongation is associated with an ancient agriculture practice known as deep planting. This tradition takes advantage of residual soil humidity and continues to be used in semiarid regions of Mexico and USA. Due to the genetic diversity of maize, some lines have developed long mesocotyls capable of deep planting while others are unable to do it. Hence, the genetic and phenetic interaction of maize lines with a robust hydrotropic response and higher mesocotyl elongation in response to water scarcity in time of global heating might be used for developing more resilient maize plants.

Increased benzoxazinoid (Bx) levels in wheat seedlings via jasmonic acid treatment and etiolation and their effects on Bx genes including Bx6

Wheat accumulates benzoxazinoid (Bx) as a defensive compound. While Bx occurs at high concentrations, particularly in the early growth stages, its mechanism of regulation remains unclear. In the present study, we first examined the effects of several plant hormones on Bx concentrations in wheat seedlings. Among the compounds tested, jasmonate (JA) elevated the concentrations of DIMBOA-Glc (2-β-D-glucoside of 2,4-dihydroxy-7-methoy-1,4-benzoxazin-3-one), the primary Bx species in intact wheat seedlings, without a significant increase in HDMBOA-Glc (4-O-methyl-DIMBOA-Glc), which is known to be upregulated by stresses. In addition, growing the plants in the dark increased DIMBOA-Glc levels. Quantification of the Bx-biosynthetic genes showed that TaBx8 (UDP-Glc:Bx glucosyltrasferase) was influenced by neither JA nor etiolation, indicating that TaBx8 is under the regulation mechanism distinct from the mechanisms influencing the others. In addition, none of the other gene expression patterns exhibited considerable correlation with DIMBOA-Glc accumulation. Since there was no correlation between transcript levels of the genes involved in Bx biosynthesis and Bx accumulation, other factors may control the levels of Bx in wheat. In the course of gene analyses, we isolated TaBx6, one of the last two genes that had not been identified in wheat in the DIMBOA-Glc biosynthetic pathway. All the four TaBx6 genes cloned in the present study were expressed in Escherichia coli and characterized their activity.

Promoter Architecture and Transcriptional Regulation of Genes Upregulated in Germination and Coleoptile Elongation of Diverse Rice Genotypes Tolerant to Submergence

Rice has the natural morphological adaptation to germinate and elongate its coleoptile under submerged flooding conditions. The phenotypic deviation associated with the tolerance to submergence at the germination stage could be due to natural variation. However, the molecular basis of this variation is still largely unknown. A comprehensive understanding of gene regulation of different genotypes that have diverse rates of coleoptile elongation can provide significant insights into improved rice varieties. To do so, publicly available transcriptome data of five rice genotypes, which have different lengths of coleoptile elongation under submergence tolerance, were analyzed. The aim was to identify the correlation between promoter architecture, associated with transcriptional and hormonal regulation, in diverse genotype groups of rice that have different rates of coleoptile elongation. This was achieved by identifying the putative cis-elements present in the promoter sequences of genes upregulated in each group of genotypes (tolerant, highly tolerant, and extremely tolerant genotypes). Promoter analysis identified transcription factors (TFs) that are common and unique to each group of genotypes. The candidate TFs that are common in all genotypes are MYB, bZIP, AP2/ERF, ARF, WRKY, ZnF, MADS-box, NAC, AS2, DOF, E2F, ARR-B, and HSF. However, the highly tolerant genotypes interestingly possess binding sites associated with HY5 (bZIP), GBF3, GBF4 and GBF5 (bZIP), DPBF-3 (bZIP), ABF2, ABI5, bHLH, and BES/BZR, in addition to the common TFs. Besides, the extremely tolerant genotypes possess binding sites associated with bHLH TFs such as BEE2, BIM1, BIM3, BM8 and BAM8, and ABF1, in addition to the TFs identified in the tolerant and highly tolerant genotypes. The transcriptional regulation of these TFs could be linked to phenotypic variation in coleoptile elongation in response to submergence tolerance. Moreover, the results indicate a cross-talk between the key TFs and phytohormones such as gibberellic acid, abscisic acid, ethylene, auxin, jasmonic acid, and brassinosteroids, for an altered transcriptional regulation leading to differences in germination and coleoptile elongation under submergence. The information derived from the current in silico analysis can potentially assist in developing new rice breeding targets for direct seeding.

Targeted mutagenesis of POLYAMINE OXIDASE 5 that negatively regulates mesocotyl elongation enables the generation of direct-seeding rice with improved grain yield

Under conditions of labor or resource scarcity, direct seeding, rather than transplantation, is the preferred mode of rice (Oryza sativa) cultivation. This approach requires varieties that exhibit uniform seedling emergence. Mesocotyl elongation (ME), the main driver of rapid emergence of rice seedlings from soil, is enhanced by darkness and inhibited by light. Plant polyamine oxidases (PAOs) oxidize polyamines (PAs) and release H2O2. Here, we established that OsPAO5 expression in rice seedlings is increased in the presence of light and inhibited by darkness. To determine its role in ME, we created OsPAO5 mutants using CRISPR/Cas9. Compared with the wild type, pao5 mutants had longer mesocotyls, released less H2O2, and synthesized more ethylene. The mutant seedlings emerged at a higher and more uniform rate, indicating their potential for use in direct seeding. Nucleotide polymorphism analysis revealed that an SNP (PAO5-578G/A) located 578 bp upstream of the OsPAO5 start codon alters its expression, and was selected during rice mesocotyl domestication. The PAO5-578G genotype conferring a long mesocotyl mainly exists in wild rice, most Aus accessions, and some Geng (Japonica) accessions. Intriguingly, knocking out OsPAO5 can remarkably increase the grain weight, grain number, and yield potential. In summary, we developed a novel strategy to obtain elite rice with higher emergence vigor and yield potential, which can be conveniently and widely used to breed varieties of direct-seeding rice.

Ethylene Signaling Facilitates Plant Adaption to Physical Barriers

The morphological changes are usually observed in the terrestrial plants to respond to physical barriers. The phytohormone ethylene plays an essential role in the morphological development of plants encountering exogenous mechanical impedance, which enables plants to grow optimally in response to physical barriers. Ethylene is shown to regulate these developmental processes directly or in concert with other phytohormones, especially auxin. In this mini review, the involvement of ethylene action in seedling emergence from the soil, root movement within the soil, and parasitic plant invasion of the host plant are described.

Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms

Ethylene is a gaseous hormone which plays important roles in both plant growth and development and stress responses. Based on studies in the dicot model plant species Arabidopsis, a linear ethylene signaling pathway has been established, according to which ethylene is perceived by ethylene receptors and transduced through CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1) and ETHYLENE-INSENSITIVE 2 (EIN2) to activate transcriptional reprogramming. In addition to this canonical signaling pathway, an alternative ethylene receptor-mediated phosphor-relay pathway has also been proposed to participate in ethylene signaling. In contrast to Arabidopsis, rice, a monocot, grows in semiaquatic environments and has a distinct plant structure. Several novel regulators and/or mechanisms of the rice ethylene signaling pathway have recently been identified, indicating that the ethylene signaling pathway in rice has its own unique features. In this review, we summarize the latest progress and compare the conserved and divergent aspects of the ethylene signaling pathway between Arabidopsis and rice. The crosstalk between ethylene and other plant hormones is also reviewed. Finally, we discuss how ethylene regulates plant growth, stress responses and agronomic traits. These analyses should help expand our knowledge of the ethylene signaling mechanism and could further be applied for agricultural purposes.

How does rice cope with too little oxygen during its early life?

Most crops cannot germinate underwater. Rice exhibits certain degrees of tolerance to oxygen deficiency for anaerobic germination (AG) and anaerobic seedling development (ASD). Direct rice seeding, whereby seeds are sown into soil rather than transplanting seedlings from the nursery, becomes an increasingly popular cultivation method due to labor shortages and opportunities for sustainable cultivation. Flooding is common under direct seeding, but most rice varieties have poor capability of AG/ASD, which is a major obstacle to broad adoption of direct seeding. A better understanding of the physiological basis and molecular mechanisms regulating AG/ASD should facilitate rice breeding for enhanced seedling vigor under flooding. This review highlights recent advances on molecular and physiological mechanisms and future breeding strategies of rice AG/ASD.

Similarities and Differences of Photosynthesis Establishment Related mRNAs and Novel lncRNAs in Early Seedlings (Coleoptile/Cotyledon vs. True Leaf) of Rice and Arabidopsis

Photosynthesis uses sunlight and carbon dioxide to produce biomass that is vital to all life on earth. In seed plants, leaf is the main organ for photosynthesis and production of organic nutrients. The seeds are mobilized to fuel post-germination seedling growth until seedling photosynthesis can be efficiently established. However, the photosynthesis and metabolism in the early growth and development have not been studied systematically and are still largely unknown. In this study, we used two model plants, rice (Oryza sativa L.; monocotyledonous) and Arabidopsis (Arabidopsis thaliana; dicotyledonous) to determine the similarities and differences in photosynthesis in cotyledons and true leaves during the early developmental stages. The photosynthesis-related genes and proteins, and chloroplast functions were determined through RNA-seq, real-time PCR, western blotting and chlorophyll fluorescence analysis. We found that in rice, the photosynthesis established gradually from coleoptile (cpt), incomplete leaf (icl) to first complete leaf (fcl); whereas, in Arabidopsis, photosynthesis well-developed in cotyledon, and the photosynthesis-related genes and proteins expressed comparably in cotyledon (cot), first true leaf (ftl) and second true leaf (stl). Additionally, we attempted to establish an mRNA-lncRNA signature to explore the similarities and differences in photosynthesis establishment between the two species, and found that DEGs, including encoding mRNAs and novel lncRNAs, related to photosynthesis in three stages have considerable differences between rice and Arabidopsis. Further GO and KEGG analysis systematically revealed the similarities and differences of expression styles of photosystem subunits and assembly factors, and starch and sucrose metabolisms between cotyledons and true leaves in the two species. Our results help to elucidate the gene functions of mRNA-lncRNA signatures.

Karrikin Signaling Acts Parallel to and Additively with Strigolactone Signaling to Regulate Rice Mesocotyl Elongation in Darkness

Seedling emergence in monocots depends mainly on mesocotyl elongation, requiring coordination between developmental signals and environmental stimuli. Strigolactones (SLs) and karrikins are butenolide compounds that regulate various developmental processes; both are able to negatively regulate rice (Oryza sativa) mesocotyl elongation in the dark. Here, we report that a karrikin signaling complex, DWARF14-LIKE (D14L)-DWARF3 (D3)-O. sativa SUPPRESSOR OF MAX2 1 (OsSMAX1) mediates the regulation of rice mesocotyl elongation in the dark. We demonstrate that D14L recognizes the karrikin signal and recruits the SCFD3 ubiquitin ligase for the ubiquitination and degradation of OsSMAX1, mirroring the SL-induced and D14- and D3-dependent ubiquitination and degradation of D53. Overexpression of OsSMAX1 promoted mesocotyl elongation in the dark, whereas knockout of OsSMAX1 suppressed the elongated-mesocotyl phenotypes of d14l and d3 OsSMAX1 localizes to the nucleus and interacts with TOPLESS-RELATED PROTEINs, regulating downstream gene expression. Moreover, we showed that the GR24 enantiomers GR245DS and GR24 ent-5DS specifically inhibit mesocotyl elongation and regulate downstream gene expression in a D14- and D14L-dependent manner, respectively. Our work revealed that karrikin and SL signaling play parallel and additive roles in modulating downstream gene expression and negatively regulating mesocotyl elongation in the dark.

The GDSL Lipase MHZ11 Modulates Ethylene Signaling in Rice Roots

Ethylene plays important roles in plant growth and development, but the regulation of ethylene signaling is largely unclear, especially in crops such as rice (Oryza sativa). Here, by analysis of the ethylene-insensitive mutant mao huzi 11 (mhz11), we identified the GDSL lipase MHZ11, which modulates ethylene signaling in rice roots. MHZ11 localized to the endoplasmic reticulum membrane and has acyl-hydrolyzing activity. This activity affects the homeostasis of sterols in rice roots and is required for root ethylene response. MHZ11 overexpression caused constitutive ethylene response in roots. Genetically, MHZ11 acts with the ethylene receptor ETHYLENE RESPONSE SENSOR2 (OsERS2) upstream of CONSTITUTIVE TRIPLE RESPONSE2 (OsCTR2) and ETHYLENE INSENSITIVE2 (OsEIN2). The mhz11 mutant maintains more OsCTR2 in the phosphorylated form whereas MHZ11 overexpression promotes ethylene-mediated inhibition of OsCTR2 phosphorylation. MHZ11 colocalized with the ethylene receptor OsERS2, and its effect on OsCTR2 phosphorylation requires ethylene perception and initiation of ethylene signaling. The mhz11 mutant overaccumulated sterols and blocking sterol biosynthesis partially rescued the mhz11 ethylene response, likely by reducing receptor-OsCTR2 interaction and OsCTR2 phosphorylation. We propose that MHZ11 reduces sterol levels to impair receptor-OsCTR2 interactions and OsCTR2 phosphorylation for triggering ethylene signaling. Our study reveals a mechanism by which MHZ11 participates in ethylene signaling for regulation of root growth in rice.

Progress of ethylene action mechanism and its application on plant type formation in crops

The plant hormone ethylene exerts a huge influence in the whole life cycle of plants, especially stress-resistance responses. With the development of functional genomics, that the action mechanism of ethylene takes part in mediated plant architecture has been clarified gradually, such as plant roots, stems, leaves, fiber elongation and so on. Accordingly, the application of ethylene on crops chemical control and genetic improvement is greatly expanded. From the view of ethylene mediated plant architecture in crops, here reviewed advances in ethylene biosynthesis and signal transduction pathway, stress-resistance responses and the yield potential enhance of crops in recently 20 years. On these grounds, the objectives of this paper were to provide scientific reference and a useful clue for the crop creation of ideal plant type.

A class B heat shock factor selected for during soybean domestication contributes to salt tolerance by promoting flavonoid biosynthesis

Soybean (Glycine max) production is severely affected in unfavorable environments. Identification of the regulatory factors conferring stress tolerance would facilitate soybean breeding. In this study, through coexpression network analysis of salt-tolerant wild soybeans, together with molecular and genetic approaches, we revealed a previously unidentified function of a class B heat shock factor, HSFB2b, in soybean salt stress response. We showed that HSFB2b improves salt tolerance through the promotion of flavonoid accumulation by activating one subset of flavonoid biosynthesis-related genes and by inhibiting the repressor gene GmNAC2 to release another subset of genes in the flavonoid biosynthesis pathway. Moreover, four promoter haplotypes of HSFB2b were identified from wild and cultivated soybeans. Promoter haplotype II from salt-tolerant wild soybean Y20, with high promoter activity under salt stress, is probably selected for during domestication. Another promoter haplotype, III, from salt-tolerant wild soybean Y55, had the highest promoter activity under salt stress, had a low distribution frequency and may be subjected to the next wave of selection. Together, our results revealed the mechanism of HSFB2b in soybean salt stress tolerance. Its promoter variations were identified, and the haplotype with high activity may be adopted for breeding better soybean cultivars that are adapted to stress conditions.

Ethephon-regulated maize internode elongation associated with modulating auxin and gibberellin signal to alter cell wall biosynthesis and modification

Ethephon efficiently regulates plant growth to modulate the maize (Zea mays L.) stalk strength and yield potential, yet there is little information on how ethylene governs a specific cellular response for altering internode elongation. Here, the internode elongation kinetics, cell morphological and physiological properties and transcript expression patterns were investigated in the ethephon-treated elongating internode. Ethephon decreased the internode elongation rate, shortened the effective elongation duration, and advanced the growth process. Ethephon regulated the expression patterns of expansin and secondary cell wall-associated cellulose synthase genes to alter cell size. Moreover, ethephon increased the activities and transcripts level of phenylalanine ammonia-lyase and peroxidase, which contributed to lignin accumulation. Otherwise, ethephon-boosted ethylene evolution activated ethylene signal and increased ZmGA2ox3 and ZmGA2ox10 transcript levels while down-regulating ZmPIN1a, ZmPIN4 and ZmGA3ox1 transcript levels, which led to lower accumulation of gibberellins and auxin. In addition, transcriptome profiles confirmed previous results and identified several transcription factors that are involved in the ethephon-modulated transcriptional regulation of cell wall biosynthesis and modification and responses to ethylene, gibberellins and auxin. These results indicated that ethylene-modulated auxin and gibberellins signaling mediated the transcriptional operation of cell wall modification to regulate cell elongation in the ethephon-treated maize internode.

Genome-wide Association Study (GWAS) for Mesocotyl Elongation in Rice (Oryza sativa L.) under Multiple Culture Conditions

Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice.

Mesocotyl elongation, an essential trait for dry-seeded rice (Oryza sativa L.): a review of physiological and genetic basis

(1) Mesocotyl elongation is responsive to abiotic stresses, such as deep sowing drought, submergence, chilling, and salinity. (2) Humus soil culture with a burial depth of 6 cm and at the temperature of 30 °C could be the optimum method for mesocotyl length phenotyping, The frequently colocalized quantitative trait loci (QTL) controlling mesocotyl elongation were located on chromosome (3) 1 (RM562-RG146), chromosome 2 (RZ288-RM145), and chromosome 3 (RM426-RM520). Dry direct-seeding is becoming a popular rice cultivation technology in many countries, which reduces water use and labor costs enormously. Meanwhile, direct-seeding rice is also facing the problems of low seedling emergence rate, poor seedling establishment, weed infestation, and high crop lodging rate. To take the full advantages of direct-seeding, both agronomic and genetic solutions are needed. Varieties with optimum mesocotyl length are desired for improving rice seedling emergence rate, particularly under deep sowing and submergence, which is adopted to reduce lodging and increase tolerance to abiotic stresses. In this review, we summarized the physiological and genetic mechanisms of mesocotyl elongation in rice. The elongation of mesocotyl is affected by light, temperature, and water, and, as a result, is responsive to sowing depth, water content, and soil salinity. Plant hormones such as abscisic acid (ABA), brassinosteroid (BR), strigolactones (SLs), cytokinin (CTK), ethylene (ETH), jasmonic acid (JA), gibberellin (GA), and indole-3-acetic acid (IAA) play important roles in regulating mesocotyl elongation. A humus soil culture protocol developed by our team was shown to be a better high-throughput method for measuring mesocotyl length in large scale. Sixty-seven QTL controlling mesocotyl length were reported, which are distributed on all the 12 chromosomes. Twelve chromosomal regions were repeatedly found to have QTL using various mapping populations and methods. These regions should be targeted in future studies to isolate genes and develop markers for molecular breeding. Two genes with very different molecular functions have been cloned, highlighting the genetic complexity of mesocotyl elongation.

Using natural variation to achieve a whole-plant functional understanding of the responses mediated by jasmonate signaling

The dramatic advances in our understanding of the molecular biology and biochemistry of jasmonate (JA) signaling have been the subject of several excellent recent reviews that have highlighted the phytohormonal function of this signaling pathway. Here, we focus on the responses mediated by JA signaling which have consequences for a plant's Darwinian fitness, i.e. the organism-level function of JA signaling. The most diverse module in the signaling cascade, the JAZ proteins, and their interactions with other proteins and transcription factors, allow this canonical signaling cascade to mediate a bewildering array of traits in different tissues at different times; the functional coherence of these diverse responses are best appreciated in an organismal/ecological context. From published work, it appears that jasmonates can function as the 'Swiss Army knife' of plant signaling, mediating many different biotic and abiotic stress and developmental responses that allow plants to contextualize their responses to their frequently changing local environments and optimize their fitness. We propose that a deeper analysis of the natural variation in both within-plant and within-population JA signaling components is a profitable means of attaining a coherent whole-plant functional perspective of this signaling cascade, and provide examples of this approach from the Nicotiana attenuata system.

Dissection of coleoptile elongation in japonica rice under submergence through integrated genome-wide association mapping and transcriptional analyses

Rice is unique among cereals for its ability to germinate not only when submerged but also under anoxic conditions. Rice germination under submergence or anoxia is characterized by a longer coleoptile and delay in radicle emergence. A panel of temperate and tropical japonica rice accessions showing a large variability in coleoptile length was used to investigate genetic factors involved in this developmental process. The ability of the Khao Hlan On rice landrace to vigorously germinate when submerged has been previously associated with the presence of the trehalose 6 phosphate phosphatase 7 (TPP7) gene. In this study, we found that, in the presence of TPP7, polymorphisms and transcriptional variations of the gene in coleoptile tissue were not related to differences in the final coleoptile length under submergence. In order to find new chromosomal regions associated with the different ability of rice to elongate the coleoptile under submergence, we used genome-wide association study analysis on a panel of 273 japonica rice accessions. We discovered 11 significant marker-trait associations and identified candidate genes potentially involved in coleoptile length. Candidate gene expression analyses indicated that japonica rice genotypes possess complex genetic elements that control final coleoptile length under low oxygen.

Binding of the Magnaporthe oryzae Chitinase MoChia1 by a Rice Tetratricopeptide Repeat Protein Allows Free Chitin to Trigger Immune Responses

To defend against pathogens, plants have developed complex immune systems, including plasma membrane receptors that recognize pathogen-associated molecular patterns, such as chitin from fungal cell walls, and mount a defense response. Here, we identify a chitinase, MoChia1 (Magnaporthe oryzae chitinase 1), secreted by M. oryzae, a fungal pathogen of rice (Oryza sativa). MoChia1 can trigger plant defense responses, and expression of MoChia1 under an inducible promoter in rice enhances its resistance to M. oryzae MoChia1 is a functional chitinase required for M. oryzae growth and development; knocking out MoChia1 significantly reduced the virulence of the fungus, and we found that MoChia1 binds chitin to suppress the chitin-triggered plant immune response. However, the rice tetratricopeptide repeat protein OsTPR1 interacts with MoChia1 in the rice apoplast. OsTPR1 competitively binds MoChia1, thereby allowing the accumulation of free chitin and re-establishing the immune response. Overexpressing OsTPR1 in rice plants resulted in elevated levels of reactive oxygen species during M. oryzae infection. Our data demonstrate that rice plants not only recognize MoChia1, but also use OsTPR to counteract the function of this fungal chitinase and regain immunity.

OsTGA2 confers disease resistance to rice against leaf blight by regulating expression levels of disease related genes via interaction with NH1

How plants defend themselves from microbial infection is one of the most critical issues for sustainable crop production. Some TGA transcription factors belonging to bZIP superfamily can regulate disease resistance through NPR1-mediated immunity mechanisms in Arabidopsis. Here, we examined biological roles of OsTGA2 (grouped into the same subclade as Arabidopsis TGAs) in bacterial leaf blight resistance. Transcriptional level of OsTGA2 was accumulated after treatment with salicylic acid, methyl jasmonate, and Xathomonas oryzae pv. Oryzae (Xoo), a bacterium causing serious blight of rice. OsTGA2 formed homo- and hetero-dimer with OsTGA3 and OsTGA5 and interacted with rice NPR1 homologs 1 (NH1) in rice. Results of quadruple 9-mer protein-binding microarray analysis indicated that OsTGA2 could bind to TGACGT DNA sequence. Overexpression of OsTGA2 increased resistance of rice to bacterial leaf blight, although overexpression of OsTGA3 resulted in disease symptoms similar to wild type plant upon Xoo infection. Overexpression of OsTGA2 enhanced the expression of defense related genes containing TGA binding cis-element in the promoter such as AP2/EREBP 129, ERD1, and HOP1. These results suggest that OsTGA2 can directly regulate the expression of defense related genes and increase the resistance of rice against bacterial leaf blight disease.

Natural selection of a GSK3 determines rice mesocotyl domestication by coordinating strigolactone and brassinosteroid signaling

Mesocotyl is the crucial organ for pushing buds out of deep water or soil after germination in monocots. Deep direct seeding or mechanized dry seeding cultivation practice requires rice cultivars having long mesocotyl. However, the mechanisms of mesocotyl elongation and domestication remain unknown. Here, our genome-wide association study (GWAS) reveals that natural variations of OsGSK2, a conserved GSK3-like kinase involved in brassinosteroid signaling, determine rice mesocotyl length variation. Variations in the coding region of OsGSK2 alter its kinase activity. It is selected for mesocotyl length variation during domestication. Molecular analyses show that brassinosteroid-promoted mesocotyl elongation functions by suppressing the phosphorylation of an U-type cyclin, CYC U2, by OsGSK2. Importantly, the F-box protein D3, a major positive component in strigolactone signaling, can degrade the OsGSK2-phosphorylated CYC U2 to inhibit mesocotyl elongation. Together, these results suggest that OsGSK2 is selected to regulate mesocotyl length by coordinating strigolactone and brassinosteroid signaling during domestication.

Membrane protein MHZ3 stabilizes OsEIN2 in rice by interacting with its Nramp-like domain

The ethylene signaling pathway has been extensively investigated in Arabidopsis, and EIN2 is the central component. Rice is a monocotyledonous model plant that exhibits different features in many aspects compared with the dicotyledonous Arabidopsis. Thus, rice provides an alternative system for identification of novel components of ethylene signaling. In this study, we identified a stabilizer of OsEIN2 through analysis of the rice ethylene-insensitive mutant mhz3. We found that MHZ3 stabilizes OsEIN2 likely by binding to its Nramp-like transmembrane domain and impeding protein ubiquitination, blocking proteasome-mediated protein degradation. This study reveals that MHZ3 is required for ethylene signaling and identifies how MHZ3 binds to OsEIN2 via the OsEIN2 N-terminal Nramp-like domain.

The phytohormone ethylene regulates many aspects of plant growth and development. EIN2 is the central regulator of ethylene signaling, and its turnover is crucial for triggering ethylene responses. Here, we identified a stabilizer of OsEIN2 through analysis of the rice ethylene-response mutant mhz3. Loss-of-function mutations lead to ethylene insensitivity in etiolated rice seedlings. MHZ3 encodes a previously uncharacterized membrane protein localized to the endoplasmic reticulum. Ethylene induces MHZ3 gene and protein expression. Genetically, MHZ3 acts at the OsEIN2 level in the signaling pathway. MHZ3 physically interacts with OsEIN2, and both the N- and C-termini of MHZ3 specifically associate with the OsEIN2 Nramp-like domain. Loss of mhz3 function reduces OsEIN2 abundance and attenuates ethylene-induced OsEIN2 accumulation, whereas MHZ3 overexpression elevates the abundance of both wild-type and mutated OsEIN2 proteins, suggesting that MHZ3 is required for proper accumulation of OsEIN2 protein. The association of MHZ3 with the Nramp-like domain is crucial for OsEIN2 accumulation, demonstrating the significance of the OsEIN2 transmembrane domains in ethylene signaling. Moreover, MHZ3 negatively modulates OsEIN2 ubiquitination, protecting OsEIN2 from proteasome-mediated degradation. Together, these results suggest that ethylene-induced MHZ3 stabilizes OsEIN2 likely by binding to its Nramp-like domain and impeding protein ubiquitination to facilitate ethylene signal transduction. Our findings provide insight into the mechanisms of ethylene signaling.

Genetic Architecture and Candidate Genes for Deep-Sowing Tolerance in Rice Revealed by Non-syn GWAS

Dry direct-seeding of rice is rapidly increasing in China, but variable planting depth associated with machine sowing can lead to low seedling emergence rates. Phenotype analysis of 621 rice accessions showed that mesocotyl length (ML) was induced by deep soil covering and was important in deep-sowing tolerance in the field. Here, we performed and compared GWAS using three types of SNPs (non-synonymous SNP, non-synonymous SNPs and SNPs within promoters and 3 million randomly selected SNPs from the entire set of SNPs) and found that Non-Syn GWAS (GWAS using non-synonyomous SNP) decreased computation time and eliminated confounding by other loci relative to GWAS using randomly selected SNPs. Thirteen QTLs were finally detected, and two new major-effect genes, named OsML1 and OsML2, were identified by an integrated analysis. There were 2 and 7 non-synonymous SNPs in OsML1 and OsML2, respectively, from which 3 and 4 haplotypes were detected in cultivated rice. Combinations of superior haplotypes of OsML1 and OsML2 increased ML by up to 4 cm, representing high emergence rate (85%) in the field with 10 cm of soil cover. The studies provide key loci and naturally occurring alleles of ML that can be used in improving tolerance to dry direct-seeding.

Diverse Roles of Ethylene in Regulating Agronomic Traits in Rice

Gaseous hormone ethylene has diverse effects in various plant processes. These processes include seed germination, plant growth, senescence, fruit ripening, biotic and abiotic stresses responses, and many other aspects. The biosynthesis and signaling of ethylene have been extensively studied in model Arabidopsis in the past two decades. However, knowledge about the ethylene signaling mechanism in crops and roles of ethylene in regulation of crop agronomic traits are still limited. Our recent findings demonstrate that rice possesses both conserved and diverged mechanism for ethylene signaling compared with Arabidopsis. Here, we mainly focused on the recent advances in ethylene regulation of important agronomic traits. Of special emphasis is its impact on rice growth, flowering, grain filling, and grain size control. Similarly, the influence of ethylene on other relevant crops will be compared. Additionally, interactions of ethylene with other hormones will also be discussed in terms of crop growth and development. Increasing insights into the roles and mechanisms of ethylene in regulating agronomic traits will contribute to improvement of crop production through precise manipulation of ethylene actions in crops.

Dynamic transcriptome and phytohormone profiling along the time of light exposure in the mesocotyl of rice seedling

Mesocotyl elongation is an important trait influencing seedling emergence and establishment in rice direct-seeding cultivation and is immediately inhibited after light exposure. Detailed researches on the molecular basis and biological processes underlying light repression of mesocotyl growth could probably provide useful information for key factors controlling this trait. Here we monitored the transcriptome and endogenous phytohormone changes specifically in the elongating mesocotyl in response to light exposure with a time-course. It was revealed that 974 transcripts were significantly differentially expressed (FDR < 0.05, |log₂ (L/D) | ≥2) after light exposure. Most of the differential expression genes associated with the responses to hormone. Metabolic pathway analysis using the KEGG system suggested plant hormone signal transduction, α-linolenic acid metabolism and diterpenoid biosynthesis were critical processes of mesocotyl growth inhibited by light. Consistent with DEGs, the endogenous IAA, tZ and GA₃ content was significantly reduced while JA level was dramatically increased, which indicated that light inhibited rice mesocotyl growth through decreasing IAA, tZ and GA₃ content and/or increasing JA level. The present results enriched our knowledge about the genes and phytohormones regulating mesocotyl elongation in rice, which may help improve future studies on associated genes and develop new varieties tolerance to deep sowing.