Gibberellic acid (GA), a ubiquitous phytohormone, has various effects on regulators of plant growth and development. GAs promote growth by overcoming growth restraint mediated by DELLA proteins (DELLAs). DELLAs, in the GRAS family of plant-specific nuclear proteins, are nuclear transcriptional regulators harboring a unique N-terminal GA perception region for binding the GA receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) and a C-terminal GRAS domain necessary for GA repression activity via interaction with multiple regulatory proteins. The N-terminal conserved region of DELLAs evolved to form a mode of GID1/DELLA-mediated GA signaling originating in bryophytes and ferns. Binding of GA to GID1 increases the affinity between DELLAs and a SCF E3 ubiquitin-ligase complex, thus promoting the eventual destruction of DELLAs by the 26S proteasome. DELLAs negatively regulate GA response by releasing transcription factors to directly activate downstream genes and indirectly regulate GA biosynthesis genes increasing GA responsiveness and feedback control by promoting GID1 transcription. GA communicates extensively with other plant hormones and uses crosstalk to regulate plant growth and development. In this review, we summarize current understanding of evolutionary DELLA-mediated gibberellin signaling and functional diversification of DELLA, focusing primarily on interactions of DELLAs with diverse phytohormones.

The LGS1 (Large grain size 1) gene, also known as GS2/GL2/OsGRF4, is involved in regulating grain size and quality in rice, but the mechanism governing grain size has not been elucidated. We performed transcriptomic, proteomic, and phosphoproteomic analyses of young rice panicles in Samba (a wild-type cultivar with extra-small grain) and NIL-LGS1 (a nearly isogenic line of LGS1 with large grain in the Samba genetic background) at three developmental stages (4-6) to identify internal dynamic functional networks determining grain size that are mediated by LGS1. Differentially expressed proteins formed seven highly functionally correlated clusters. The concordant regulation of multiple functional clusters may be key features of the development of grain length in rice. In stage 5, 16 and 24 phosphorylated proteins were significantly up-regulated and down-regulated, and dynamic phosphorylation events may play accessory roles in determining rice grain size by participating in protein-protein interaction networks. Transcriptomic analysis in stage 5 showed that differentially expressed alternative splicing events and dynamic gene regulatory networks based on 39 transcription factors and their highly correlated target genes might contribute to rice grain development. Integrative multilevel omics analysis suggested that the regulatory network at the transcriptional and posttranscriptional levels could be directly manifested at the translational level, and this analysis also suggested a regulatory mechanism, regulation of protein translation levels, in the biological process that extends from transcript to protein to the development of grain. Functional analysis suggested that biological processes including MAPK signaling, calcium signaling, cell proliferation, cell wall, energy metabolism, hormone pathway, and ubiquitin-proteasome pathway might be involved in LGS1-mediated regulation of grain length. Thus, LGS1-mediated regulation of grain size is affected by dynamic transcriptional, posttranscriptional, translational and posttranslational changes.

In flowering plants, the inflorescence meristem (IM) provides founder cells to form successive floral meristems, which are precursors of fruits and seeds. The activity and developmental progression of IM are thus critical for yield production in seed crops. In some cereals, such as rice (Oryza sativa) and maize (Zea mays), the size of undifferentiated IM, which is located at the inflorescence apex, is positively associated with yield traits such as spikelet number. However, the relationship between IM size and yield-related spike traits remains unknown in the Triticeae tribe. Here we report that IM size has a negative correlation with yield traits in barley (Hordeum vulgare). Three FASCIATED EAR (FEA) orthologs, HvFEA2, HvFEA3, and HvFEA4, regulate IM size and spike morphogenesis and ultimately affect yield traits. Three HvFEAs genes are highly expressed in developing spikes, and all three loss-of-function mutants exhibit enlarged IM size, shortened spikes, and reduced spikelet number, which may lead to reduced grain yield. Natural variations identified in HvFEAs indicate selection events during barley domestication. We further reveal that HvFEA4, as a transcription factor, potentially targets multiple pathways during reproductive development, including transcriptional control, phytohormone signaling, and redox status. The roles of barley FEA genes in limiting IM size and promoting spikelet formation suggest the potential of increasing yield by manipulating IM activity.

The study of yield traits can reveal the genetic architecture of grain yield for improving maize production. In this study, an association panel comprising 362 inbred lines and a recombinant inbred line population derived from X178 × 9782 were used to identify candidate genes for nine yield traits. High-priority overlap (HPO) genes, which are genes prioritized in a genome-wide association study (GWAS), were investigated using coexpression networks. The GWAS identified 51 environmentally stable SNPs in two environments and 36 pleiotropic SNPs, including three SNPs with both attributes. Seven hotspots containing 41 trait-associated SNPs were identified on six chromosomes by permutation. Pyramiding of superior alleles showed a highly positive effect on all traits, and the phenotypic values of ear diameter and ear weight consistently corresponded with the number of superior alleles in tropical and temperate germplasm. A total of 61 HPO genes were detected after trait-associated SNPs were combined with the coexpression networks. Linkage mapping identified 16 environmentally stable and 16 pleiotropic QTL. Seven SNPs that were located in QTL intervals were assigned as consensus SNPs for the yield traits. Among the candidate genes predicted by our study, some genes were confirmed to function in seed development. The gene Zm00001d016656 encoding a serine/threonine protein kinase was associated with five different traits across multiple environments. Some genes were uniquely expressed in specific tissues and at certain stages of seed development. These findings will provide genetic information and resources for molecular breeding of maize grain yield.

Plant height (PH) is associated with lodging resistance and planting density, which is regulated by a complicated gene network. In this study, we identified a spontaneous dwarfing mutation in maize, m30, with decreased internode number and length but increased internode diameter. A candidate gene, ZmCYP90D1, which encodes a member of the cytochrome P450 family, was isolated by map-based cloning. ZmCYP90D1 was constitutively expressed and showed highest expression in basal internodes, and its protein was targeted to the nucleus. A G-to-A substitution was identified to be the causal mutation, which resulted in a truncated protein in m30. Loss of function of ZmCYP90D1 changed expression of hormone-responsive genes, in particular brassinosteroid (BR)-responsive genes which is mainly involved in cell cycle regulation and cell wall extension and modification in plants. The concentration of typhasterol (TY), a downstream intermediate of ZmCYP90D1 in the BR pathway, was reduced. A haplotype conferring dwarfing without reducing yield was identified. ZmCYP90D1 was inferred to influence plant height and stalk diameter via hormone-mediated cell division and cell growth via the BR pathway.

Nitrogen (N) fertilization is necessary for obtaining high rice yield. But excessive N fertilizer reduces rice plant N efficiency and causes negative effects such as environmental pollution. In this study, we assembled key genes involved in different nodes of N pathways to boost nitrate and ammonium uptake and assimilation, and to strengthen amino acid utilization to increase grain yield and nitrogen use efficiency (NUE) in rice. The combinations OsNPF8.9a × OsNR2, OsAMT1;2 × OsGS1;2 × OsAS1, and OsGS2 × OsAS2 × OsANT3 optimized nitrate assimilation, ammonium conversion, and N reutilization, respectively. In co-overexpressing rice lines obtained by co-transformation, the tiller number, biomass, and grain yield per plant of the OsAMT1;2 × OsGS1;2 × OsAS1-overexpressing line exceeded those of wild-type ZH11, the OsNPF8.9a × OsNR2 × OsGS1;2 × OsAS1-overexpressing line, and the OsGS2 × OsAS2 × OsANT3-overexpressing line. The glutamine synthase activity, free amino acids, and nitrogen utilization efficiency (NUtE) of the OsAMT1;2 × OsGS1;2 × OsAS1-overexpressing line exceeded those of ZH11 and other lines that combined key genes. N influx efficiency was increased in the OsAMT1;2 × OsGS1;2 × OsAS1-overexpressing line and OsNPF8.9a × OsNR2 × OsGS1;2 × OsAS1-overexpressing line under a low ammonium and a low nitrate treatment, respectively. We propose that combining overexpression of OsAMT1;2, OsGS1;2, and OsAS1 is a promising breeding strategy for systematically increasing rice grain yield and NUE by focusing on key nodes in the N pathway.

Trehalose (Tre) is a non-reducing disaccharide found in many species, including bacteria, fungi, invertebrates, yeast, and even plants, where it acts as an osmoprotectant, energy source, or protein/membrane protector. Despite relatively small amounts in plants, Tre concentrations increase following exposure to abiotic stressors. Trehalose-6-phosphate, a precursor of Tre, has regulatory functions in sugar metabolism, crop production, and stress tolerance. Among the various abiotic stresses, temperature extremes (heat or cold stress) are anticipated to impact crop production worldwide due to ongoing climate changes. Applying small amounts of Tre can mitigate negative physiological, metabolic, and molecular responses triggered by temperature stress. Trehalose also interacts with other sugars, osmoprotectants, amino acids, and phytohormones to regulate metabolic reprogramming that underpins temperature stress adaptation. Transformed plants expressing Tre-synthesis genes accumulate Tre and show improved stress tolerance. Genome-wide studies of Tre-encoding genes suggest roles in plant growth, development, and stress tolerance. This review discusses the functions of Tre in mitigating temperature stress—highlighting genetic engineering approaches to modify Tre metabolism, crosstalk, and interactions with other molecules—and in-silico approaches for identifying novel Tre-encoding genes in diverse plant species. We consider how this knowledge can be used to develop temperature-resilient crops essential for sustainable agriculture.

Salinity impairs plant growth, limiting agricultural development. It is desirable to identify genes responding to salt stress and their mechanism of action. We identified a function of the Zea mays WRKY transcription factor, ZmWRKY104, in salt stress response. ZmWRKY104 was localized in the nucleus and showed transcriptional activation activity. Phenotypic and physiological analysis showed that overexpression of ZmWRKY104 in maize increased the tolerance of maize to salt stress and alleviated salt-induced increases in O₂^- accumulation, malondialdehyde (MDA) content, and percent of electrolyte leakage. Further investigation showed that ZmWRKY104 increased SOD activity by regulating ZmSOD4 expression. Yeast one-hybrid, electrophoretic mobility shift test, and chromatin immunoprecipitation-quantitative PCR assay showed that ZmWRKY104 bound directly to the promoter of ZmSOD4 by recognizing the W-box motif in vivo and in vitro. Phenotypic, physiological, and biochemical analysis showed that ZmSOD4 increased salt tolerance by alleviating salt-induced increases in O₂^- accumulation, MDA content, and percent of electrolyte leakage under salt stress. Taken together, our results indicate that ZmWRKY104 positively regulates ZmSOD4 expression to modulate salt-induced O₂^- accumulation, MDA content, and percent of electrolyte leakage, thus affecting salt stress response in maize.

The delta-1-pyrroline-5-carboxylate synthetase (P5CS) gene exercises a protective function in stressed plants. However, the relationship between proline accumulation caused by P5CS and abiotic stress tolerance in plants is not always clear, as P5CS overexpression has been reported to repress plant growth under normal conditions in several reports. We re-evaluated the role of P5CS in drought-tolerant rice breeding by expressing the AtP5CS1 and feedback-inhibition-removed AtP5CS1 (AtP5CS1^F128A) genes under the regulation of an ABA-inducible promoter to avoid the potential side effects of P5CS overexpression under normal conditions. ABA-inducible AtP5CS1 and AtP5CS1^F128A increased seedling growth in a nutrient solution (under osmotic stress) and grain yield in pot plants. However, the evidently deleterious effects of AtP5CS1 on grain quality, tiller number, and grain yield in the field indicated the unsuitability of P5CS for drought-tolerance breeding.

The genetic pathways of rice seedling growth have a major impact on seedling emergence from soil and development. In this study, we identified a new bHLH transcription factor, BEAR1, from rice RNAi mutant library. Both the BEAR1-RNAi and bear1 CRISPR mutants had accelerated seedling growth. Histological section of leaves showed accelerated development of lacuna and vascular bundles in bear1 mutant. GUS staining revealed that BEAR1 was highly expressed in coleoptiles and leaves at seedling stage. Expression analysis of gibberellin (GA) biosynthesis and metabolic genes and content determination of active GAs indicated that the expression of GA biosynthesis genes, especially OsKS4 and OsCPS2, were upregulated and the GAs content were significantly increased in bear1, which correlated with the seedling phenotype of bear1 mutant. Molecular and biochemical assays revealed that BEAR1 directly binds to the promoter of OsKS4, thereby repressing its expression. Haplotypes analysis showed clear differentiation in indica and japonica rice varieties, and a strong correlation with seedling height. These findings provide novel insights into the regulation of seedling growth in rice.

Foliar nitrogen (N) application is an effective strategy to improve protein content and quality in wheat kernels, but the specific effects of N forms remain unclear. In a two-year field study, foliar application of various N forms (NO₃^-, urea, NH₄⁺) at anthesis was performed to measure their effects on wheat grain protein accumulation, quality formation, and the underlying mechanisms. Foliar application of three N forms showed varying effects in improving grain gluten proteins and quality traits. Under NH₄⁺ application, there was more post-anthesis N uptake for grain filling, with relatively strong increase in enzyme activities and gene expression associated with N metabolism in flag leaves at 8-20 days after anthesis (DAA), whereas its promotion of grain N metabolism became weaker after 20 DAA than those under NO₃^- and urea treatments. More N was remobilized from source organs to grain under treatment with foliar NO₃^- and urea. Genes controlling the synthesis of gluten protein and disulfide bonds were upregulated by NO₃^- and urea at 20-28 DAA, contributing to increased grain protein content and quality. Overall, foliar applications of NO₃^- and urea were more effective than those of NH₄⁺ in increasing grain N filling. These findings show that manipulating the source-sink relationship by reinforcing grain N metabolism and N remobilization is critical for optimizing grain protein accumulation and quality formation.

Interaction between the embryo and endosperm affects seed development, an essential process in yield formation in crops such as rice. Signals that mediate communication between embryo and endosperm are largely unknown. We used the notched-belly (NB) mutant with impaired communication between embryo and endosperm to investigate the effect of the embryo on developmental staging of the endosperm and signaling pathways in the embryo that regulate endosperm development. Hierachical clustering of mRNA datasets from embryo and endosperm samples collected during development in NB and a wild type showed a delaying effect of the embryo on the developmental transition of the endosperm by extension of the middle stage. K-means clustering further identified coexpression modules of gene sets specific to embryo and endosperm development. Combined gene expression and biochemical analysis showed that T6P-SnRK1, gibberellin and auxin signaling by the embryo regulate endosperm developmental transition. We propose a new seed developmental staging system for rice and identify the most detailed signature of rice grain formation to date. These will direct genetic strategies for rice yield improvement.

Pre-harvest sprouting (PHS) is one of the serious global issues in wheat production. Identification of quantitative trait loci (QTL) and closely-linked markers is greatly helpful for wheat improvement. In the present study, a recombinant inbred line (RIL) population derived from the cross of Zhongmai 578 (ZM578)/Jimai 22 (JM22) and parents were phenotyped in five environments and genotyped by the wheat 50 K single-nucleotide polymorphism (SNP) array. Two QTL of germination index (GI), QGI.caas-3A and QGI.caas-5A, were detected, explaining 4.33%-5.58% and 4.43%-8.02% of the phenotypic variances, respectively. The resistant effect of QGI.caas-3A was contributed by JM22, whereas that of QGI.caas.5A was from ZM578. The two QTL did not correspond to any previously identified genes or genetic loci for PHS-related traits according to their locations in the Chinese Spring reference genome, indicating that they are likely to be new loci for PHS resistance. Four kompetitive allele-specific PCR (KASP) markers K_AX-109605367and K_AX-179559687 flanking QGI.caas-3A, and K_AX-111258240 and K_AX-109402944 flanking QGI.caas-5A, were developed and validated in a natural population of 100 wheat cultivars. The distribution frequency of resistance alleles at Qphs.caas-3A and Qphs.caas-5A loci were 82.7% and 57.1%, respectively, in the natural population. These findings provide new QTL and tightly linked KASP markers for improvement of PHS resistance in wheat.

Kernel size, one of the traits that determine wheat yield, is controlled by multiple quantitative trait loci. Polish wheat (Triticum polonicum) has elongated and plump kernel and is a valuable material for breeding high-yielding wheat cultivars. However, genes or loci determining kernel length (KL) in Polish wheat are unknown. We identified and validated a major KL gene, KL-PW, at the P1 locus in Polish wheat. KL-PW is VRT-A2, which encodes a MIKC-type MADS-box protein (MADS55). An insertion/deletion mutation in intron 1 of VRT-A2^PW led to an alternatively spliced transcript, VRT-A2^PW2. Quantitative PCR analysis showed that VRT-A2^PW was more highly expressed in developing seeds than was VRT-A2^Ailanmai. Brassinosteroid (BR) sensitivity experiment and the expression of BR-related genes indicated that VRT-A2^PW functions as a positive regulator of BR responses. VRT-A2^PW significantly increased KL of wheat. These findings not only reveal the molecular basis of KL-PW in controlling KL, but also provide a valuable genetic resource for increasing kernel size in wheat.

The development of rice cultivars with improved nitrogen use efficiency (NUE) is desirable for sustainable agriculture. Achieving this goal depends in part on understanding how rice responds to low soil nitrogen (N) and identifying causative genes underlying this trait. To identify quantitative trait loci (QTL) or genes associated with low N response, we conducted a genome-wide association study (GWAS) using a diverse panel of 230 rice accessions and performed a transcriptomic investigation of rice accessions with differential responses to low N stress at two N levels. We detected 411 GWAS-associated genes in 5 QTL and 2722 differentially expressed genes in response to low N, of which 24 were identified by both methods and ranked according to gene annotations, literature queries, gene expression, and genetic diversity analysis. The large-scale datasets obtained from this study reveal low N-responsive characteristics and provide insights towards understanding the regulatory mechanisms of N-deficiency tolerance in rice, and the candidate genes or QTL would be valuable resources for increasing rice NUE via molecular biotechnology.

Phytophthora sojae infection severely impairs soybean production. We previously identified a dirigent protein, GmDRR1 (Glycine max Disease Resistant Response 1), that increases soybean resistance to P. sojae. However, the molecular basis of GmDRR1 function remained largely uncharacterized. In the present study, analysis of GmDRR1-RNAi, GmDRR1-overexpressing, and CRISPR/Cas9-derived Gmdrr1 mutant lines revealed that GmDRR1 expression significantly restricted P. sojae growth. Combining co-immunoprecipitation with liquid chromatography-tandem mass spectrometry revealed a GmDRR1-interacting protein, GmDRR2, which is homologous to GmDRR1. An E-coniferyl alcohol coupling assay indicated that GmDRR1 promotes the synthesis of (+)-pinoresinol, which helps to protect plants from P. sojae. The GmNAC1 (Glyma.05G025500) transcription factor bound to the GmDRR1 promoter both in vitro and in vivo to upregulate GmDRR1 expression. Soybean resistance to P. sojae was increased by overexpression of GmNAC1. Our findings suggest a novel signaling pathway involving a NAC transcription factor that mediates soybean resistance to P. sojae. Specifically, GmNAC1 directly induces GmDRR1 expression to increase resistance of soybean plants to P. sojae.

Puccinia striiformis Westend. f. sp. tritici (Pst) pathotype CYR34 is widely virulent and prevalent in China. Here, we report identification of a strpie rust resistance (Yr) gene, designated Yr041133, in winter wheat line 041133. This line produced a hypersensitive reaction to CYR34 and conferred resistance to 13 other pathotypes. Resistance to CYR34 in line 041133 was controlled by a single dominant gene. Bulked segregant RNA sequencing (BSR-Seq) was performed on a pair of RNA bulks generated by pooling resistant and susceptible recombinant inbred lines. Yr041133 was mapped to a 1.7 cM genetic interval on the chromosome arm 7BL that corresponded to a 0.8 Mb physical interval (608.9-609.7 Mb) in the Chinese Spring reference genome. Based on its unique physical location Yr041133 differred from the other Yr genes on this chromosome arm.

The jasmonic acid (JA) signaling pathway is involved in plant growth, development, and response to abiotic or biotic stresses. MYC2, a bHLH transcription factor, is a regulatory hub in the pathway. The function of ZmMYC7, a putative MYC2 ortholog, in jasmonate-signaled defense responses of maize has not been reported. In this study, we found that ZmMYC7 possesses JID, TAD, bHLH and Zip domains and essential characteristics of transcription factors: a nuclear location and transactivation activity. The ZmMYC7 mutants showed markedly increased sensitivity to Fusarium graminearum and Setosphaeria turcica. The expression levels of the defense-associated genes ZmPR1, ZmPR2, ZmPR3, ZmPR5, ZmPR6, and ZmPR7 in response to F. graminearum infection were downregulated in ZmMYC7 mutants, while ZmPR4 and ZmPR10 were up-regulated. ZmMYC7 interacted with members of the ZmJAZ family, including ZmJAZ8, ZmJAZ11, and ZmJAZ12. ZmMYC7 physically interacted with G-box cis-elements in the ZmERF147 promoter in vitro and transcriptional activation of ZmERF147 by ZmMYC7 was inhibited by ZmJAZ11 and ZmJAZ12. ZmERF147 mutants were more susceptible to F. graminearum infection than inbred line B73 with concomitant down-regulation of all defense-associated ZmPRs except ZmPR4. These findings indicate that ZmMYC7 functions in maize resistance to F. graminearum and sheds light on maize defense responses to pathogenic fungi via the JA signaling pathway.

Rye (Secale cereale genome RR), a close relative of common wheat, possesses valuable resistance genes for wheat improvement. Due to the co-evolution of pathogen virulence and host resistance, some resistance genes derived from rye have lost effectiveness. Development and identification of new, effective resistance genes from rye is thus required. In the current study, wheat-rye line WR56 was produced through distant hybridization, embryo rescue culture, chromosome doubling and backcrossing. WR56 was then proved to be a wheat-rye 2RL ditelosomic addition line using GISH (genomic in situ hybridization), mc-FISH (multicolor fluorescence in situ hybridization), ND-FISH (non-denaturing FISH), mc-GISH (multicolor GISH) and rye chromosome arm-specific marker analysis. WR56 exhibited a high level of adult plant resistance to powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt). This resistance was carried by the added 2RL telosomes and presumed to be different from Pm7 which is also located on chromosome arm 2RL but confers resistance at the seedling and adult stages. WR56 will be a promising bridging parent for transfer of the resistance to a more stable wheat breeding line. A newly developed 2RL-specific KASP (kompetitive allele specific PCR) marker should expedite that work.

Wheat tiller angle (TA) is an important agronomic trait that contributes to grain production by affecting plant architecture. It also plays a crucial role in high-yield wheat breeding. An association panel and a recombinant inbred line (RIL) population were used to map quantitative trait loci (QTL) for TA. Results showed that 470 significant SNPs with 10.4%-28.8% phenotypic variance explained (PVE) were detected in four replicates by a genome-wide association study (GWAS). Haplotype analysis showed that the TA_Hap_4B1 locus on chromosome 4B was a major QTL to regulate wheat TA. Ten QTL were totally detected by linkage mapping with the RIL population, and QTA.hau-4B.1 identified in six environments with the PVE of 7.88%-18.82% was a major and stable QTL. A combined analysis demonstrated that both TA_Hap_4B1 and QTA.hau-4B.1 were co-located on the same region. Moreover, QTA.hau-4B.1 was confirmed by bulked segregant RNA-Seq (BSR-Seq) analysis. Phenotypic analysis showed that QTA.hau-4B.1 was also closely related to yield traits. Furthermore, TraesCS4B02G049700 was considered as a candidate gene through analysis of gene sequence and expression. This study can be potentially used in cloning key genes modulating wheat tillering and provides valuable genetic resources for improvement of wheat plant architecture.

The size and shape of rice grains influence their yield and commercial value. We investigated the role of OsDA1, a rice homolog of the Arabidopsis DA1 gene, in regulating grain size and shape. OsDA1 was highly expressed in young spikelets and glumes. Its overexpression led to enlarged seeds with increased width and decreased length/width ratio (LWR) and knocking out OsDA1 reduced grain width and increased grain length and LWR. A R310K point mutation in the DA1-like domain is a potential target for breeding for increased grain width and length. OsDA1 interacted with TCP gene-family proteins to regulate grain size and shape. Our findings deepen our understanding of the molecular mechanisms underlying grain size regulation and provide useful information for improving grain yield.

Cotton architecture is partly determined by shoot branching and flowering patterns. GhBRC1 was previously identified by RNA-seq analysis of nulliplex-branching and normal-branching cotton. However, the roles of GhBRC1 in cotton remain unclear. In the present study, investigations of nuclear localization and transcriptional activity indicated that GhBRC1 has characteristics typical of transcription factors. Gene expression analysis showed that GhBRC1 was highly expressed in axillary buds but displayed different expression patterns between the two branching types. Overexpression of GhBRC1 in Arabidopsis significantly inhibited the number of branches and promoted flowering. In contrast, silencing GhBRC1 in cotton significantly promoted seedling growth. GhBRC1 was induced by multiple hormones, including strigolactones, which promoted seedling growth and seed germination of Arabidopsis plants overexpressing GhBRC1. Consistent with these findings, RNA-seq analysis of virus-induced gene silencing treated cotton revealed that a large number of genes were differentially expressed between GhBRC1-silenced and control plants, and these genes were significantly enriched in plant hormone signalling pathways. Together, our data indicates that GhBRC1 regulates plant branching and flowering through multiple regulatory pathways, especially those regulating plant hormones, with functions partly differing from those of Arabidopsis BRC1. These results provide insights into the molecular mechanisms controlling plant architecture, which is important for breeding cotton with ideal plant architecture and high yield.

Global food security is threatened by rice blast disease caused by the filamentous fungus Magnaporthe oryzae. An understanding of rice resistance mechanisms is fundamental to developing strategies for disease control. In this review, we summarize recent advances in pathogen-associated molecular pattern-triggered immunity, effector-triggered immunity, defense regulator-mediated immunity, and effects of nutrient elements on rice blast resistance. We outline strategies used for breeding rice cultivars with improved disease resistance. We also present the major research challenges for rice blast disease resistance and propose approaches for future investigation.

Genetic recombination produces new allelic combinations, thereby introducing variation for domestication. Allopolyploidization has increased the evolutionary potential of hexaploid common wheat by conferring the advantages of heterosis and gene redundancy, but whether a relationship exists between allopolyploidization and genetic recombination is currently unknown. To study the impact of allopolyploidization on genetic recombination in the ancestral D genome of wheat, we generated new synthetic hexaploid wheats by crossing tetraploid Triticum turgidum with multiple diploid Aegilops tauschii accessions, with subsequent chromosome doubling, to simulate the evolutionary hexaploidization process. Using the DArT-Seq approach, we determined the genotypes of two new synthetic hexaploid wheats with their parents, F₂ plants in a diploid population (2x, D₁D₁ × D₂D₂) and its new synthetic hexaploid wheat-derived population (6x, AABBD₁D₁ × AABBD₂D₂). About 11% of detected SNP loci spanning the D genome of Ae. tauschii were eliminated after allohexaploidization, and the degree of segregation distortion was increased in their hexaploid offspring from the F₂ generation. Based on codominant genotypes, the mean genetic interval length and recombination frequency between pairs of adjacent and linked SNPs on D genome of the hexaploid F₂ population were 2.3 fold greater than those in the diploid F₂ population, and the recombination frequency of Ae. tauschii was increased by their hexaploidization with T. turgidum. In conclusion, allopolyploidization increases genetic recombination of the ancestral diploid D genome of wheat, and DNA elimination and increased segregation distortion also occur after allopolyploidization. Increased genetic recombination could have produced more new allelic combinations subject to natural or artificial selection, helping wheat to spread rapidly to become a major global crop and thereby accelerating the evolution of wheat via hexaploidization.

Plant AT-rich sequence and zinc binding (PLATZ) transcription factors are a class of plant specific zinc-dependent DNA-binding proteins that function in abiotic stress response and plant development. In this study, 31 GmPLATZ genes were identified in soybean. GmPLATZ17 was down-regulated by drought and exogenous abscisic acid. Transgenic Arabidopsis and soybean hairy roots overexpressing GmPLATZ17 showed drought sensitivity and inhibition of stress-associated gene transcription. In contrast, suppressed expression of GmPLATZ17 led to increased drought tolerance in transgenic soybean hairy roots. The GmPLATZ17 protein was verified to interact physically with the GmDREB5 transcription factor, and overexpression of GmDREB5 increased drought tolerance in soybean hairy roots. Interaction of GmPLATZ17 with GmDREB5 was shown to interfere with the DRE-binding activity of GmDREB5, suppressing downstream stress-associated gene expression. These results show that GmPLATZ17 inhibits drought tolerance by interacting with GmDREB5. This study sheds light on PLATZ transcription factors and the function of GmPLATZ17 in regulating drought sensitivity.

Cotton fiber is a raw material for the global textile industry and fiber quality is essential to its industrial application. Carotenoids are plant secondary metabolites that may serve as dietary components, regulate light harvesting, and scavenge reactive oxygen species. Although carotenoids accumulate predominantly in rapidly elongating cotton fibers, their roles in cotton fiber development remain poorly understood. In this study, a fiber-specific promoter proSCFP was applied to drive the expression of GhOR1^Del, a positive regulator of carotenoid accumulation, to upregulate the carotenoid level in cotton fiber in planta. Fiber length, strength, and fineness were increased in proSCFP:GhOR1^Del transgenic cotton and abscisic acid (ABA) and ethylene contents were increased in elongating fibers. The ABA downstream regulator GhbZIP27a stimulated the expression of the ethylene synthase gene GhACO3 by binding to its promoter, suggesting that ABA promoted fiber elongation by increasing ethylene production. These findings suggest the involvement of carotenoids and ABA signaling in promoting cotton fiber elongation and provide a strategy for improving cotton fiber quality.

A biparental soybean population of 364 recombinant inbred lines (RILs) derived from Zhongdou 41 × ZYD 02.878 was used to identify quantitative trait loci (QTL) associated with hundred-seed weight (100-SW), pod length (PL), and pod width (PW). 100-SW, PL, and PW showed moderate correlations among one another, and 100-SW was correlated most strongly with PW (0.64-0.74). Respectively 74, 70, 75 and 19 QTL accounting for 38.7%-78.8% of total phenotypic variance were identified by inclusive composite interval mapping, restricted two-stage multi-locus genome-wide association analysis, 3 variance-component multi-locus random-SNP-effect mixed linear model analysis, and conditional genome-wide association analysis. Of these QTL, 189 were novel, and 24 were detected by multiple methods. Six loci were associated with 100-SW, PL, and PW and may be pleiotropic loci. A total of 284 candidate genes were identified in colocalizing QTL regions, including the verified gene Seed thickness 1 (ST1). Eleven genes with functions involved in pectin biosynthesis, phytohormone, ubiquitin-protein, and photosynthesis pathways were prioritized by examining single nucleotide polymorphism (SNP) variation, calculating genetic differentiation index, and inquiring gene expression. The prediction accuracies of genomic selection (GS) for 100-SW, PL, and PW based on single trait-associated markers reached 0.82, 0.76, and 0.86 respectively, but selection index (SI)-assisted GS strategy did not increase GS efficiency and inclusion of trait-associated markers as fixed effects reduced prediction accuracy. These results shed light on the genetic basis of 100-SW, PL, and PW and provide GS models for these traits with potential application in breeding programs.

The emergence and spread of wheat blast caused by fungal pathogen Magnaporthe oryzae pathotype Triticum is a threat to global wheat production. The resistance level and genetic loci for blast resistance in Chinese germplasm remain unknown. A panel of 266 bread wheat accessions from China, CIMMYT-Mexico and other countries was screened for head blast resistance under 12 field experiments in Bolivia and Bangladesh. Subsequently, a genome-wide association study was performed to understand the genetic basis of wheat blast resistance. The average blast index of all the accessions was 53.7% ± 12.7%, and 10 accessions including Chinese accessions Yumai 10 and Yu 02321 showed moderate to high levels of blast resistance, accounting for only 3.8% in the panel. Fifty-eight significant SNPs clustered in a 28.9 Mb interval on the 2AS/2NS translocation region, explaining phenotypic variation between 10.0% and 35.0%. The frequency of the 2AS/2NS translocation in the Chinese accessions was as low as 4.5%. These results indicated that the 2NS fragment was the only major locus conferring resistance to wheat blast in this panel, and the resistant and moderately resistant lines identified could be deployed in breeding.

Low temperature in early spring impairs wheat growth and grain yield. However, little is known about the cytological and molecular mechanisms underlying low temperature regulation of wheat spike development. Microstructure observation and transcriptome sequencing of wheat spikes under low temperature were conducted. Low temperature slowed spike development, reduced the yield-component parameters of wheat spikes at the harvest stage, delayed the formation of lateral spikelets and tissue development, and induced the early differentiation of terminal spikelets. Low temperature increased the content of abscisic acid and caused the upregulation of genes in the abscisic acid signaling pathway, including those encoding PP2Cs, SnRK2s, and bZIP transcription factors. Low temperature also induced the upregulation of 33 cold-responsive genes involved in wheat response to low-temperature stress and regulation of abscisic acid biosynthesis and metabolism of other substances. The wheat spike adapted to cold conditions by changing the expression levels of genes involved in spike morphogenesis, including the transcription-factor genes MADS6, ERF4, ERF78, WOX6, and NAC48. These findings suggest that low temperature in early spring delays wheat spike development by increasing abscisic acid content or affecting the expression of genes involved in morphogenesis.

Wheat production is seriously influenced by extreme hot weather, which has attracted increasing attention. It is important to compare wheat responses to heat at seedling and reproductive stages, to explore the potential relationship between the performances at different growing stages and the possibility of early selection to accelerate heat tolerance breeding. In this study, forty wheat genotypes were screened under heat stress at both seedling and adult stages. It was found that root lengths at seedling stage were severely reduced by heat stress with significant variations among wheat genotypes. Heat-tolerant genotypes at seedling stage showed less root length decrease than susceptible ones. Wheat genotypes tolerant at seedling stage showed higher yield at adult stage after heat treatment. The performances of wheat genotypes screened under heat stress at seedling and adult stages were ranked by seedling damage index and adult damage index. A significant positive relationship was found between heat tolerance at seedling stage and at adult stage (r=0.6930), suggesting a similar tolerant/susceptible mechanism at different plant growth stages and the possibility of early selection at seedling stage for breeding heat tolerance. Extremely tolerant and susceptible genotypes with consistent performances at seedling and adult stages were genetically compared and associated SNP markers and linked candidate genes were identified.

Knowledge of rice (Oryza sativa L.) genes and various DNA markers can be used in genomic breeding programs aimed at developing improved elite rice cultivars. We used an efficient genomic breeding approach to pyramid four resistance genes (Pi2, Xa23, Bph14, and Bph15) in the popular photoperiod- and thermo-sensitive genic male sterile (PTGMS) rice line Feng39S. We performed foreground selection for the target genes, followed by recombinant selection and background selection. This process reduced the sizes of the genomic segments harboring the target genes (566.8 kb for Pi2, 1143.9 kb for Xa23, 774.7 kb for Bph14, and 1574.9 kb for Bph15) and accelerated the recovery of the recurrent parent genome to proportions ranging from 98.77% to 99.16%, thus resulting in four near-isogenic lines. To assemble the four resistance genes in Feng39S, we performed a double-way cross combined with foreground and background selection to generate two improved lines of Feng39S (Pi2 + Xa23 + Bph14 + Bph15) with a recurrent parent genome recovery of 98.98%. The two lines showed agronomic performance, grain quality, and fertility-sterility transition characteristics similar to those of the original Feng39S line. The newly developed PTGMS lines and corresponding hybrid combinations were resistant to various field blast isolates and seven representative isolates of bacterial blight. At the seedling stage, the lines also showed resistance against brown planthopper. This study provides an efficient and accurate genomic breeding approach for introducing desirable traits into PTGMS lines.

Maize ear development determines the crop yield, and many important transcription factors (TFs) have been identified to function in this process. However, their transcriptional regulation mechanisms are still elusive. In this study, we generated the genome-wide DNA binding sites for 8 TFs which are known to function or highly expressed in inflorescence by applying the tsCUT&Tag method in maize leaf protoplast. We exposed a regulatory grid of 4 WUSCHEL-related homeobox (WOX) genes and revealed their potential regulatory mechanisms. In addition, a hierarchical regulation network for the determinacy and specification of maize inflorescence meristems were also constructed using the binding profiles of a floral development gene INDETERMINATE FLORAL APEX1 (IFA1) and 3 MADS-box genes. Our study provides an in-depth understanding and new insights of the regulatory mechanisms during maize inflorescence development.

CRISPR-Cas9 is a common tool for gene editing, and appropriate sgRNAs are the key factor for successful editing. In this study, the effect of sgRNA length and number on editing efficiency was analyzed in rice using CYP81A6 as the target gene. A series of CRISPR-Cas9 plant expression vectors containing single sgRNAs with different lengths (17, 18, 19, 20, 21, 22, 23 nt) or two sgRNAs were constructed and introduced into rice cultivar Zhonghua11 by Agrobacterium-mediated transformation. Analysis of the editing status of 1283 transgenic rice plants showed that 371 were successfully edited with base preference. Single A or T insertions were the most frequent among the six edited types. The editing efficiency of transgenic rice with two sgRNAs was higher than that with a single sgRNA. Editing efficiency and sgRNA length showed a normal distribution with 20 nt sgRNA (25%) being the most efficient. The editing efficiency decreased slightly with decreases of 1-2 bases (19 nt 20%, 18 nt 21%), but decreased significantly with a decrease of 3 bases (17 nt 4.5%). Editing efficiency was significantly reduced by adding 1 to 3 bases (21 nt 16.8%, 22 nt 13%, 23 nt 13%) to the sgRNA. These results provide data for successful gene editing or rice by CRISPR-Cas9.

Root hairs are fast growing, ephemeral tubular extensions of the root epidermis that aid nutrient and water uptake. The aim of the present study was to identify QTL for root hair length (RHL) using 227 F₈ recombinant inbred lines (RILs) derived from a cross of Zhou 8425B (Z8425B) and Chinese Spring (CS), and to develop convenient molecular markers for marker-assisted breeding in wheat. Analysis of variance of root hair length showed significant differences (P < 0.01) among RILs. The genetic map for QTL analysis consisted of 3389 unique SNP markers. Using composite interval mapping, four major QTL (LOD > 2.5) for RHL were identified on chromosomes 1B (2), 2D and 6D and four putative QTL (2 ≤ LOD ≤ 2.5) were detected on chromosomes 1A, 3A, 6B, and 7B, explaining 3.32%-6.52% of the phenotypic variance. The positive alleles for increased RHL of QTL on chromosomes 2D, 6B and 6D (QRhl.cau-2D, qRhl.cau-6B, and QRhl.cau-6D) were contributed by Z8425B, and CS contributed positive QTL alleles on chromosomes 1A (qRhl.cau-1A), 1B (QRhl.cau-1B.1 and QRhl.cau-1B.2), 3A (qRhl.cau-3A) and 7B (qRhl.cau-7B). STARP markers were developed for QRhl.cau-1B.1, QRhl.cau-2D, QRhl.cau-6D, and qRhl.cau-7B. Haplotype and association analysis indicated that the positive allele of QRhl.cau-6D had been strongly selected in Chinese wheat breeding programs. Collectively, the identified QTL for root hair length are likely to be useful for marker-assisted selection.

Chloroplasts are essential for plant growth and development, as they play a key role in photosynthesis. The chloroplast biogenesis process is complex and its regulatory mechanism remains elusive. We characterized a spontaneous Brassica napus (rapeseed) mutant, ytg, that showed a delayed greening phenotype in all green organs and retarded growth. We identified BnaA02.YTG1 encoding a chloroplast-localized tetratricopeptide repeat protein widely expressed in rapeseed tissues. We speculated that the ytg phenotype was caused by the deletion of BnaA02.YTG1 based on sequence comparison of 4608 (with normal green leaves, isolated from the elite Chinese rapeseed cultivar ZS11) and ytg combined with transcriptome data and CRISPR/Cas9 gene editing results. The homologous gene (BnaC02.YTG1) restored the phenotype of the mutant. BnaA02.YTG1 interacted with MORF2, MORF8, and OZ1. RNA editing of the ndhD-2, ndhF-290, petL-5, and ndhG-50 plastid transcripts was affected in ytg. These findings suggested that BnaA02.YTG1 participates in RNA editing events. We predicted 29 RNA editing sites in the chloroplast of Brassica napus by comparison with the Arabidopsis chloroplast genome. We conclude that BnaA02.YTG1 affects the posttranscriptional regulation of plastid gene expression and suggest that a tetratricopeptide repeat protein is involved in the chloroplast RNA editing in rapeseed.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases threatening the yield and stability of wheat production in China and many other countries. Identification and utilization of new genes for durable stripe rust resistance are important for ongoing control of this disease. The objectives of this study were to identify quantitative trait loci (QTL) associated with adult-plant stripe rust resistance in the Chinese wheat landrace Yibinzhuermai (YBZR) and to provide wheat breeders with new sources of potentially durable resistance. A total of 117 recombinant inbred lines (RILs) (F_5:8) derived from a cross between YBZR and highly susceptible cultivar Taichung 29 (TC29) were assessed for stripe rust severity in field experiments at Wenjiang in 2016 and 2017 and Chongzhou in 2016, 2017, 2018, and 2019 in Sichuan following inoculation with a mixture of current Pst races. The RILs were genotyped using the Wheat55K single nucleotide polymorphism (SNP) array. Three QTL were identified on chromosome arms 6AL, 5BL and 7DS. QYr.YBZR-6AL and QYr.YBZR-7DS conferred major effects in all field environments, explaining 10.6% to 14.7% and 11.5% to 21.2% of phenotypic variation, respectively. The QTL on 5BL and 7DS likely correspond to previously known QTL, whereas QYr.YBZR-6AL is probably novel. Haplotype analysis revealed that the resistance allele at QYr.YBZR-6AL was present in 2.8% of 324 Chinese wheat landraces. SNP markers closely linked with QYr.YBZR-6AL were converted to kompetitive allele-specific PCR markers and validated in the RIL population and a subset of 92 wheat cultivars. QYr.YBZR-6AL and its markers should be useful in breeding programs to improve the level and durability of stripe rust resistance.

Drought stress caused by insufficient irrigation or precipitation impairs agricultural production worldwide. In this study, a two-year field experiment was conducted to investigate the effect of coronatine (COR), a functional analog of jasmonic acid (JA), on maize drought resistance. The experiment included two water treatments (rainfed and irrigation), four COR concentrations (mock, 0 μmol L^-1; A1, 0.1 μmol L^-1; A2, 1 μmol L^-1; A3, 10 μmol L^-1) and two maize genotypes (Fumin 985 (FM985), a drought-resistant cultivar and Xianyu 335 (XY335), a drought-sensitive cultivar). Spraying 1 μmol L^-1 COR at seedling stage increased surface root density and size, including root dry matter by 12.6%, projected root area by 19.0%, average root density by 51.9%, and thus root bleeding sap by 28.2% under drought conditions. COR application also increased leaf area and SPAD values, a result attributed to improvement of the root system and increases in abscisic acid (ABA), JA, and salicylic acid (SA) contents. The improvement of leaves and roots laid the foundation for increasing plant height and dry matter accumulation. COR application reduced anthesis and silking interval, increasing kernel number per ear. COR treatment at 1 μmol L^-1 increased the yield of XY335 and FM985 by 7.9% and 11.0%, respectively. Correlation and path analysis showed that grain yields were correlated with root dry weight and projected root area, increasing maize drought resistance mainly via leaf area index and dry matter accumulation. Overall, COR increased maize drought resistance mainly by increasing root dry weight and root area, with 1 μmol L^-1 COR as an optimal concentration.

Cytokinins (CKs) function in plant development and during stress responses, but their role in drought tolerance in wheat is unknown. In the present study, 24 isopentenyltransferase (IPT) genes, encoding rate-limiting enzymes in CK biosynthesis were identified in the wheat genome. The chromosomal locations and structures of the genes, protein properties, and phylogenetic relationships were characterized. ATP/ADP TaIPT genes showed tissue-specific expression. TaIPT2, TaIPT7, and TaIPT8 expression was rapidly induced by 0.5-1 h drought treatments, which decreased to low levels after 2 h drought treatment, as did most other TaIPT genes. TaIPT8-5a/5b/5d triple mutants showed decreased levels of tZ-type CK under normal and drought conditions and reduced drought tolerance, which, however, did not manifest as phenotype alterations. By contrast, transgenic wheat plants with drought-induced TaIPT8 showed increased drought tolerance. Our study provides a foundation for further investigation of TaIPT genes and novel insights into the role of CKs in the drought response of wheat.