Strigolactones (SLs), which are biosynthesized mainly in roots, modulate various aspects of plant growth and development. Here, we review recent research on the role of SLs and their cross-regulation with auxin, cytokinin, and ethylene in the modulation of root growth and development. Under nutrient-sufficient conditions, SLs regulate the elongation of primary roots and inhibit adventitious root formation in eudicot plants. SLs promote the elongation of seminal roots and increase the number of adventitious roots in grass plants in the short term, while inhibiting lateral root development in both grass and eudicot plants. The effects of SLs on the elongation of root hairs are variable and depend on plant species, growth conditions, and SL concentration. Nitrogen or phosphate deficiency induces the accumulation of endogenous SLs, modulates root growth and development. Genetic analyses indicate cross-regulation of SLs with auxin, cytokinin, and ethylene in regulation of root growth and development. We discuss the implications of these studies and consider their potential for exploiting the components of SL signaling for the design of crop plants with more efficient soil-resource utilization.

Hessian fly (HF), Mayetiola destructor (Say) is an important pest of wheat in North Africa, North America, Southern Europe, Northern Kazakhstan, Northwestern China, and New Zealand. It can cause up to 30% yield losses and sometimes can result in complete crop failure if infestation coincides with young stage of the wheat crop. Studies to-date have shown the availability of genetic diversity in the wheat genetic resources (landraces, wild relatives, cultivars, etc.) for resistance to Hessian fly. About 37 resistance genes have been reported from these wheat genetic resources for resistance to Hessian fly, of which, some have been deployed singly or in combination in the breeding programs to develop high yielding varieties with resistance to HF. Deployment of resistant varieties in different agro-ecologies with other integrated management measures plays key role for the control of HF. This paper summarizes the importance, life cycle, mechanisms of resistance, gene mining, and wheat breeding efforts for HF resistance.

Grain protein content (GPC) is an indicator of cereal nutritional quality. Identification of genes involved in the regulation of GPC provides targets for molecular breeding for crop protein quality. We characterized a maize gene encoding the putative amino acid transporter ZmAAP6, a gene expressed mainly in immature seeds, especially in the basal endosperm transfer layer. Total protein and zein contents were decreased in ZmAAP6 null mutants and increased in ZmAAP6 overexpression (OE) lines, consistent with their changed in the size of protein bodies. Metabolic and transcriptomic analysis supported the regulatory role of ZmAAP6 in amino acid transportation. These results suggest that ZmAAP6 functions as a positive regulator of GPC in maize, shedding new light on the genetic basis of GPC regulation.

Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty. However, knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited. In this study, we characterized transcriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors. We identified 144,827, 99,609, and 219,379 Tn5 transposase-hypersensitive sites (THSs) in Gossypium arboreum, G. raimondii, and G. hirsutum, respectively, and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression. This observation was consistent with analysis of transcription-factor binding sites (TFBS) for 262 known motifs: genes with higher TFBS conservation scores (CS) showed less change than those genes with lower TFBS CS in expression levels. TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton. We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development (fiber-related genes). Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits.

Salt stress limits plant growth and development. In this study, changes in membrane lipids were investigated in leaves of sorghum seedlings subjected to salt stress (150 mmol L⁻¹ NaCl). Galactolipids (DGDG and MGDG) accounted for more than 65% of the total glycerolipids in sorghum leaves. The predominance of C36 molecular species in MGDG suggested that sorghum is an 18:3 plant. Under NaCl treatment, the content of major phospholipids (PC and PE) increased, accompanied by the activation of their metabolism pathways at the transcriptional level. In contrast, the proportion of MGDG and PG dropped drastically, leading to a decreased ratio of plastidic to non-plastidic lipids. An adjustment of glycerolipid pathway between the cytosolic and plastidic compartments was triggered by salt stress, as reflected by the increased conversion of PC to PA, providing precursors for galactolipid synthesis. The elevated DGDG resulted in increased DGDG/MGDG and bilayer/non-bilayer lipid ratios. The double-bond index of PC, PE, and DGDG increased markedly, evidently owing to the increased expression of FAD3 and FAD8. These findings will be helpful for understanding dynamic membrane lipid changes and adaptive lipid remodeling in sorghum response to salt stress.

Heading date (or flowering time), an important agronomic trait in crop species, is closely associated with regional adaptation and yield. Members of the Pseudo-Response Regulator (PRR) family play key roles in regulating flowering. However, their role and molecular mechanism controlling heading date in rice is not very clear. Here, we identified rice OsPRR protein, OsPRR59, which delayed heading under long-day conditions. OsPRR59 positively regulates yield by affecting plant height, secondary branches number per panicle, grain number per panicle, seed setting rate, and grain weight per plant. OsPRR59 is expressed in most tissues and its protein is localized to the nucleus. We also found that OsPRR59 directly binds to the promoter of Ehd3 to inhibit its expression. Compared with the WT, osprr59 ehd3 showed a significantly delayed heading phenotype, as did the ehd3 mutant. This was opposite to the phenotype of the osprr59 mutant, confirming that Ehd3 acted downstream of OsPRR59 in regulating rice flowering. Our results identified a direct regulator of Ehd3, and revealed a novel molecular mechanism of clock component OsPRR proteins in regulating heading date and provide a new genetic resource for fine-tuning heading date in rice.

Leaf inclination, a component of crop architecture, influences photosynthetic efficiency and planting density. Various factors, particularly the phytohormones auxin and brassinosteroids (BRs), function in regulating lamina joint bending, and understanding of the genetic control of leaf inclination will help to elucidate the relevant regulatory network. Screening a rice T-DNA insertion population revealed a mutant that was insensitive to auxin and displayed an enlarged leaf angle due to increased cell length on the adaxial side of the lamina joint. Genetic analysis revealed that the increased leaf inclination was caused by T-DNA insertion in the promoter region of OsIAA6, resulting in elevated OsIAA6 expression. Further study showed that OsIAA6 interacts with OsARF1 to suppress auxin signaling and regulates leaf inclination. OsIAA6 mediates the BR effects on lamina joint development, and OsBZR1, the key transcription factor in BR signaling, binds directly to the promoter of OsIAA6 to stimulate its transcription. These results indicate the roles of the OsIAA6-OsARF1 module in regulating rice leaf inclination and suggest the synergistic effects of the phytohormones auxin and BR.

The root system is fundamental for maize growth and yield. Characterizing its heterogeneity and cell type-specific response to nitrate at the single-cell level will shed light on root development and nutrient uptake. We profiled the transcriptomes of >7000 cells derived from root tips of maize seedlings grown on media with or without nitrate, and identified 11 major cell types or tissues and 85 cell type-specific nitrate-response genes, including several known nitrate metabolic genes. A pseudotime analysis showed a continuous pseudotime series with the beginning at meristematic zone cells and showed that the root hair cell was derived by differentiation of a subset of epidermal cells. Interspecies comparison of root cells between maize and rice revealed the conservation and divergence of the root cell types and identified 57, 216, and 80 conserved orthologous genes in root hair, endodermis, and phloem cells respectively. This study provides a global view of maize root tip developmental processes and responses to nitrate at the single-cell level. The genes described in the present work could serve as targets for further genetic analyses and accurate regulation of gene expression and phenotypic variation in specific cell types or tissues.

Drought stress impairs crop growth and productivity. Stress-associated proteins (SAPs), a class of zinc finger proteins containing the A20/AN1 domain, function in various stress responses in plants. However, little is known about the function of SAPs in drought-stress responses in soybean, an oil and protein crop. We report that a GmSAP5 protein confers drought tolerance by increasing sensitivity to abscisic acid (ABA) and reducing stomatal aperture. Overexpression and RNA interference of GmSAP5 in soybean hairy roots resulted in elevated resistance and sensitivity to drought stress, respectively. ABA and proline contents increased in GmSAP5-overexpressing plants under water-deficit conditions. Lower water loss rates and higher relative water contents were observed in GmSAP5-overexpressing plants, resulting in increased drought-stress resistance. A yeast one-hybrid assay and luciferase transient transcriptional activity assay showed that GmAREB3, an AREB/ABF transcription factor, could bind to the promoter of GmSAP5 and activate its expression. These results suggest that GmSAP5 acts downstream of GmAREB3 and improves drought-stress resistance by mediating ABA signaling.

Rice (Oryza sativa L.) is a staple cereal for more than two thirds of the world’s population. Soil salinity severely limits rice growth, development, and grain yield. It is desirable to elucidate the mechanism of rice’s salt-stress response. As the major source of H₂O₂, NADPH oxidase (Rboh) is believed to be involved in salt-stress tolerance. However, the function and mechanism of rice Rboh in salt stress response remain unclear. In this study, we found that the expression of OsRbohA was up-regulated by NaCl treatment in the shoots and roots of rice seedlings. Knockout of OsRbohA reduced the tolerance of rice to salt stress. Knockout of OsRbohA blocked NaCl-induced increases of NADPH activity and H₂O₂ content in roots. OsRbohA knockout inhibited root growth and disrupted K⁺ homeostasis by reducing the expression of K⁺ transporters and channel-associated genes (OsGORK, OsAKT1, OsHAK1, and OsHAK5) in roots under NaCl treatment. Under NaCl treatment, OsRbohA knockout also reduced subcellular K⁺ contents of the plasma membrane and soluble fraction. Overexpression of OsRbohA increased the expression of K⁺ transporters and channel-associated genes and reduced the loss of K⁺ ions in roots. These results indicate that OsRbohA-mediated H₂O₂ accumulation modulates K⁺ homeostasis, thereby increasing salt tolerance in rice.

Nitrate (NO₃⁻) uptake involves a finely regulated and complex multilevel response system. Elucidating the molecular mechanism of nitrate uptake may lead to improving the growth and productivity of plants in the presence of dynamic variation in nitrate concentration. In this study, we identified three lateral organ boundaries domain (LBD) transcription factors, OsLBD37, OsLBD38, and OsLBD39, as regulators of nitrate uptake in response to nitrogen (N) availability. OsLBD37, OsLBD38, and OsLBD39 were induced by ammonium and glutamine in rice roots. Individual or collective knockout of OsLBD37, OsLBD38, and OsLBD39 led to increased concentrations of nitrate and increased expression of OsNRT2.1, OsNRT2.2, and OsNRT2.3 respectively under high-N conditions, whereas overexpression of each of these three LBD genes produced opposite effects where N accumulation was reduced. Dual-luciferase reporter assay further confirmed that OsLBD37, OsLBD38, and OsLBD39 possessed transcription inhibitory activities in rice protoplast cells, downregulating the expression of OsNRT2.1/OsNRT2.2/OsNRT2.3. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsLBD37 interacted with OsLBD37, OsLBD38, and OsLBD39 in the nucleus. Together, these results show that OsLBD37, OsLBD38, and OsLBD39 collaborate to inhibit the expression of OsNRT2.1/OsNRT2.2/OsNRT2.3 transporters under N-sufficient conditions, thereby helping rice plants avoid excessive nitrate accumulation that may affect their growth.

Because high temperatures impair rice production, it is desirable to elucidate the regulatory mechanisms involved in rice response to heat stress. The objectives of this study were to identify candidate genes and characterize their response patterns during rice adaptation to high temperatures at the seedling stage. Ten heat-associated quantitative-trait loci were identified in a genome-wide association study. Comparison of transcript abundances in heat-sensitive and heat-tolerant rice pools under heat stress revealed approximately 400 differentially expressed genes. The expression of genes from heat-sensitive accessions changed more than those from heat-tolerant accessions under heat stress. Alternative splicing (AS) events responded to heat stress in rice. The types of AS variants significant different between the heat-sensitive and heat-tolerant accessions. Expression patterns differing between the heat-sensitive and heat-tolerant accessions were identified for genes known to be involved in heat stress. We identified eleven genes associated with rice heat stress response. These genes could be pyramided to breed heat-tolerant rice accessions.

Phytophthora root rot (PRR), caused by Phytophthora sojae, is a devastating disease of soybean. The NBS-LRR gene family is a class of plant genes involved in disease resistance. miRNA mediates plant response to biotic stresses by regulating the expression of target genes at the transcriptional or post-translational level. Glyma.16G135500, encoding an NBS-LRR-type protein, is a target of gma-miR1510 that responds to pathogen infections. We cloned and overexpressed Glyma.16G135500 (naming it GmTNL16) and knocked down miR1510 using short tandem target mimic technology to identify the roles of the GmTNL16/gma-miR1510 pair in the interaction of soybean and the oomycete. By overexpressing GmTNL16 in transgenic hairy roots of soybean, we showed that biomass of P. sojae was lower in overexpressing hairy roots than in control roots. Thus, miR1510 expression was reduced upon P. sojae infection, reflecting the induced expression of GmTNL16 conferring resistance to P. sojae in soybean. Differentially expressed genes were enriched in plant-pathogen interaction, plant hormone signal transduction, and secondary metabolism by RNA sequencing analyze. In particular, jasmonate and salicylic acid pathway-associated genes, including JAZ, COI1, TGA, and PR, responded to P. sojae infection. All of these results indicate that the GmTNL16/gma-miR1510 pair participates in soybean defense response via the JA and SA pathways.

Soybean (Glycine max) responds to ambient light variation by undergoing multiform morphological alterations, influencing its yield potential and stability in the field. Phytochromes (PHYs) are plant-specific red (R) and far-red (FR) light photoreceptors mediating photomorphogenesis and photoperiodic flowering. As an ancient tetraploid, soybean harbors four PHYA, two PHYB, and two PHYE paralogs. Except for GmPHYA2/E4 and GmPHYA3/E3, which have been identified as photoperiod-dependent flowering repressors, the functions of GmPHYs are still largely unclear. We generated a series of individual or combined mutations targeting the GmPHYA or GmPHYB genes using CRISPR/Cas9 technology. Phenotypic analysis revealed that GmPHYB1 mediates predominantly R-light induced photomorphogenesis, whereas GmPHYA2/E4 and GmPHYA3/E3, followed by GmPHYA1 and GmPHYB2, function redundantly and additively in mediating FR light responses in seedling stage. GmPHYA2/E4 and GmPHYA3/E3, with weak influence from GmPHYA1 and GmPHYA4, delay flowering time under natural long-day conditions. This study has demonstrated the diversified functions of GmPHYAs and GmPHYBs in regulating light response, and provides a core set of phytochrome mutant alleles for characterization of their functional mechanisms in regulating agronomic traits of soybean.

Grain number and seed-setting rate are components of crop yield. Cytokinin influences grain yield. However, emerging studies suggest that high cytokinin signals often lead to reduced branching or seed-setting rate, leading to reduced grain yield, although the mechanisms remain unclear. In this study, we identified and characterized the rice (Oryza sativa L.) gene LONELY GUY-LIKE 8 (LOGL8), based on analysis of the LOGL8-pm (promoter mutant of LOGL8) mutant, which harbors a T-DNA insertion in the promoter of this gene. The mutation in LOGL8-pm causes ectopic hyperexpression of LOGL8 in inflorescence organs, resulting in plants with smaller panicles and defective ovules lacking archesporial cells and integuments. Knockout of LOGL8 caused pollen abortion, leading to a reduced seed-setting rate. LOGL8 encodes a putative cytokinin-activating enzyme. Our results showed that LOGL8 directly catalyzes the biosynthesis of bioactive cytokinins. Therefore, we propose that the ectopic expression of LOGL8 disrupts cytokinin spatiotemporal distribution and causes inhibition of LONELY GUY (LOG), which affects panicle branching and female organ development. These findings reveal the important role of LOGL8 in male development, and highlight the delicate balance of local cytokinin levels during panicle branching and female organ development.

Manganese (Mn) toxicity-induced leaf chlorosis limits crop production in acidic soils, but its underlying mechanisms remain unknown. The effects of excessive Mn on chlorophyll (Chl) biosynthesis in sugarcane (Saccharum officinarum L.) leaves were investigated. Under Mn treatment, Chl concentration decreased with Mn accumulation and chlorosis appeared in expanding leaves. Before that, levels of the initial Chl precursor 5-aminolevulinic acid (ALA) and its downstream intermediates decreased, whereas magnesium-protoporphyrin IX monomethyl ester (MgPME) accumulated. Overaccumulation of Mn in leaves downregulated the ALA biosynthetic gene GluTR (encoding glutamyl-tRNA reductase) and MgPME conversion gene MgPMEC (encoding MgPME cyclase), upregulated the ALA biosynthesis inhibitor FLU (encoding FLUORESCENT), but had no significant effect on the expression of other Chl biosynthetic genes. The above Mn-induced changes of Chl precursors and expression of corresponding genes commenced before the Chl decline and leaf chlorosis, and were reversed by ALA supplementation. Thus, excessive Mn-induced chlorosis in sugarcane is mediated by a Chl-biosynthesis disorder resulting from the inhibition of ALA synthesis and MgPME conversion.

Plant cytoplasmic male sterility (CMS) is maternally inherited and often manifested as aborted pollen development, but the molecular basis of abortion remains to be identified. To facilitate an investigation of CMS in cotton, the complete sequence of cotton mitochondrial (mt) genome for CMS-D2 line ZBA was determined. The mt genome was assembled as a single circular molecule with 634,036 bp in length. A total of 194 ORFs, 36 protein‐coding genes, six rRNAs, and 24 tRNAs were identified. Several chimeric genes encoding hypothetical proteins with transmembrane domains were identified. Among them, a previously unknown chimeric gene, orf610a, which is composed of atp1 and a 485-bp downstream sequence of unknown nature, was identified. RT-PCR and qRT-PCR validation indicated that orf610a was expressed specifically in a sterile line. Ectopic expression of orf610a in yeast resulted in excessive accumulation of reactive oxygen species and reduction in ATP content, in addition to inhibition of cellular growth. Transgenic A. thaliana overexpressing orf610a fused with a mitochondrial targeting peptide displayed partial male sterility. Interaction between ORF610a and the nuclear-encoded protein RD22 indicated an association between ORF610a and pollen abortion. Positive feedback during transcriptional regulation between nuclear regulatory factors and the mt CMS gene may account for the male sterility of ZBA.

Fusarium head blight (FHB), also known as scab, is a devastating fungal disease of wheat that causes significant losses in grain yield and quality. Quantitative inheritance and cumbersome phenotyping make FHB resistance a challenging trait for direct selection in wheat breeding. Genomic selection to predict FHB resistance traits has shown promise in several studies. Here, we used univariate and multivariate genomic prediction models to evaluate the prediction accuracy (PA) for different FHB traits using 476 elite and advanced breeding lines developed by South Dakota State University hard winter wheat breeding program. These breeding lines were assessed for FHB disease index (DIS), and percentage of Fusarium damaged kernels (FDK) in three FHB nurseries in 2018, 2019, and 2020 (TP18, TP19, and TP20) and were evaluated as training populations (TP) for genomic prediction (GP) of FHB traits. We observed a moderate PA using univariate models for DIS (0.39 and 0.35) and FDK (0.35 and 0.37) using TP19 and TP20, respectively, while slightly higher PA was observed (0.41 for DIS and 0.38 for FDK) when TP19 and TP20 (TP19 + 20) were combined to leverage the advantage of a large training population. Although GP with multivariate approach including plant height and days to heading as covariates did not significantly improve PA for DIS and FDK over univariate models, PA for DON increased by 20% using DIS, FDK, DTH as covariates using multi-trait model in 2020. Finally, we used TP19, TP20, and TP19 + 20 in forward prediction to calculate genomic-estimated breeding values (GEBVs) for DIS and FDK in preliminary breeding lines at an early stage of the breeding program. We observed moderate PA of up to 0.59 for DIS and 0.54 for FDK, demonstrating the promise in genomic prediction for FHB resistance in earlier stages using advanced lines. Our results suggest GP for expensive FHB traits like DON and FDK can facilitate the rejection of highly susceptible materials at an early stage in a breeding program.

Development of hybrid rice with high yield and grain quality is a goal of rice breeding. To investigate the genetic mechanism of heterosis for rice milling and appearance quality in indica/xian rice, QTL mapping was conducted using 1061 recombinant inbred lines (RILs) derived from a cross of the xian rice cultivars Quan9311B (Q9311B) and Wu-shan-si-miao (WSSM), and a backcross F₁ (BC₁F₁) population developed by crossing the RILs with Quan9311A (Q9311A), combined with phenotyping in two environments. The F₁ hybrid (Q9311A × WSSM) showed various degrees of heterosis for milling and appearance quality. A total of 142 main-effect QTL (M-QTL) and 407 pairs of epistatic QTL (E-QTL) were identified for five milling and appearance quality traits and grain yield per plant (GYP) in the RIL, BC₁F₁ and mid-parental heterosis (H_MP) populations. Differential detection of QTL in three populations revealed that most additive loci detected in the RILs did not show heterotic effects, but some of them did contribute to BC₁F₁ trait performance. Unlike heterosis of GYP, single-locus overdominance and epistasis were the main contributors to heterosis for milling and appearance quality. Epistasis contributed more to the heterosis for milling quality than to that for appearance quality. Three (four) QTL regions harboring opposite (consistent) directions of favorable allele effects for GYP and grain quality were identified, indicating the presence of partial genetic overlaps between GYP and grain quality. Three strategies are proposed to develop hybrid rice with high yield and good grain quality: 1) pyramiding favorable alleles with consistent directions of gene effects for GYP and grain quality at the M-QTL on different chromosomes; 2) introgressing favorable alleles for GYP and grain quality into the parents and then pyramiding and fixing these additive effects in hybrids; and 3) pyramiding overdominant and dominant loci and minimizing or eliminating underdominant loci from the parents.

Wheat bread-making quality can be improved by use of high-molecular-weight glutenin subunits (HMW-GSs) from wild relatives. Aegilops longissima is a close relative of wheat that contains a number of HMW-GS-encoding genes including 1S^lx2.3*. In this study, transgenic wheat lines overexpressing 1S^lx2.3* were obtained by Agrobacterium-mediated transformation and used to investigate the genetic contribution of 1S^lx2.3* to wheat flour-processing quality. The 1S^lx2.3* transgene was stably inherited and expressed over generations. Expression of 1S^lx2.3* increased the relative expression of 1Dx2 and 1Dy12 and reduced that of 1By18 during grain development. In general, integration of 1S^lx2.3* stimulated the accumulation of endogenous HMW-GSs and low-molecular-weight glutenin subunits in wheat kernels, greatly increasing the glutenin:gliadin ratio and resulting in faster formation of protein bodies in the endosperm during grain development. A wheat material with improved flour-making quality was developed in which 1S^lx2.3* improved wheat bread-making quality.

Greenbug (Schizaphis graminum Rondani) is a destructive insect pest that not only damages plants, but also serves as a vector for many viruses. Host plant resistance is the preferred strategy for managing greenbug. Two greenbug resistance genes, Rsg1 and Rsg2, have been reported in barley. To breed cultivars with effective resistance against various greenbug biotypes, additional resistance genes are urgently needed to sustain barley production. Wild barley accession WBDC053 (PI 681777) was previously found to be resistant to several greenbug biotypes. In this study, a recombinant inbred line (RIL) population derived from Weskan × WBDC053 was evaluated for response to two greenbug biotypes (E and TX1) and genotyped using genotyping by sequencing (GBS). A set of 3347 high quality GBS-derived single nucleotide polymorphisms (SNPs) were then used to map the greenbug resistance gene in this wild barley accession. Linkage analysis placed the greenbug resistance gene in a 2.35 Mb interval (0-2,354,645 bp) in the terminal region of the short arm of chromosome 2H. This interval harbors 15 genes with leucine-rich-repeat (LRR) protein domains. An allelism test indicated that the greenbug resistance gene in WBDC053, designated Rsg2.a3, is likely allelic or closely linked to Rsg2. GBS-SNPs 2H_1318811 and 2H_1839499 co-segregating with Rsg2.a3 in the RIL population were converted to Kompetitive allele specific PCR (KASP) markers KASP-Rsg2.a3-1 and KASP-Rsg2.a3-2, respectively. The two KASP markers can be used to select Rsg2.a3 and have the potential to tag Rsg2 in barley improvement programs.

Wheat production is under continuous threat by various fungal pathogens. Identification of multiple-disease resistance genes may lead to effective disease control via the development of cultivars with broad-spectrum resistance. Plant Lysin-motif (LysM)-type pattern-recognition receptors, which elicit innate immunity by recognizing fungal pathogen associated molecular patterns such as chitin, are potential candidates for such resistance. In this study, we cloned a LysM receptor-like kinase gene, CERK1-V, from the diploid wheat relative Haynaldia villosa. CERK1-V expression was induced by chitin and Blumeria graminis f. sp. tritici, the causal agent of wheat powdery mildew. Heterologous overexpression of CERK1-V in wheat inhibited the development of three fungal pathogens, thereby increased resistance to powdery mildew, yellow rust, and Fusarium head blight. CERK1-V physically interacted with the wheat LysM protein TaCEBiPs. CERK1-V/TaCEBiPs interaction promoted chitin recognition and activated chitin signal transduction in wheat. Transgenic plants with excessively high CERK1-V expression showed high resistance but abnormal plant growth, whereas plants with moderate expression level showed adequate resistance level with no marked impairment of plant growth. In transgenic lines, RNA-seq showed that gene expression involved in plant innate immunity was activated. Expression of genes involved in photosynthesis, ER stress and multiple phytohormone pathways was also activated. Optimized expression of CERK1-V in wheat can confer disease resistance without compromising growth or defense fitness.

Erianthus arundinaceus is a wild relative of sugarcane (Saccharum officinarum L.) with many desirable agronomic traits for sugarcane genetic improvement. However, limited knowledge of the complex genome of hexaploid E. arundinaceus has impeded the development of required molecular tools. Dissecting complex genomes into single chromosomes can simplify analyses. The flow-cytometric sorting of a single chromosome of E. arundinaceus in a Saccharum-Erianthus introgression line is reported. A novel approach called genomic in situ hybridization in suspension was used to discriminate the alien chromosome from sugarcane chromosomes at the same size. A total of 218,000 E. arundinaceus chromosome 1 (EaC1) were sorted to >97% purity and amplified DNA was sequenced using Illumina and PacBio technologies. The resulting assembly had a 70.93 Mb contig sequence with an N50 of 19.62 kb. A total of 56.69 Mb repeat sequences were predicted, accounting for 79.1% of the chromosome and 2646 genes having a total length of 1.84 Mb that represented 2.59% of the chromosome. Of these genes, 1877 (70.9%) genes were functionally annotated. The phylogenetic relationship of E. arundinaceus with other species using the chromosome 1 sequence revealed that E. arundinaceus was distantly related to Oryza sativa and Zea mays, followed by Sorghum bicolor, and was closely related to S. spontaneum and Saccharum spp. hybrids. This study provides the first insights into the characteristics of EaC1, and the results will provide tools to support molecular improvement and alien introgression breeding of sugarcane.

Serotonin is ubiquitous across all forms of life and functions in responses to biotic and abiotic stresses. In rice, the conversion of tryptamine to serotonin is catalyzed by Sekiguchi lesion (SL). Previous studies have identified an sl mutation (a null mutation of SL) in several rice varieties and confirmed its increase of resistance and cell death. However, a systematic understanding of the reprogrammed cellular processes causing cell death and resistance is lacking. We performed a multi-omics analysis to clarify the fundamental mechanisms at the protein, gene transcript, and metabolite levels. We found that cell death and Magnaporthe oryzae (M. oryzae) infection of the sl-MH-1 mutant activated plant hormone signal transduction involving salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) in multiple regulatory layers. We characterized the dynamic changes of several key hormone levels during disease progression and under the cell death conditions and showed that SA and JA positively regulated rice cell death and disease resistance. SL-overexpressing lines confirmed that the sl-MH-1 mutant positively regulated rice resistance to M. oryzae. Our studies shed light on cell death and facilitate further mechanistic dissection of programmed cell death in rice.

Fresh-seed germination (FSG) impairs peanut production, especially in areas where the peanut harvest season coincides with rainy weather. Developing FSG-resistant cultivars by molecular breeding is expected to mitigate yield loss and quality impairment caused by FSG. However, the genetic control of FSG awaits elucidation. In this study, FSG at 1, 3, 5, 7, and 9 days post-imbibition in three environments were tested, and quantitative-trait loci (QTL) associated with FSG were mapped in a peanut recombinant inbred line population by leveraging existing high-density peanut genetic maps. Of 24 QTL identified in 13 linkage groups, qFSGA04 was a stable major QTL on linkage group 04 (LG04). It was consistently detected in five germination stages and three environments. By designing and validating DNA markers in the confidence interval of qFSGA04, we identified one single-nucleotide polymorphism and one InDel closely associated with FSG that could be used as linked markers for FSG resistance in peanut breeding.

Sustainable intensification is an agricultural development direction internationally. However, little is known about the yield sustainability of winter wheat (Triticum aestivum L.) under limited irrigation schemes on the North China Plain (NCP). A 28-year field experiment from 1991 to 2018 at Wuqiao Experimental Station was used to characterize long-term yield, evapotranspiration (ET), and water use efficiency (WUE) trends under three irrigation treatments (W1, irrigation just before sowing; W2, irrigation before sowing and at jointing stage; W3, irrigation before sowing, at jointing stage, and at anthesis). Yield gaps and the effects of genetic improvement, climate change, and climate variables on wheat yield and key phenological stages were estimated using the Agricultural Production Systems Simulator (APSIM) model. Grain yield and WUE of winter wheat increased during the 28 years under the three irrigation treatments, and the upward trend of WUE followed a saturation curve pattern. ET increased slightly. Simulation results showed that genetic improvement dramatically prolonged the phenological stages of vegetative growth period and contributed to yield increase by 0.03%-15.6%. The rapid increase in yield with lower water use was associated mainly with an increase in biomass with genetic improvement and partly with an increase in harvest index. A curvilinear relationship between WUE and yield emphasized the importance of obtaining high yields for high WUE. The yield gaps between potential yield and yield under W1 treatment increased from 1991 to 2018 but were relatively constant for the W2 and W3 treatments. Elevated atmospheric CO₂ concentration offset the negative effects of temperature increase on yield, leading to minor (−2.3% to 0.3%) changes in yield under climate change. Thus, genetic improvement played a dominant role in yield increase, and limited-irrigation schemes (W2 and W3) can increase wheat yield and promote sustainability of crop production on the NCP.

Because of the higher nitrogen (N) recovery efficiency (NRE) of panicle-stage fertilization compared with basal and tillering fertilization, increasing the proportion of N topdressing at the booting stage (panicle-N) is recommended and commonly practiced in parts of China. To investigate the effects of increasing panicle-N on grain yield and N use efficiency (NUE) and the relationships of the increase and the rice cultivar and soil fertility status, we increased the percentage of panicle-N from 20% to 40% by correspondingly reducing the N amount applied only at the tillering stage in both high- and low-fertility blue clayey paddy fields in 2018 and 2019. Four indica cultivars with diverse panicle types were used, and their grain yield, dry matter accumulation, and NUE were compared. In high-fertility soil, increasing topdressing panicle-N from 20% to 40% reduced tillering ability and reduced the effective panicle numbers of the multi- and medium-panicle cultivars Huanghuazhan (HHZ), C Liangyouhuazhan (CHZ), and Tianyouhuazhan (THZ). These cultivars gave the greatest yield when 30% of N was supplied as panicle fertilizer, whereas the yield, NRE, N agronomic efficiency (NAE), and nitrogen physiological efficiency (NPE) of the heavy-panicle inbred cultivar Yangdao 6 (YD6) continued to increase, resulting in improved dry matter accumulation and grain filling in the late growth stage. The yield, NAE, NRE, and NPE of YD6 peaked when the panicle-N constituted 40%. While in low-fertility soil, the multipanicle cultivar HHZ showed the greatest yield when 30% of fertilizer-N was applied once at the panicle initiation (PI) stage, while the medium-panicle cultivar CHZ showed the greatest yield when the panicle-N percentage was 40%. Our results suggest that the percentage of panicle-N fertilizer should not exceed 30% for multipanicle cultivars, while can be appropriately increased to 40% for heavy-panicle indica cultivars. The effect of increasing topdressing panicle-N on the yield of medium-panicle cultivars was related to soil fertility. The optimum panicle-N percentage was 30% in the high-fertility soil and 40% in the low-fertility soil.

Application of slow-release fertilizer (SF) is a nutrient-management measure aimed at improving maize nutrient use and yield and saving labor cost. One-time application of SF at sowing usually results in nutrient deficiency during the post-silking stage, owing to the long growth period of spring maize. This study was conducted to investigate the effects on spring maize of SF application stage (zero, three-, and six-leaf stages, designated as SF0, SF3, and SF6, respectively) on grain yield, total soil rhizosphere nitrogen (N) content, and root activity, in comparison with the conventional fertilization mode (CF, application of compound fertilizer at sowing time, and topdressing urea at six-leaf and tasseling stages) at the same fertilization level as the control. Compared with no fertilization (F0) and CF, SF increased grain number and weight. The maize cultivars Suyu 30 (SY30) and Jiangyu 877 (JY877) produced the highest grain yield and net return under SF6 treatment over the three years. SF6 increased enzymatic activities including oxidoreductase, hydrolase, transferase, and lyase in rhizosphere soil at silking (R1) and milking stages (R3). SF6 increased the total N contents of rhizosphere soil by 7.1% at R1 and 9.2% R3 stages compared with SF0. The activities of antioxidant enzymes in roots were increased under SF6 treatments at R1 and R3. The mean root activities of SF0, SF3, and SF6 increased by 7.1%, 12.8%, and 20.5% compared with CF at R1 and by 8.8%, 13.0%, and 23.5% at R3. Delaying the application time of SF could increase grain yield by increasing total N content of rhizosphere soil, delaying root senescence, and increasing root activity at the late reproductive stage. Applying SF at the six-leaf stage is recommended as an effective fertilization strategy for the sustainable production of spring maize in southern China.

Zinc (Zn) deficiency is the most widespread micronutrient deficiency, affecting yield and quality of crops worldwide. Identifying genes associated with Zn-deficiency tolerance in maize is a basis for elucidating its genetic mechanism. A K22 × CI7 recombinant inbred population consisting of 210 lines and an association panel of 508 lines were used to identify genetic loci influencing Zn-deficiency tolerance. Under -Zn and -Zn/CK conditions, 15 quantitative trait loci (QTL) were detected, each explaining 5.7%-12.6% of phenotypic variation. Sixty-one significant single-nucleotide polymorphisms (SNPs) were identified at P < 10⁻⁵ by genome-wide association study (GWAS), accounting for 5%-14% of phenotypic variation. Among respectively 198 and 183 candidate genes identified within the QTL regions and the 100-kb regions flanking these significant SNPs, 12 were associated with Zn-deficiency tolerance. Among these candidate genes, four genes associated with hormone signaling in response to Zn-deficiency stress were co-localized with QTL or SNPs, including the genes involved in the auxin (ZmARF7), and ethylene (ZmETR5, ZmESR14, and ZmEIN2) signaling pathways. Three candidate genes were identified as being responsible for Zn transport, including ZmNAS3 detected by GWAS, ZmVIT and ZmYSL11 detected by QTL mapping. Expression of ZmYSL11 was up-regulated in Zn-deficient shoots. Four candidate genes that displayed different expression patterns in response to Zn deficiency were detected in the regions overlapping peak GWAS signals, and the haplotypes for each candidate gene were further analyzed.

Grain size is a determinant of rice grain yield. In plants, mitochondria supply energy for cellular metabolism via the mitochondrial electron transport chain. Here we report that OsNDB2, which encodes a putative rotenone-insensitive type II NAD(P)H dehydrogenase (ND), negatively regulates grain size and weight in rice. Six ND members representing three major types of rice were identified, and the predicted OsNDB2 protein was localized to mitochondria. Contents of OsNDB2 transcripts were higher in young panicles and leaf blades. OsNDB2 overexpression reduced grain length, grain width, and 1000-grain weight and moderately influenced plant height, while knockout of OsNDB2 increased grain size and 1000-grain weight. Allelic mutations of OsNDB2 were associated with diverse grain appearances. Cellular observations revealed that variations in grain size of transgenic lines were caused by change in cell expansion but not cell proliferation in spikelet hulls. Our study sheds light on OsNDB2 function and provides a new potential breeding approach for increasing rice grain size and weight.

Soluble sugar is a key quality trait of soybean seeds. We developed rapid and economic extraction and quantification methods for seed soluble sugars using an ultra-high performance liquid chromatography system with a refractive index detector. We evaluated the soluble sugar compositions of 1164 soybean accessions collected from diverse ecoregions and grown in multiple locations and years. Total soluble sugar (TSS) content was influenced by accession type, year of cultivation, and ecoregion. The mean contents of fructose, glucose, sucrose, raffinose, stachyose and TSS were 3.31, 5.21, 55.60, 6.60, 35.47, and 106.19 mg g⁻¹, respectively. The highest mean TSS content (108.71 mg g⁻¹) was observed in accessions from Northern Region of China. Cultivars contained higher contents of sucrose, raffinose, and TSS, whereas landraces had a higher content of stachyose. Fourteen accessions with mean TSS contents >130 mg g⁻¹ were identified as elite soybean resources. TSS was correlated with sucrose, raffinose, stachyose, protein, oil and total tocopherol. The main soluble sugar components were correlated with latitude and longitude, indicating that the geographical origin of the accessions affected their seed soluble sugar compositions. The developed methods and elite identified accessions can be used in the food and feed industry and in soybean breeding programs aimed at improving soybean seed nutrition.