Autophagy is an evolutionarily conserved degradation pathway of lysosomes (in mammals) and vacuoles (in yeasts and plants) from lower yeasts to higher mammals. It wraps unwanted organelles and damaged proteins in a double-membrane structure to transport them to vacuoles for degradation and recycling. In plants, autophagy functions in adaptation to the environment and maintenance of growth and development. This review systematically describes the autophagy process, biological functions, and regulatory mechanisms occurring during plant growth and development and in response to abiotic stresses. It provides a basis for further theoretical research and guidance of agricultural production.

Maize (Zea mays L.) is an indispensable crop worldwide for food, feed, and bioenergy production. Fusarium verticillioides (F. verticillioides) is a widely distributed phytopathogen and incites multiple destructive diseases in maize: seedling blight, stalk rot, ear rot, and seed rot. As a soil-, seed-, and airborne pathogen, F. verticillioides can survive in soil or plant residue and systemically infect maize via roots, contaminated seed, silks, or external wounds, posing a severe threat to maize production and quality. Infection triggers complex immune responses: induction of defense-response genes, changes in reactive oxygen species, plant hormone levels and oxylipins, and alterations in secondary metabolites such as flavonoids, phenylpropanoids, phenolic compounds, and benzoxazinoid defense compounds. Breeding resistant maize cultivars is the preferred approach to reducing F. verticillioides infection and mycotoxin contamination. Reliable phenotyping systems are prerequisites for elucidating the genetic structure and molecular mechanism of maize resistance to F. verticillioides. Although many F. verticillioides resistance genes have been identified by genome-wide association study, linkage analysis, bulked-segregant analysis, and various omics technologies, few have been functionally validated and applied in molecular breeding. This review summarizes research progress on the infection cycle of F. verticillioides in maize, phenotyping evaluation systems for F. verticillioides resistance, quantitative trait loci and genes associated with F. verticillioides resistance, and molecular mechanisms underlying maize defense against F. verticillioides, and discusses potential avenues for molecular design breeding to improve maize resistance to F. verticillioides.

Stem growth habit dictates plant architecture and influences flowering and podding (seed setting), making it an essential morphological and breeding agronomic trait of soybean (Glycine max). Stem growth habit in soybean is affected by photoperiod and environment and is determined by genetic variation at major genes. Classical genetic analysis identified two critical loci, designated Determinacy 1 (Dt1) and Determinacy 2 (Dt2). Dt1 is an ortholog of Arabidopsis thaliana TERMINAL FLOWER1 (TFL1) and specifies an indeterminate stem growth habit, whereas Dt2 specifies a semi-determinate growth habit. MADS-box proteins, including Dt2, SUPPRESSOR OF OVEREXPRESSION OF CO1 (GmSOC1) and MADS-box genes downregulated by E1 (GmMDE), repress Dt1 expression. Photoreceptors encoded by the E3 and E4 loci regulate the expression of soybean FLOWERING LOCUS T (GmFT) orthologs via circadian clock genes and E1, and GmFTs compete with Dt1 to regulate stem growth habit. Study of the molecular mechanism underlying the regulation of stem growth habit in soybean has focused on the repression of Dt1 expression. Here we provide an overview of progress made in elucidating the genetic and molecular bases of stem growth habit in soybean, with emphasis on the molecular components responsible for integrating photoperiodic flowering and stem growth habit.

Plants adaptively change their cell wall composition and structure during their growth, development, and interactions with environmental stresses. Dirigent proteins (DIRs) contribute to environmental adaptations by dynamically reorganizing the cell wall and/or by generating defense compounds. A maize DIR, ZmDRR206, was previously reported to play a dominant role in regulation of storage nutrient accumulation in endosperm during maize kernel development. Here we show that ZmDRR206 mediates maize seedling growth and disease resistance by coordinately regulating biosynthesis of cell wall components for cell-wall integrity (CWI) maintenance. Expression of ZmDRR206 was induced in maize seedlings upon pathogen infection. ZmDRR206 overexpression in maize resulted in reduced seedling growth and photosynthetic activity but increased disease resistance and drought tolerance, revealing a tradeoff between growth and defense. Consistently, ZmDRR206 overexpression reduced the contents of primary metabolites and down-regulated genes involved in photosynthesis, while increasing the contents of major cell wall components, defense phytohormones, and defense metabolites, and up-regulated genes involved in defense and cell-wall biosynthesis in seedlings. ZmDRR206-overexpressing seedlings were resistant to cell-wall stress imposed by isoxaben, and ZmDRR206 physically interacted with ZmCesA10, which is a cellulose synthase unit. Our findings suggest a mechanism by which ZmDRR206 coordinately regulates biosynthesis of cell-wall components for CWI maintenance during maize seedling growth, and might be exploited for breeding strong disease resistance in maize.

Trichomes are specialized structures that originate from epidermal cells of organs in higher plants. The cotton fiber is a unique single-celled trichome that elongates from the seed coat epidermis. Cotton (Gossypium hirsutum) fibers and trichomes are models for cell differentiation. In an attempt to elucidate the intercellular factors that regulate fiber and trichome cell development, we identified a plasmodesmal β-1,3-glucanase gene (designated GhPdBG) controlling the opening and closing of plasmodesmata in cotton fibers. Structural and evolutionary analysis showed haplotypic variation in the promoter region of the GhPdBG gene among 352 cotton accessions, but high conservation in the coding region. GhPdBG was expressed predominantly in cotton fibers and localized to plasmodesmata (PD). Expression patterns of PdBG that corresponded to PD permeability were apparent during fiber development in G. hirsutum and G. barbadense. The PdBG- mediated opening-closure of PD appears to be involved in fiber development and may account for the contrasting fiber traits of these two species. Ectopic expression of GhPdBG revealed that it functions in regulating fiber and trichome length and/or density by modulating plasmodesmatal permeability. This finding suggests that plasmodesmal targeting of GhPdBG, as a switch of intercellular channels, regulates single-celled fiber and trichome development in cotton.

The plant natural product scopolin, a coumarin secondary metabolite, has been extensively exploited in flavor, cosmetic, medicine, and other industrial fields. Melilotus albus, a leguminous rotation crop, contains high concentrations of coumarin. The transcriptional regulatory network that controls the flow through the scopolin biosynthesis pipeline in M. albus remains poorly understood. MabHLH11 encodes a basic helix-loop-helix (bHLH) transcription factor whose transcription is positively associated with scopolin accumulation and with the expression of MaMYB4, the bHLH partner of the MYB-bHLH complex. Phylogenetic analysis grouped MabHLH11 in the TRANSPARENT TESTA 8 (TT8) clade of the bHLH IIIf subgroup. The MabHLH11 protein contained an MYB-interacting region and physically interacted with MaMYB4 in yeast and tobacco leaves. Co-overexpression of MabHLH11 with MaMYB4 in M. albus additively increased the expression of UDP-glucosyltransferase (MaUGT79) and induced more scopolin accumulation than occurred under the expression of MabHLH11 alone. MabHLH11 directly targeted the promoter of MaUGT79 and the activation of MabHLH11 was strengthened by the presence of MaMYB4. Thus, MaMYB4 enhanced the function of MabHLH11 in upregulating scopolin biosynthesis in M. albus, providing a theoretical basis for scalable production of a high-value plant natural product.

Photosynthesis affects crop growth and yield. The roles of microRNAs (miRNAs) in photosynthesis are little known. In the present study, the role of the OsNF-YB7-OsMIR5810-OsMRLP6 regulatory module in photosynthesis was investigated. The malectin-like protein gene OsMRLP6 was identified as a target gene of osa-miR5810 (miR5810). Overexpression in rice of miR5810 or down-expression of OsMRLP6 resulted in reduced expression of genes involved in chloroplast development and photosynthesis and decreased net photosynthetic rate, finally leading to lower shoot biomass and grain yield. Down-expression of miR5810 and overexpression of OsMRLP6 showed the opposite effect. Overexpression of transcription factor OsNF-YB7 elevated expression of OsMIR5810 in rice seedlings by binding to its promoter. The OsNF-YB7-OsMIR5810-OsMRLP6 regulatory module affects photosynthesis to mediate growth and grain yield.

Flower development and plant architecture determine the efficiency of mechanized harvest and seed yield in Brassica napus. Although TERMINAL FLOWER 1 (AtTFL1) is a regulator of flower development in Arabidopsis thaliana, the function and regulatory mechanism of TFL1 orthologs in B. napus remains unclear. Six BnTFL1 paralogs in the genome of the B. napus inbred line ‘K407’ showed steadily increasing expression during vernalization. CRISPR/Cas-induced mutagenesis of up to four BnTFL1 paralogs resulted in early flowering and alteration of plant architecture, whereas seed yield was not altered in BnTFL1 single, double, or triple mutants. Six BnTFL1 paralogs, but not BnaA02.TFL1, showed an additive and conserved effect on regulating flowering time, total and terminal flower number, and plant architecture. BnaA10.TFL1 regulates flower development by interacting with BnaA08.FD through the protein BnaA05.GF14nu, resulting in the transcriptional repression of floral integrator and floral meristem identity genes. These findings about the regulatory network controlling flower development and plant architecture present a promising route to modifying these traits in B. napus.

Plant trichomes are a specialized cellular tissue that functions in resistance to biotic and abiotic stresses. In rice, three transcription-factor genes: OsWOX3B, HL6, and OsSPL10, have been found to control trichome development. Although studies have shown interactions between the three genes, their full relationship in trichome development is unclear. We found that the expression levels of OsWOX3B and HL6 were both reduced in OsSPL10-knockout plants but increased in OsSPL10-overexpression plants, suggesting that OsSPL10 positively regulates their expression. Physical interaction between OsSPL10 and OsWOX3B was found both in vivo and in vitro and attenuated their abilities to bind to the promoter of HL6 to activate its transcription. This mechanism may regulate trichome length by adjusting the expression of HL6. A rice gene network regulating trichome development is proposed.

Nuclear factor Y (NF-Y), a group of conserved transcription-factor complexes that consist of NF-YA, B, and C subunits, is essential for developmental regulation and for responses to environmental changes in eukaryotes. We previously found that some NF-Y genes, such as OsNF-YA8, were expressed specifically in the endosperm of rice. In the present study, overexpression of OsNF-YA8 in rice resulted in reduced plant height due to suppressed cell elongation in internodes. Gibberellin (GA) biosynthetic genes, including OsCPS1, OsGA20ox1, and OsGA20ox2, were down-regulated. OsNF-YA8 bound to the promoters of these genes to repress their expression. Endogenous GA content was decreased in OsNF-YA8 overexpressors, whose dwarf phenotype could be partially rescued by exogenous GA treatment. The findings suggested that ectopic expression of OsNF-YA8 causes defective GA biosynthesis in vegetative stage. Heading date in OsNF-YA8 overexpressors was delayed, especially under short-day conditions. OsNF-YA8 bound to the promoter of Heading Date 3a (Hd3a), the florigen gene in rice, to negatively regulate flowering. Either ectopic activation or knockout of OsNF-YA8 impaired seed development, as indicated by reduced seed size and increased grain chalkiness. These results suggest that ectopic expression of the endosperm-specific OsNF-YA8 in rice disrupts both vegetative and reproductive development.

Mitochondrial protein translation that is essential for aerobic energy production includes four essential steps of the mitochondrial ribosome cycle, namely, initiation, elongation, termination of the polypeptide, and ribosome recycling. Translation termination initiates when a stop codon enters the A site of the mitochondrial ribosome where it is recognized by a dedicated peptide release factor (RF). However, RFs and mechanisms involved in translation in plant mitochondria, especially in monocotyledons, remain largely unknown. Here, we identified a crumpled kernel (crk5 allele) mutant, with significantly decreased kernel size, 100-kernel weight, and an embryo-lethal phenotype. The Crk5 allele was isolated using map-based cloning and found to encode a mitochondrial localization RF2a. As it is an ortholog of Arabidopsis mitochondrial RF2a, we named the gene ZmmtRF2a. ZmmtRF2a is missing the 5th-7th exons in the crk5 resulting in deletion of domains containing motifs GGQ and SPF that are essential for release activity of RF, mitochondrial ribosome binding, and stop codon recognition. Western blot and qRT-PCR analyses indicate that the crk5 mutation results in abnormal mitochondrion structure and function. Intriguingly, we observed a feedback loop in the crk5 with up-regulated transcript levels detected for several mitochondrial ribosome and mitochondrial-related components, in particular mitochondrial complexes CI, CIV, and a ribosome assembly related PPR. Together, our data support a crucial role for ZmmtRF2a in regulation of mitochondrial structure and function in maize.

Gibberellin (GA) functions in plant growth and development. However, genes involved in the biosynthesis and regulation of GA in crop plants are poorly understood. We isolated the mutant gad5-1 (GA-Associated Dwarf 5), characterized by dwarfing, short internodes, and dark green and short leaves. Map-based gene cloning and allelic verification confirmed that ZmGAD5 encodes ent-kaurenoic acid oxidase (KAO), which catalyzes KA (ent- kaurenoic acid) to GA12 conversion during GA biosynthesis in maize. ZmGAD5 is localized to the endoplasmic reticulum and is present in multiple maize organs. In gad5-1, the expression of ZmGAD5 is severely reduced, and the levels of the direct substrate of KAO, KA, is increased, leading to a reduction in GA content. The abnormal phenotype of gad5-1 was restored by exogenous application of GA₃. The biomass, plant height, and levels of GA₁₂ and GA₃ in transgenic Arabidopsis overexpressing ZmGAD5 were increased in comparison with the corresponding controls Col-0. These findings deepen our understanding of genes involved in GA biosynthesis, and could lead to the development of maize lines with improved architecture and higher planting-density tolerance.

Salt and drought stress are common abiotic factors that exert a detrimental influence on seed germination, potentially leading to significantly impaired growth and production in rice. Gaining a comprehensive understanding of the molecular response of seeds to abiotic stress during the germination is of paramount importance. In the present study, we identified two R3-MYB genes in rice, namely OsTCL1 and OsTCL2, and characterized their roles in regulating seed germination under salt and drought stress. Plants with tcl1 and tcl2 mutant alleles exhibited delayed seed germination, particularly under stress conditions. The tcl1 tcl2 double mutant showed an even more pronounced reduction in germination during initial stages of germination, thereby indicating a redundant regulatory function of OsTCL1 and OsTCL2 in seed germination under abiotic stresses. Furthermore, we demonstrated that the transcript levels of several phospholipase D (PLD) genes were downregulated in the tcl1 tcl2 mutant, resulting in a decreased level of the phosphatidic acid (PA) product. Application of 1-butanol, a competitive substrate inhibitor of PLD-dependent production of PA, attenuated the stress response of the tcl1 tcl2 mutant. This suggests that OsTCL1 and OsTCL2 partially modulate seed germination through the PLD-PA signaling pathway. Moreover, there were alterations in the expression of genes involved in abscisic acid (ABA) biosynthesis, metabolism and signaling transduction in the double mutant. These changes affected the endogenous ABA level and ABA response, thereby influencing seed germination. Application of both 1-butanol and ABA synthesis inhibitor sodium tungstate (Na₂WO₄) nearly eliminated the differences in stress response between wild type and the tcl1 tcl2 mutant. This indicates that OsTCL1 and OsTCL2 synergistically coordinate seed germination under abiotic stresses through both the PLD-PA signaling and ABA-mediated pathways.

Soybean (Glycine max) is a major oil and feed crop worldwide. Soybean mosaic virus (SMV) is a globally occurring disease that severely reduces the yield and quality of soybean. Here, we characterized the role of the clock gene TIMING OF CAB EXPRESSION 1b (GmTOC1b) in the resistance of soybean to SMV. Homozygous Gmtoc1b mutants exhibited increased tolerance to SMV strain SC3 due to the activation of programmed cell death triggered by a hypersensitive response. Transcriptome deep sequencing and RT-qPCR analysis suggested that GmTOC1b likely regulates the expression of target genes involved in the salicylic acid (SA) signaling pathway. GmTOC1b binds to the promoter of GmWRKY40, which encodes a protein that activates the expression of SA-mediated defense-related genes. Moreover, we revealed that the GmTOC1b^H1 haplotype, which confers increased tolerance to SMV, was artificially selected in improved cultivars from the Northern and Huang-Huai regions of China. Our results therefore identify a previously unknown SMV resistance component that could be deployed in the molecular breeding of soybean to enhance SMV resistance.

The Triticum-Aegilops complex provides ideal models for the study of polyploidization, and mitochondrial genomes (mtDNA) can be used to trace cytoplasmic inheritance and energy production following polyploidization. In this study, gapless mitochondrial genomes for 19 accessions of five Triticum or Aegilops species were assembled. Comparative genomics confirmed that the BB-genome progenitor donated mtDNA to tetraploid T. turgidum (genome formula AABB), and that this mtDNA was then passed on to the hexaploid T. aestivum (AABBDD). T urartu (AA) was the paternal parent of T. timopheevii (AAGG), and an earlier Ae. tauschii (DD) was the maternal parent of Ae. cylindrica (CCDD). Genic sequences were highly conserved within species, but frequent rearrangements and nuclear or chloroplast DNA insertions occurred during speciation. Four highly variable mitochondrial genes (atp6, cob, nad6, and nad9) were established as marker genes for Triticum and Aegilops species identification. The BB/GG-specific atp6 and cob genes, which were imported from the nuclear genome, could facilitate identification of their diploid progenitors. Genic haplotypes and repeat-sequence patterns indicated that BB was much closer to GG than to Ae. speltoides (SS). These findings provide novel insights into the polyploid evolution of the Triticum/Aegilops complex from the perspective of mtDNA, advancing understanding of energy supply and adaptation in wheat species.

Cotton is a major crop that provides the most important renewable textile fibers in the world. Studies of the taxonomy and evolution of cotton species have received wide attentions, not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin, evolution, and cultivation of polyploid species. Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation. Whereas, with only a few mitogenomes assembled in the cotton genus Gossypium, our knowledge about their roles in cotton evolution and speciation is still scarce. To close this gap, here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades (A-G, K, and AD genomes) and 5 cotton relatives using short and long sequencing reads. Systematic analyses uncovered a high level of mitochondrial gene sequence conservation, abundant sequence repeats and many insertions of foreign sequences, as well as extensive structural variations in cotton mitogenomes. The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general, while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content, RNA editing, and gene expression level. Interestingly, we further revealed the specific presence and expression of two novel mitochondrial open reading frames (ORFs) in lint-fiber cotton species. Finally, these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.

Superior inbred lines are central to maize breeding as sources of natural variation. Although many elite lines have been sequenced, less sequencing attention has been paid to newly developed lines. We constructed a genome assembly of the elite inbred line KA105, which has recently been developed by an artificial breeding population named Shaan A and has shown desirable characteristics for breeding. Its pedigree showed genetic divergence from B73 and other lines in its pedigree. Comparison with the B73 reference genome revealed extensive structural variation, 58 presence/absence variation (PAV) genes, and 1023 expanded gene families, some of which may be associated with disease resistance. A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes, of which eight were induced by at least one kind of stress, participating in gene modules responding to stress such as drought and southern leaf blight disease. More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development. The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.

Sugarcane mosaic virus (SCMV) is the main etiological agent of sugarcane mosaic disease, which affects sugarcane and other grass crops. Despite the extensive characterization of quantitative trait loci controlling resistance to SCMV in maize, the genetic basis of this trait in sugarcane is largely unexplored. Here, a genome-wide association study was performed and machine learning coupled with feature selection was used for genomic prediction of resistance to SCMV in a diverse sugarcane panel. Nine single-nucleotide polymorphisms (SNPs) explained up to 29.9% of the observed phenotypic variance and a 73-SNP set predicted resistance with high accuracy, precision, recall, and F1 scores (the harmonic mean of precision and recall). Both marker sets were validated in additional sugarcane genotypes, in which the SNPs explained up to 23.6% of the phenotypic variation and predicted resistance with a maximum accuracy of 69.1%. Synteny analyses suggested that the gene responsible for the majority of SCMV resistance in maize is absent in sugarcane, explaining why this major resistance source has not been identified in this crop. Finally, using sugarcane RNA-Seq data, markers associated with resistance to SCMV were annotated, and a gene coexpression network was constructed to identify the predicted biological processes involved in resistance. This network allowed the identification of candidate resistance genes and confirmed the involvement of stress responses, photosynthesis, and the regulation of transcription and translation in resistance to SCMV. These results provide a practical marker-assisted breeding approach for sugarcane and identify target genes for future studies of SCMV resistance.

A large amount of genome-wide association study (GWAS) panels together with quantitative-trait locus (QTL) information associated with breeding-targeted traits have been described in wheat (Triticum aestivum L.). However, the application of mapping results from a GWAS panel to conventional wheat breeding remains a challenge. In this study, we first report a general genetic map which was constructed from 44 published linkage maps. It permits the estimation of genetic distances between any two genetic loci with physical map positions, thereby unifying the linkage relationships between QTL, genes, and genomic markers from multiple genetic populations. Second, we describe QTL mapping in a wheat GWAS panel of 688 accessions, identifying 77 QTL associated with 12 yield and grain-quality traits. Because these QTL have known physical map positions, they could be mapped onto the general map. Finally, we present a design approach to wheat breeding by using known QTL information and computer simulation. Potential crosses between parents in the GWAS panel may be evaluated by the relative frequency of the target genotype, trait correlations in simulated progeny populations, and genetic gain of selected progenies. It is possible to simultaneously improve yield and grain quality by suitable parental selection, progeny population size, and progeny selection scheme. Applying the design approach will allow identifying the most promising crosses and selection schemes in advance of the field experiment, increasing predictability and efficiency in wheat breeding.

More than 170 years after causing the potato famine in Ireland, late blight is still considered one of the most devastating crop diseases. Commercial potato breeding efforts depend on natural sources of resistance to protect crops from the rapidly evolving late blight pathogen, Phytophthora infestans. We have identified and mapped a novel broad-spectrum disease resistance gene effective against P. infestans from the wild, diploid potato species Solanum bulbocastanum. Diagnostic resistance gene enrichment sequencing (dRenSeq) was used to confirm the uniqueness of the identified resistance. RenSeq and GenSeq-based mapping of the resistance, referred to as Rpi-blb4, alongside recombinant screening, positioned the locus responsible for the resistance to potato chromosome 5. The interval spans approximately 2.3 Mb and corresponds to the DM reference genome positions of 11.25 and 13.56 Mb.

Wheat resistance to Fusarium head blight (FHB) has often been associated with some undesirable agronomic traits. To study the relationship between wheat FHB resistance and agronomic traits, we constructed a linkage map of single nucleotide polymorphisms (SNPs) using an F_6:8 population from G97252W × G97380A. The two hard winter wheat parents showed contrasts in FHB resistance, plant height (HT), heading date (HD), spike length (SL), spike compactness (SC), kernel number per spike (KNS), spikelet number per spike (SNS), thousand-grain weight (TGW) and grain size (length and width). Quantitative trait locus (QTL) mapping identified one major QTL (QFhb.hwwg-2DS) on chromosome arm 2DS for the percentage of symptomatic spikelets (PSS) in the spike, deoxynivalenol (DON) content and Fusarium damaged kernel (FDK). This QTL explained up to 71.8% of the phenotypic variation for the three FHB-related traits and overlapped with the major QTL for HT, HD, SL, KNS, SNS, TGW, and grain size. QTL on chromosome arms 2AL, 2DS, 3AL and 4BS were significant for the spike and grain traits measured. G97252W contributed FHB resistance and high SNS alleles at QFhb.hwwg-2DS, high KNS alleles at the QTL on 2AL and 2DS, and high TGW and grain size alleles at QTL on 3AL; whereas G97380A contributed high TGW and grain size alleles at the QTL on 2AL and 2DS, respectively, and the high KNS allele at the 4BS QTL. Combining QFhb.hwwg-2DS with positive alleles for spike and grain traits from other chromosomes may simultaneously improve FHB resistance and grain yield in new cultivars.

Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is a destructive wheat disease. Although it can be easily overcome by deployment of resistance genes, the resistance is often quickly compromised by pathogen virulence. Thus, exploration and characterization of new resistance genes is always ongoing. Line NJ3946 derived from a cross of einkorn wheat accessions TA2032 and M389 showed resistance to powdery mildew. Inheritance analysis of an F₂ population derived from a cross of NJ3946 and M389 suggested that the resistance was conferred by a dominant allele. With polymorphic markers identified through bulked segregant analysis (BSA), this gene was mapped to a novel locus on chromosome 3A, and was designated as PmNJ3946. Bulked segregant RNA-seq analysis (BSR-seq) was conducted to obtain more closely linked markers, which allowed delimitation of the PMNJ3946 locus to a 0.9 cM interval covering a physical distance of less than 1 Mb. PMNJ3946 was flanked by Xwgrc5153 and SNP-derived marker CHS21_3A008915069, and co-segregated with SNP-derived markers CHS21_3A008939814 and CHS21_3A008943175. The PmNJ3946 discovery expands the diversity of powdery mildew resistance genes and is useful for wheat breeding.

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), threatens global wheat production. Development of cultivars with increased resistance to stem rust by identification, mapping, and deployment of resistance genes is the best strategy for controlling the disease. In this study, we performed fine mapping and characterization of the all-stage stem rust resistance (Sr) gene Sr8155B1 from the durum wheat line 8155-B1. In seedling tests of biparental populations, Sr8155B1 was effective against six Chinese Pgt races tested. In a segregating population of 5060 gametes, Sr8155B1 was mapped to a 0.06-cM region flanked by markers Pku2772 and Pku43365, corresponding to 1.5- and 2.7-Mb regions in the Svevo and Chinese Spring reference genomes. Both regions include several typical nucleotide-binding leucine-rich repeat (NLR) and protein kinase genes that represent candidate genes. Among them, three NLR genes and three receptor-like protein kinases were highly polymorphic between the parental lines and their transcripts were upregulated in the homozygous resistant line TdR2 relative to its susceptible sister line TdS4. Four markers (Pku2772, Pku43365, Pku2950, and Pku3721) developed in this study, together with seedling resistance responses, correctly predicted Sr8155B1 absence or presence in 78 tetraploid wheat genotypes tested. The presence of Sr8155B1 in tetraploid wheat accessions CItr 14916, PI 197492, and PI 197493 was confirmed by mapping in three F₂ populations. The genetic map and linked markers developed in this study may accelerate the deployment of Sr8155B1-mediated resistance in wheat breeding programs.

Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a bacterial disease affecting rice production in Asia and Africa, whose severity is expected to increase with climate change. Identification of new quantitative-trait loci (QTL) or resistance genes for BLS resistance is essential for developing resistant rice. A genome-wide association study to identify QTL associated with BLS resistance was conducted using phenotypic and genotypic data from 429 rice accessions. Of 47 QTL identified, 45 were novel and two co-localized with previously reported QTL or genes conferring BLS resistance. qBLS6.2 on chromosome 6 explained the greatest phenotypic variation. Combined analysis of differential expression and annotations of predicted genes near qBLS6.2 based on haplotype and disease phenotype identified OsBLS6.2 (LOC_Os06g02960) as a candidate gene for qBLS6.2. OsBLS6.2 knockout plants showed higher resistance to Xoc than wild-type plants. Many other candidate genes for resistance to Xoc were identified.

Water and nitrogen fertilization are the key factors limiting maize productivity. The genetic basis of interactions between maize genotype, water, and nitrogen is unclear. A recombinant inbred line (RIL) maize population was evaluated for seven yield and five agronomic traits under four water and nitrogen conditions: water stress and low nitrogen, water stress and high nitrogen, well-watered and low nitrogen, and well-watered and high nitrogen. Respectively eight, six, and six traits varied in response to genotype-water interactions, genotype-nitrogen interactions, and genotype-water-nitrogen interactions. Using a linkage map consisting of 896 single-nucleotide polymorphism markers and multiple-environmental quantitative-trait locus (QTL) mapping, we identified 31 QTL, including 12 for genotype-water-nitrogen interaction, across the four treatments. A set of 8060 genes were differentially expressed among treatments. Integrating genetic analysis, gene co-expression, and functional annotation revealed two candidate genes controlling genotype-water-nitrogen interactions, affecting both leaf width and grain yield. Genes involved in abscisic acid biosynthesis and bZIP, NAC, and WRKY transcription factors participated in maize response to water and nitrogen conditions. These results represent a step toward understanding the genetic regulatory network of maize that responds to water and nitrogen stress and provide a theoretical basis for the genetic improvement of both water- and nitrogen-use efficiency.

Genomic prediction (GP) in plant breeding has the potential to predict and identify the best-performing hybrids based on the genotypes of their parental lines. In a GP experiment, 34 elite inbred lines were selected to make 285 single-cross hybrids in a partial-diallel cross design. These lines represented a mini-core collection of Chinese maize germplasm and comprised 18 inbred lines from the Stiff Stalk heterotic group and 16 inbred lines from the Non-Stiff Stalk heterotic group. The parents were genotyped by sequencing and the 285 hybrids were phenotyped for nine yield and yield-related traits at two locations in the summer sowing area (SUS) and three locations in the spring sowing area (SPS) in the main maize-producing regions of China. Multiple GP models were employed to assess the accuracy of trait prediction in the hybrids. By ten-fold cross-validation, the prediction accuracies of yield performance of the hybrids estimated by the genomic best linear unbiased prediction (GBLUP) model in SUS and SPS were 0.51 and 0.46, respectively. The prediction accuracies of the remaining yield-related traits estimated with GBLUP ranged from 0.49 to 0.86 and from 0.53 to 0.89 in SUS and SPS, respectively. When additive, dominance, epistasis effects, genotype-by-environment interaction, and multi-trait effects were incorporated into the prediction model, the prediction accuracy of hybrid yield performance was improved. The ratio of training to testing population and size of training population optimal for yield prediction were determined. Multiple prediction models can improve prediction accuracy in hybrid breeding.

Despite the longstanding importance of silage as a critical feed source for ruminants, its quality improvement has been largely overlooked. Although numerous quantitative trait loci (QTL) and genes affecting silage quality in maize have been reported, only a few have been effectively incorporated into breeding programs. Addressing this gap, the present study undertook a comprehensive meta-QTL (MQTL) analysis involving 523 QTL associated with silage-quality traits collected from 14 published studies. Of the 523 QTL, 405 were projected onto a consensus map comprising 62,424 genetic markers, resulting in the identification of 60 MQTL and eight singletons. The average confidence interval (CI) of the MQTL was 3.9-fold smaller than that of the source QTL. Nine of the 60 identified MQTL were classified as breeder’s MQTL owing to their small CIs, involvement of more QTL, and large contribution to phenotypic variation. One-third of the MQTL co-localized with DNA marker-trait associations identified in previous genome-wide association mapping studies. A set of 78 high-confidence candidate genes influencing silage quality were identified in the MQTL regions. These genes and associated markers may advance marker-assisted breeding for maize silage quality.

Carotenoid biosynthesis and accumulation are important in determining nutritional and commercial value of crop products. Yellow pigmentation of mature kernels caused by carotenoids is considered a vital quality trait in foxtail millet, an ancient and widely cultivated cereal crop across the world. Genomic regions associated with yellow pigment content (YPC), lutein and zeaxanthin in foxtail millet grains were identified by genome-wide association analysis (GWAS), and SiPSY1 (Phytoene synthase 1 which regulates formation of the 40-carbon backbone of carotenoids) was confirmed as the main contributor to all three components by knockout and overexpression analysis. SiPSY1 was expressed in seedlings, leaves, panicles, and mature seeds, and was subcellularly localized to chloroplasts. Transcription of SiPSY1 in 15 DAP immature grains was responsible for YPC in mature seeds. Selection of SiPSY1 combined with increased YPC in mature grains during domestication of foxtail millet was confirmed. Haplotype analysis suggested that expression level of SiPSY1 could be a selection target for future breeding programs, and a KASP marker was developed for selection of favorable SiPSY1 alleles in breeding. The results of this work will benefit nutritional and commercial improvement of foxtail millet varieties, as well as other cereal crops.

Rice yield stability is a breeding goal, particularly for short-growth duration rice, but its underlying mechanisms remain unclear. In an attempt to identify the relationship between yield stability and source-sink characteristics in short-growth duration rice, a field experiment was conducted at three sites (Yueyang, Liuyang, and Hengyang) in 2021 and 2022. This study compared yield, yield components, source-sink characteristics, and their stability between two stable-yielding short-growth duration rice cultivars, Zhongzao 39 (Z-39) and Lingliangyou 268 (L-268), and two unstable-yielding short-growth duration rice cultivars, Zhongjiazao 17 (Z-17) and Zhuliangyou 819 (Z-819). The stability of agronomic parameters was represented by the coefficient of variation (CV). The respective CVs of yield in Z-17, Z-819, Z-39, and L-268 were 10.2%, 10.1%, 4.5%, and 5.7% in 2021 and 19.7%, 15.0%, 5.4%, and 6.5% in 2022. The respective CVs of grain weight were 6.3%, 5.7%, 3.4%, and 4.5% in Z-17, Z-819, Z-39, and L-268 in 2021, and 8.1%, 6.3%, 1.5%, and 0.8% in 2022. The mean source capacity per spikelet and pre-heading non-structural carbohydrate reserves per spikelet (NSC_pre) were 7%-43% and 7%-72% lower in Z-819 and Z-17 than in L-268 and Z-39 in 2021 and 2022. The mean quantum yield of photosystem II photochemistry of leaf, leaf area index, and specific leaf weight of L-268 and Z-39 were higher than those of Z-819 and Z-17 at the heading stage. This study suggests that high NSC_pre, caused by great leaf traits before heading, increases source capacity per spikelet and its stability, thereby increasing the stability of grain weight and yield. Increasing NSC_pre is critical for achieving grain weight and yield stability in short-growth duration rice.

Relay cropping of Poaceae and Fabaceae promotes high yield and land-use efficiency by allowing a double harvest. However, it is difficult to increase yield synergistically because of the reduced photosynthetic abilities of legume leaves under the shade of graminoids. Leaf photosynthetic capacity in relay cropping systems is associated with ecological niche differentiation and photosynthetic compensation after restoration of normal light. We conducted a field experiment in southwest China in 2020-2021 to evaluate the effects of three cropping patterns: maize-soybean relay cropping (IMS), monoculture maize (MM), and monoculture soybean (SS), and N application levels: no N application (NN:0 kg N ha⁻¹), reduced N (RN: 180 kg N ha⁻¹), and conventional N (CN: 240 kg N ha⁻¹). Compared to monocropping, relay cropping increased the stay-green traits of maize and soybean by 13% and 89%, respectively. Relay cropping prolonged the leaf stay-green duration in the maize and soybean lag phase by almost 4 and 8 days, respectively. Relay cropping maize (IM) increased the leaf area index (LAI) by 79.4% to 88.5% under NN and 55.5% to 148% under RN. Relay cropping soybean (IS) increased the LAI from 115% to 437% at days 40 to 50 after anthesis. IM increased yield by 65.6%. IS increased yield by 9.7%. HI and system yield were at their highest values under RN. In the relay cropping system, reduced N application extended green leaf duration, increased photosynthesis inside the canopy at multiple levels, ultimately increases soybean yield synergistically.

Rice is one of the three most important food crops in the world. Increasing rice yield is an effective way to ensure food security. Grain size is a key factor affecting rice yield; however, the genetic and molecular mechanisms regulating grain size have not been fully investigated. In this study, we identified a rice mutant, wide grain 4-D (wg4-D), that exhibited a significant increase in grain width and a decrease in grain length. Histological analysis demonstrated that WG4 affects cell expansion thereby regulating grain size. MutMap-based gene mapping and complementary transgenic experiments revealed that WG4 encodes an alpha-tubulin, OsTubA1. A SNP mutation in WG4 affected the arrangement of cortical microtubules and caused a wide-grain phenotype. WG4 is located in nuclei and cytoplasm and expressed in various tissues. Our results provide insights into the function of tubulin in rice and identifies novel targets the regulation of grain size in crop breeding.

Ferredoxins (Fds) in plastids are the most upstream stromal electron receptors shuttling electrons to downstream metabolic systems and function in various physiological processes of dicots, but their roles in monocots’ response to stresses are still unclear. In this study, the functions of OsFd4, the major non-photosynthetic type Fd in rice, were characterized under oxidative stress and Xanthomonas oryzae pv. oryzae (Xoo) infection. OsFd4-knockout mutants displayed no defects in key agronomic traits and blast resistance, but were more sensitive to hydrogen peroxide (H₂O₂) treatment than the wild type. Transient expression of OsFd4 alleviated H₂O₂- induced rice cell death, suggesting that OsFd4 contributes to rice tolerance to exogenous oxidative stress. Deletion of OsFd4 enhanced rice immune responses against Xoo. OsFd4 formed a complex in vivo with itself and OsFd1, the major photosynthetic Fd in rice, and OsFd1 transcripts were increased in leaf and root tissues of the OsFd4- knockout mutants. These results indicate that OsFd4 is involved in regulating rice defense against stresses and interplays with OsFd1.

In animals, serotonin is a neurotransmitter and mood regulator. In plants, serotonin functions in energy acquisition, tissue maintenance, delay of senescence, and response to biotic and abiotic stresses. In this study, we examined the effect of serotonin enrichment of rice endosperm on plant growth, endosperm development, and grain quality. To do so, TDCs and T5H were selected as targets for serotonin fortification. Overexpression of TDC1 or TDC3 increased serotonin accumulation relative to overexpression of T5H in rice grain. Transgenic lines of target genes driven by the Gt1 promoter showed better field performance than those driven by the Ubi promoter. Overexpression of T5H showed little effect on plant growth or grain physicochemical quality. In neuronal cell culture assays, serotonin induced neuroprotective action against apoptosis. Breeding of rice cultivars with high serotonin content may be beneficial for health and nutrition.