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.

Plant photosynthetic capacity directly determines crop yield. Light quality regulates photosynthetic capacity. This review discusses plant responses to far-red light from the phenotypic to the molecular level, focusing specifically on the improvement of photosynthetic capacity by adjustment of photosynthetic electron transport and the path of light energy. Far-red light can also regulate leaf angle and increase plant height and leaf area, via expression of associated genes, to capture more light energy. Thus, far-red light regulates plant morphology and photosynthetic capacity. Identifying the mechanism of this regulation may lead to increased crop yields.

Xanthine dehydrogenase, a member of the molybdenum enzyme family, participates in purine metabolism and catalyzes the generation of ureides from xanthine and hypoxanthine. However, the mechanisms by which xanthine dehydrogenase affects rice growth and development are poorly understood. In the present study, we identified a mutant with early leaf senescence and reduced tillering that we named early senescence and less-tillering 1 (esl1). Map-based cloning revealed that ESL1 encodes a xanthine dehydrogenase, and it was expressed in all tissues. Chlorophyll content was reduced and chloroplast maldevelopment was severe in the esl1 mutant. Mutation of ESL1 led to decreases in allantoin, allantoate, and ABA contents. Further analysis revealed that the accumulation of reactive oxygen species in esl1 resulted in decreased photosynthesis and impaired chloroplast development, along with increased sensitivity to abscisic acid and abiotic stresses. Ttranscriptome analysis showed that the ESL1 mutation altered the expression of genes involved in the photosynthesis process and reactive oxygen species metabolism. Our results suggest that ESL1 is involved in purine metabolism and the induction of leaf senescence. These findings reveal novel molecular mechanisms of ESL1 gene-mediated plant growth and leaf senescence.

Heterosis contributes greatly to crop production, but the genetic basis of heterosis is not fully understood. To identify heterotic loci (HLs) for grain yield, 12 yield traits were evaluated in four rice (Oryza sativa L.) mapping populations: one parental population of chromosome segment substitution lines derived from a cross between the japonica cultivar Nipponbare and indica cultivar 9311 and three connected test populations in either a homozygous 9311 genetic background or a heterozygous background. A total of 390 HLs were detected for the measured traits in two environments. The genetic bases of heterosis differed between the backcross and testcross populations. At least 10 HLs were confirmed in F₁ hybrids between 9311 and near-isogenic lines, each of which carried a heterotic locus of interest in the same 9311 background. All 10 showed overdominant or dominant effects on grain yield and yield components. Among them, three were verified as being associated with yield heterosis and colocalized in the same regions as those containing previously reported heterosis-associated genes. Five HLs were identified to be promising candidate loci that could be used to achieve more than 15% yield heterosis in several commercial rice hybrids. These findings suggest the potential of indica or japonica introgression for increasing yield in hybrid rice breeding programs.

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.

Boron (B) is an essential micronutrient for vascular plant growth. Both B deficiency and toxicity can impair tissue development in diverse plant species, but little is known about the effect of B on reproductive panicle development and grain yield. In this study, a mutant of Setaria italica exhibiting necrotic panicle apices was identified and designated as sibor1. Sequencing revealed a candidate gene, SiBOR1, with a G-to-A alteration at the seventh exon. Knockout transgenic lines generated by clustered regularly interspaced short palindromic repeats and their associated protein-9 also had necrotic panicles, verifying the function of SiBOR1. SiBOR1 encoded a membrane-localized B efflux transporter, co-orthologous to the rice BOR1 protein. SiBOR1 was dominantly expressed in panicles and displayed a distinct expression pattern from those of its orthologs in other species. The induced mutation in SiBOR1 caused a reduction in the B content of panicle primary branches, and B deficiency-associated phenotypes such as thicker cell walls and higher cell porosity compared with Yugu 1. Transcriptome analysis indicated that differentially expressed genes involved in cell wall biogenesis, jasmonic acid synthesis, and programmed cell death response pathways were enriched in sibor1. qPCR analysis identified several key genes, including phenylalanine ammonia-lyase (SiPAL) and jasmonate-ZIM-domain (SiJAZ) genes, responsive to B-deficient conditions. These results indicate that SiBOR1 helps to regulate panicle primary branch development to maintain grain yield in S. italica. Our findings shed light on molecular mechanisms underlying the relationship between B transport and plant development in S. italica.

Saline-alkaline (SA) stress is characterized by high salinity and high alkalinity (high pH), which severely inhibit plant growth and cause huge losses in crop yields worldwide. Here we show that a moderate elevation of endogenous abscisic acid (ABA) levels by RNAi-mediated suppression of OsABA8ox1 (OsABA8ox1-kd), a key ABA catabolic gene, significantly increased tolerance to SA stress in rice plants. We produced OsABA8ox1-kd lines in two different japonica cultivars, Dongdao 4 and Nipponbare. Compared with non-transgenic control plants (WT), the OsABA8ox1-kd seedlings accumulated 25.9%-55.7% higher levels of endogenous ABA and exhibited reduced plasmalemma injury, ROS accumulation and Na⁺/K⁺ ratio, and higher survival rates, under hydroponic alkaline conditions simulated by 10, 15, and 20 mmol L^-1 of Na₂CO₃. In pot trials using SA field soils of different alkali levels (pH 7.59, 8.86, and 9.29), OsABA8ox1-kd plants showed markedly higher seedling survival rates and more vigorous plant growth, resulting in significantly higher yield components including panicle number (85.7%-128.6%), spikelets per panicle (36.9%-61.9%), branches (153.9%-236.7%), 1000-kernel weight (20.0%-28.6%), and percentage of filled spikelets (96.6%-1340.8%) at harvest time. Under severe SA soil conditions (pH = 9.29, EC = 834.4 μS cm^-1), OsABA8ox1-kd lines showed an 194.5%-1090.8% increase in grain yield per plant relative to WT plants. These results suggest that suppression of OsABA8ox1 to increase endogenous ABA levels provides a new molecular approach for improving rice yield in SA paddies.

Base editing using CRISPR technologies is an invaluable tool for crop breeding. One of the major base editors, the adenine base editor (ABE), has been successfully used in both model plants and many crops. However, owing to limited editing efficiency, the ABE has been difficult to apply in polyploid crops such as allohexaploid bread wheat that often require simultaneous mutation of multiple alleles for fast breeding. We have designed a wheat high-efficiency ABE (WhieABE), using the newly developed high-activity adenosine deaminase TadA8e. In vivo and in vitro analysis demonstrated the improved applicability of TadA8e over the commonly used TadA7.10. Dinitroaniline is a widely used herbicide with high effectiveness and low toxicity to animals. However, wheat cultivars with tolerance to dinitroaniline are rare, limiting the application of dinitroaniline in wheat planting. Using A-to-G editing with WhieABE, we found that a Met-to-Thr mutation in wheat tubulin alleles located on chromosomes 1A, 1B, 1D, 4A, and 4D increased the resistance of wheat to dinitroaniline, revealing a dosage effect of edited tubulins in resistance. The WhieABE promises to be a valuable editing tool for accelerating crop improvement and developing herbicide-resistant wheat germplasm.

Drought and salinity are major environmental stresses that impair crop growth and productivity worldwide. Improving drought and salt tolerance of crops with microbial mutualists is an effective and environmentally sound strategy to meet the demands of the ever-growing world population. In the present study, we found that the Streptomyces albidoflavus OsiLf-2, a moderately salt-tolerant endophytic actinomycete, produced abundant osmolytes, including proline, polysaccharides, and ectoine. Inoculation with OsiLf-2 increased the osmotic-adjustment ability of the rice host by increasing the proline content (by 250.3% and 49.4%) and soluble sugar (by 20.9% and 49.4%) in rice under drought and salt conditions, relative to the uninoculated control. OsiLf-2 increased stress responses in the rice host at the physiological and biochemical levels (photosynthesis efficiency, osmolytes and antioxidant content), and the gene level (osmolytes synthesis, stress-responsive and ion-transport related genes), raising rice yields under both greenhouse and saline-alkaline soil conditions. The use of endophytic actinomycetes offers a promising biotechnological approach to developing stress-tolerant plants.

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.

Rice has a large number of nitrate or peptide transporter family (NPF) genes, but the effects of most members on rice growth and development are unknown. We report that OsNPF5.16, a nitrate transporter gene with natural variation in its promoter sequence, is essential for rice growth and yield. The promoter sequence showed various differences between indica and japonica cultivars, and higher expression of OsNPF5.16 was found in indica cultivars with higher plant weight and more tillers than japonica cultivars. OsNPF5.16 was highly expressed in roots, tiller basal parts, and leaf sheaths, and its protein was localized on the plasma membrane. In cRNA-injected Xenopus laevis oocytes, OsNPF5.16 transport of nitrate at high nitrate concentration depended on pH. Overexpression of OsNPF5.16 increased nitrate content and total nitrogen content in leaf sheath as well as biomass and tiller bud length in rice. Elevated expression of OsNPF5.16 increased rice tiller number and grain yield by regulating cytokinin levels. Inhibition of OsNPF5.16 expression showed the opposite effects. Regulating OsNPF5.16 expression has potential for improving rice grain yield.

Fusarium crown rot (FCR), caused by Fusarium spp., is a chronic and severe plant disease worldwide. In the last years, the incidence and severity of FCR in China has increased to the point that it is now considered a threat to local wheat crops. In this study, for the first time, the metabolites and transcripts responsive to FCR infection in the partial resistant wheat cultivar 04 Zhong 36 (04z36) and susceptible cultivar Xinmai 26 (XM) were investigated and compared at 20 and 25 days post inoculation (dpi). A total of 443 metabolites were detected, of which 102 were significantly changed because of pathogen colonization. Most of these 102 metabolites belonged to the flavonoid, phenolic acid, amino acid and derivative classes. Some metabolites, such as proline betaine, lauric acid, ribitol, and arabitol, were stably induced by Fusarium pseudograminearum (Fp) infection at two time points and may have important roles in FCR resistance. In line with the reduced seedling height of 04z36 and XM plants, RNA-seq analysis revealed that FCR infection significantly affected the photosynthesis activities in two cultivars. Furthermore, 15 jasmonate ZIM-domain genes (JAZ) in the significantly enriched ‘regulation of jasmonic acid mediated signaling pathway’ in 04z36 were down-regulated. The down-regulation of these JAZ genes in 04z36 may cause a strong activation of the jasmonate signaling pathway. Based on combined data from gene expression and metabolite profiles, two metabolites, benzoxazolin-2-one (BOA) and 6-methoxy-benzoxazolin-2-one (MBOA), involved in the benzoxazinoid-biosynthesis pathway, were tested for their effects on FCR resistance. Both BOA and MBOA significantly reduced fungal growth in vitro and in vivo, and, thus, a higher content of BOA and MBOA in 04z36 may contribute to FCR resistance. Above all, the current analysis extends our understanding of the molecular mechanisms of FCR resistance/susceptibility in wheat and will benefit further efforts for the genetic improvement of disease resistance.

Intercropping cereals and legumes is practiced widely in the world for improving yields and economic benefits. Shorter legume crops in intercropping are shaded by taller cereals, substantially reducing legume growth and yield. Reducing shade in intercropping by shortening the plant height of cereals by seedling defoliation has been proposed as a practical approach to increase crop yields and land productivity. A two-year field experiment was conducted to investigate the effect of defoliation of cereal crops at seedling stage on the growth and yield of peanut (Arachis hypogaea L.) intercropped with corn (Zea mays L.) or millet (Setaria italica L.). In comparison with non-defoliation controls, defoliation reduced final plant height by 29 cm on average for corn and 18 cm for millet. Photosynthetically active radiation on peanut in intercropping systems with corn or millet intercropping was respectively 27.0% and 22.8% higher than those in controls, significantly improving the light environment of intercropped peanut. Net photosynthetic rates of peanut were on average 25.5% higher in corn and peanut intercropping and 19.6% higher in millet and peanut intercropping than those in non-defoliation controls. Total biomass of intercropped peanut increased owing to increased root growth. Across two years, yield of peanut intercropped with corn was 27.7% and with millet 32.8% higher than those of controls. Defoliation of cereal crops did not affect corn yield but significantly decreased millet yield by 24.5%. Our results suggest that applying seedling defoliation in intercropped corn could increase peanut yield without compromising corn yield in an intercropping system.

Southern corn rust (SCR) is a destructive maize disease caused by Puccinia polysora Underw. To investigate the mechanism of SCR resistance in maize, a highly resistant inbred line, L119A, and a highly susceptible line, Lx9801, were subjected to gene mapping and transcriptome analysis. Bulked-segregant analysis coupled with whole-genome sequencing revealed several quantitative trait loci (QTL) on chromosomes 1, 6, 8, and 10. A set of 25 genes, including two coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) genes, were identified as candidate genes for a major-effect QTL on chromosome 10. To investigate the mechanism of SCR resistance in L119A, RNA-seq of P. polysora-inoculated and non-inoculated plants of L119A and Lx9801 was performed. Unexpectedly, the number of differentially expressed genes in inoculated versus non-inoculated L119A plants was about 10 times that of Lx9801, with only 29 common genes identified in both lines, suggesting extensive gene expression changes in the highly resistant but not in the susceptible line. Based on the transcriptome analysis, one of the CC-NBS-LRR candidate genes was confirmed to be upregulated in L119A relative to Lx9801 independently of P. polysora inoculation. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that transcription factors, as well as genes involved in defense responses and metabolic processes, were dominantly enriched, with the phenylpropanoid biosynthesis pathway most specifically activated. Consistently, accumulation of phenylpropanoid-derived lignin, especially S lignin, was drastically increased in L119A after P. polysora inoculation, but remained unchanged in Lx9801, suggesting a critical role of lignin in SCR resistance. A regulatory network of defense activation and metabolic change in SCR-resistant maize upon P. polysora infection is described.

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.

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.

Common bean (Phaseolus vulgaris) is an annual legume crop that is grown worldwide for its edible dry seeds and tender pods. Marsh spot (MS) of the seeds is a physio-genic stress disease affecting seed quality in beans. Studies have suggested that this disease involves a nutritional disorder caused by manganese deficiency, but the inheritance of resistance to this disease has not been reported. A biparental genetic population composed of 138 recombinant inbred lines (RILs) was developed from a cross between an MS resistant cultivar ‘Cran09’ and an MS susceptible cultivar ‘Messina’. The 138 RILs and their two parents were evaluated for MS resistance during five consecutive years from 2015 to 2019 in sandy and heavy clay soils in Morden, Manitoba, Canada. The MS incidence (MSI) and the MS resistance index (MSRI) representing disease severity were shown to be both highly correlated heritable traits that had high broad-sense heritability values (H²) of 86.5% and 83.2%, respectively. No significant differences for MSI and MSRI were observed between the two soil types in all five- (MSI) or four-year (MSRI) data collection, but significant correlations among years were observed despite MS resistance was moderately affected by year. The MSIs and MSRIs displayed a right-skewed distribution, indicating a mixed genetic model involving a few major genes and polygenes. Using the joint segregation analysis method, the same four major genes with additive-epistasis effects showed the best fit for both traits, explaining 84.4% and 85.3% of the phenotypic variance for MSI and MSRI, respectively. For both traits, the M1, M2, M3 and m4 acted as the favorable (resistant) alleles for the four genes where M and m represent two alleles of each gene. However, due to epistatic effects, only the individuals of the M1M2M3M4 haplotype appeared to be highly resistant, whereas those of the m1m2m3M4 haplotype were the most susceptible. The m4 allele significantly suppressed the additive effects of M1M2M3 on resistance, but decreased susceptibility due to the additive effects of m1m2m3. Further quantitative trait locus (QTL) mapping is warranted to identify and validate individual genes and develop molecular markers for marker-assisted selection of resistant cultivars.

A set of 45 diverse Asian and African origin/bred populations of pearl millet were investigated multi-locationally for morphological traits including grain yield and assessed for their fertility restoration ability on three cytoplasmic male sterility (CMS) systems in two contrasting seasons. Significant genetic variation was found for all the yield linked traits. Multivariate analysis for grain yield and its component traits grouped these populations into five clusters. Most of the Asian origin populations grouped into single cluster (Cluster III) and separated from the rest of the African origin populations indicating the presence of correspondence between clustering pattern and geographical origin of the populations. Clusters dominated with Asian populations (As-As) had linkages with early flowering, short plant height, more number of tillers, small and thin panicles, small seeded and low grain yield compared to the clusters dominated by African populations (Af-Af) or African origin and Asian bred (Af-As) populations. Genetically related populations having common parentage were found grouped in same clusters. Fertility restoration/maintainer frequency of 45 populations on three diverse CMS systems revealed that overall fertility restoration frequency was highest for A₁ (86%) followed by A₄ (37%) and for A₅ (7%) CMS system. Five populations were identified as potential sources for developing maintainer lines for all three CMS systems and eight populations were identified specifically for A₄ and A₅ CMS systems. A set of 11 and four populations were identified for restorer line development exclusively for A₁ and A₅ CMS system, respectively. Six populations were identified for the development of dual restorers for both A₁ and A₄ CMS system.

Stable yield of staple grains must be ensured to satisfy food demands for daily dietary energy requirements against the backdrop of global climate change. Summer maize, a staple crop, suffers severe yield losses due to extreme rainfall events, threatening food security. A randomized block experiment with four treatments: control, no water stress (CK); waterlogging for 6 days at the third leaf, sixth leaf stage, and 10th day after tasseling, was conducted to investigate the mechanism of waterlogging-induced yield losses of summer maize. Waterlogging delayed plant growth and impaired tassel and ear differentiation, leading to high grain yield losses of Denghai 605 (DH605). Waterlogging at third leaf (V3) stage reduced the photosynthesis of DH605, reducing total dry matter weight. Waterlogging at V3 stage reduced sucrose-cleaving enzymes activities in spike nodes and ears, reducing the carbon partitioned to ears (-53.1%), shanks (-46.5%), and ear nodes (-71.5%) but increasing the carbon partitioned to ear leaves (9.6%) and tassels (43.9%) in comparison with CK. The reductions in total carbon assimilate together with the reduced carbon partitioning to ears resulted in poor development of spikes (with respectively 15.2% and 20.6% reductions in total florets and fertilized florets) and lengthened the anthesis-silking interval by around 1 day, leading to high yield losses.

Leaf rust (LR) and stripe rust (YR) are important diseases in wheat producing areas worldwide and cause severe yield losses under favorable environmental conditions when susceptible varieties are grown. We determined the genetic basis of resistance to LR and YR in variety Borlaug 100 by developing and phenotyping a population of 198 F₆ recombinant inbred lines derived from a cross with the susceptible parent Apav#1. LR and YR phenotyping were conducted for 4 and 3 seasons, respectively, at CIMMYT research stations in Mexico under artificial epidemics. Mendelian segregation analyses indicated that 3-5 LR and 2 YR genes conferred resistance in Borlaug 100. Lr46/Yr29 (1BL), Yr17 (2AS) and Yr30 (3BS) were present in the resistant parent and segregated in the RIL population based on characterization by molecular markers linked to these genes. When present alone, Lr46/Yr29 caused average 13% and 16% reductions in LR and YR severities, respectively, in RILs. Similarly, Yr17 and Yr30 reduced YR severities by 57% and 11%, respectively. The Yr30 and the Yr17 translocation were also associated with 27% and 14% reductions, respectively, in LR severity, indicating that the 3BS and 2AS chromosomal regions likely carry new slow rusting LR resistance genes, temporarily designated as LrB1 and LrB2, respectively. Additive effects of Yr30*Yr17, Yr29*Yr17 and Yr29*Yr30 on YR and LR were significant and reduced YR severities by 56%, 55%, and 45%, respectively, and LR severities by 34%, 40%, and 45%, respectively. Furthermore, interaction between the three genes was also significant, with mean reductions of 70% for YR and 54% for LR severities. Borlaug 100, or any one of the 21 lines with variable agronomic traits but carrying all three co-located resistance loci, can be used as resistance sources in wheat breeding programs.

Bacterial blight (BB), which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is an important rice disease responsible for significant yield losses. In the rice-growing regions of South China where BB outbreaks are common, the resistance of cultivars with BB resistance genes Xa4 and Xa21 has been lost because of rapid changes in the Xoo population structure and virulence. In this study, 421 diverse rice accessions were evaluated regarding their resistance to two Xoo strains, namely GD1358 (C5) and IV, which are prevalent pathotypes in South China and overcame the resistance of Xa4 and Xa21, respectively. Using the 4.8mio filtered SNP dataset, we conducted a genome-wide association study, which identified 13 loci associated with BB resistance, including eight new quantitative trait loci (QTL) and five QTL harboring known BB resistance genes: Xa3/Xa26, xa5, Xa35(t), Xa36(t), Xa40, Xa43(t), and xa44(t). Intriguingly, a steep peak was detected on chromosomes 5 and 11. Six QTL including three new ones, were distributed on chromosome 11, whereas a new QTL qBB5.1 and a known QTL were detected on chromosome 5. Haplotype analyses indicated that the LOC_Os05g01610 (OsPRAF2) gene within the qBB5.1 region, which encodes a PRAF protein, is associated with BB resistance. Furthermore, OsPRAF2 knockout lines generated using the CRISPR-Cpf1 system were significantly more resistant to Xoo strains than the wild-type plants. Our results provide researchers and breeders with useful information regarding QTL and gene resources, which may be relevant for developing new BB-resistant rice cultivars.

The market success of perennial ryegrass (Lolium perenne L.) cultivars depends on sufficient seed production, as they are propagated by seed. However, breeding for high quality forage production reduces seed yield, and breaking the negative correlation would help to overcome the problem. The foliar disease crown rust is another factor affecting reproductive capacity and thereby seed yield. We evaluated seed yield-related traits and resistance to crown rust in a collection of commercial cultivars and ecotypes of perennial ryegrass and identified genome-wide markers associated with the traits. The study revealed high variation between the ecotype and cultivar groups as well as between years. A genome-wide association study identified 17 DNA single-nucleotide polymorphisms (SNPs) of which eight were associated with crown rust and nine with flag-leaf length. The SNP markers were located within or near predicted genes functioning in defense against pathogens. The identified genes are strong candidates for a further in-depth functional study to continue unravel determination of leaf architecture and crown rust resistance in perennial ryegrass.

Labor scarcity requires double-season rice to be planted by direct seeding as an alternative to transplanting. Only ultrashort-duration varieties can be used in direct-seeded, double-season rice (DSD) in central China where thermal time is limited. Whether ultrashort-duration varieties grown in DSD can be as productive and efficient in nitrogen (N) use as transplanted double-season rice (TPD) remains unclear. Field experiments were conducted in Hubei province, central China with two establishment methods (DSD, TPD) and three N rates in the early and late seasons of 2017 and 2018. Nitrogen treatments included zero-N control (N0), total N rate of 60 kg N ha^-1 with equal splits at basal, midtillering, and panicle initiation (N1), and weekly N application at 15 kg ha^-1 from seeding/transplanting to heading (N2). Both early- and late-season rice under DSD matured within 95 days, on average 9 days shorter than rice under TPD. The grain yield of DSD was comparable to or higher than that of TDP in both seasons, although the daily yield was significantly higher under DSD than under TDP. Before heading, DSD had higher leaf area, stem number, intercepted radiation, and radiation use efficiency than TPD, which compensated for the negative effect of short growth duration on biomass production. Total dry weight and harvest index under DSD were comparable to or higher than those under TDP. In general, the recovery efficiency of fertilizer-N under DSD was higher than that under TPD, but the reverse was true for physiological N use efficiency. Thus, there was no significant difference in agronomic N use efficiency between DSD and TPD. These results suggested that DSD with ultrashort-duration varieties is a promising alternative to TPD in central China for maintaining high grain yield and N fertilizer use efficiency with less labor input.

Doubled haploid (DH) technology is important in modern maize breeding. Haploid inducers determine the efficiency of both haploid induction and identification. It has taken decades to improve the efficiency, haploid induction rate (HIR), from the ～2% of the ancestor haploid inducer, stock6, to the ～10% of modern haploid inducers. Improvement of kernel oil content (KOC) would further enhance haploid identification efficiency. Using molecular marker-assisted selection, in combine with the number of haploids per ear as phenotypic criterion, we developed a new high-oil haploid inducer line, CHOI4, with a mean HIR of 15.8% and mean KOC of 11%. High KOC of CHOI4 can achieve a mean accuracy greater than 90% in identification of haploids of different backgrounds, with reduced false discovery rates and false negative rates in comparison with the previous high-oil haploid inducer line, CHOI3. Comparison of phenotypic selection strategies suggested that the number of haploids per ear can be used as a phenotyping criterion during haploid inducer line development. CHOI4 could further increase the efficiency of large-scale DH breeding programs with lower cost.

The grain of rye (Secale cereale L.) used for baking contains a large amount of non-starch polysaccharides, making it an excellent component of functional foods. But rye grain intended for alcohol production and forage use should have a reduced content of these polysaccharides. A comprehensive parameter that can predict the best field of application for winter rye grain is the viscosity of its wholemeal water extract. However, our understanding of the genetic background underlying this key trait and associated features of rye grain is poor. By analyzing six Russian winter rye cultivars, we identified the most contrasting forms and characterized the peculiarities of their water-soluble carbohydrates capable of influencing the viscosity of water extracts. Then, using phylogenetic and transcriptomic analyses, we identified in the rye genome many genes encoding putative glycosyltransferases and glycosylhydrolases responsible for the synthesis and degradation of arabinoxylans, mixed-linkage glucans, cellulose, and some other polysaccharides. We determined the dynamics of mRNA abundance for these genes at three stages of kernel development. Comparisons of gene expression levels in two contrasting cultivars revealed specific members of multigene families that may serve as promising targets for manipulating non-starch polysaccharide content in rye grain. High-viscosity cultivars were characterized by up-regulation of many glycosyltransferases involved in the biosynthesis of arabinoxylans and other cell-wall polysaccharides, whereas low-viscosity cultivars showed up-regulation of several genes encoding polysaccharide-degrading enzymes.

Computational efficiency has become a key issue in genomic prediction (GP) owing to the massive historical datasets accumulated. We developed hereby a new super-fast GP approach (SHEAPY) combining randomized Haseman-Elston regression (RHE-reg) with a modified Algorithm for Proven and Young (APY) in an additive-effect model, using the former to estimate heritability and then the latter to invert a large genomic relationship matrix for best linear prediction. In simulation results with varied sizes of training population, GBLUP, HEAPY|A and SHEAPY showed similar predictive performance when the size of a core population was half that of a large training population and the heritability was a fixed value, and the computational speed of SHEAPY was faster than that of GBLUP and HEAPY|A. In simulation results with varied heritability, SHEAPY showed better predictive ability than GBLUP in all cases and than HEAPY|A in most cases when the size of a core population was 4/5 that of a small training population and the training population size was a fixed value. As a proof of concept, SHEAPY was applied to the analysis of two real datasets. In an Arabidopsis thaliana F₂ population, the predictive performance of SHEAPY was similar to or better than that of GBLUP and HEAPY|A in most cases when the size of a core population (200) was 2/3 of that of a small training population (300). In a sorghum multiparental population, SHEAPY showed higher predictive accuracy than HEAPY|A for all of three traits, and than GBLUP for two traits. SHEAPY may become the GP method of choice for large-scale genomic data.

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.

Chlorosis at leaf margins is a typical symptom of potassium (K) deficiency, but inappropriate application of K with other nutrients often masks symptoms of K deficiency. A two-year field experiment was conducted to measure the interactive effects of N and K on leaf photosynthesis and dry matter accumulation and the resulting growth dilution effect on K concentration and leaf K deficiency symptoms. N application aggravated the imbalance of N and K nutrients and further exacerbated K deficiency symptoms under K limitation. Synergistic effects of N and K promoted plant growth, amplified the growth dilution effect, and reduced the critical K concentration in leaves. Using 90% of the maximum shoot biomass as a threshold, the critical K concentration was 0.72% at the recommended N (N₁₈₀) fertilization level. The critical K concentration increased by 62.5% owing to the reduced biomass under insufficient N (N₉₀) supply. In contrast, high N (N₂₇₀) reduced the critical K concentration (0.64%), accelerating chlorophyll decomposition and exacerbating K deficiency symptoms. The basis of changing the critical K concentration by magnifying growth dilution effect was the functional synergistic effect of N and K on photosynthetic characteristics. Under insufficient N, the low maximum carboxylation rate (V_cmax) limited the net photosynthetic rate (A_n) and necessitated more K to maintain high CO₂ transmission capacity, to improve the total conductance g_tot /V_cmax ratio. High N supply increased g_tot and V_cmax, possibly mitigating the effect of K reduction on photosynthesis. In conclusion, it is unwise to judge K status of plants only by K concentration without accounting for crop mass (or dilution effect), critical K concentration and deficiency symptoms are affected by N fertilization, and the synergistic effect of N and K on leaf photosynthesis is the foundation of maximal growth of plants under diverse critical K concentrations.

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.

Screening for agronomic traits associated with grain moisture is important for mechanical grain-harvesting of maize. Cob color as a visual indicator has received limited attention, though it has been subjected to artificial selection, and may have some association with threshability. To investigate the relationships between cob color and grain moisture and other agronomic traits, field experiments were conducted during 2016-2017 using 23 commercial hybrids with red or white cobs. Kernels of red-cob hybrids dehydrated faster, showing lower moisture content at harvest than white-cob hybrids. A cob color index (CCI) was established as a quantitative measure of cob color in the hybrid panel. Ranging from 0 (whitest) to 17.98 (reddest), CCI correlated well with grain dehydration and other agronomic traits associated with growth ontogeny, plant morphology, and plant N content. Strong selection of red cob for recently released hybrids suitable for mechanical grain-harvesting indirectly validated the observed link between cob color and grain dehydration. We propose that cob color and CCI could be used in future selection of maize cultivars bred for mechanical grain-harvesting.