Plant glutamine synthetase (GS, EC6.3.1.2) catalyzes the synthesis of glutamine from glutamate and ammonium ions and acts as a key enzyme in the nitrogen metabolic pathway in organisms. Nitrogen is an essential element for plant growth and development and plays an important role in crop yield and quality formation. Therefore, GS is crucial in many physiological processes in plants. Currently, nitrogen regulation by GS in plants is well-studied in terms of its effect on plant growth and development. This article reviews the regulatory role of plant GS and its molecular mechanism in mitigating stress injury, such as low or high temperature, salinity, drought and oxidation. The function of plant GS in stress tolerance response is focused. The review aims to provide a reference for the utilization of plant GS in crop stress tolerance breeding.

The Asian cultivated rice Oryza sativa can be classified into two major subspecies: japonica/geng and indica/xian. There are large physiological and phenotypic differences between the two subspecies, with each having its advantages and disadvantages. Understanding the differences between xian and geng could provide a foundation for cultivar improvement based on hybridization between subspecies in order to synthesize favorable traits. We review the origin and domestication of xian and geng rice, compare their differences in terms of physiological and phenotypical traits, and describe the molecular mechanism differences between the subspecies. Based on this knowledge, we propose an ideal plant architecture of geng rice varieties for northern regions.

Alfalfa (Medicago sativa L.) is a nutritious forage crop with wide ecological adaptability. The molecular breeding of alfalfa is restricted by its heterozygous tetraploid genome and the difficult genetic manipulation process. Under time and resource constraints, we applied a more convenient approach. We investigated two MtGA3ox genes, MtGA3ox1 and MtGA3ox2, of Medicago truncatula, a diploid legume model species, finding that MtGA3ox1 plays a major role in GA-regulated plant architecture. Mutation of neither gene affected nitrogenase activity. These results suggest that MtGA3ox1 can be used in semidwarf and prostrate alfalfa breeding. Based on the M. truncatula MtGA3ox1 sequence, MsGA3ox1 was cloned from alfalfa, and two knockout targets were designed. An efficient CRISPR/Cas9-based genome editing protocol was used to generate msga3ox1 mutants in alfalfa. We obtained three lines that carried mutations in all four alleles in the T0 generation. Fifteen clonal plants were vegetatively propagated from each transgenic line using shoot cuttings. The plant height and internode length of msga3ox1 null mutants were significantly decreased. The number of total lateral branches, leaf/stem ratio and crude protein content of aerial plant parts of msga3ox1 mutants were significantly increased. Thus, we obtained semi-dwarf and prostrate alfalfa by gene editing.

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

Plant architecture strongly influences rice grain yield. We report the cloning and characterization of the LTA1 gene, which simultaneously controls tiller angle and yield of rice. LTA1 encodes a chloroplast-localized protein with a conserved YbaB DNA-binding domain, and is highly expressed in photosynthetic tissues including leaves and leaf sheaths. Disrupting the function of LTA1 leads to large tiller angle and yield reduction of rice. LTA1 affects the gravity response by mediating the distribution of endogenous auxin, thereby regulating the tiller angle. An lta1 mutant showed abnormal chloroplast development and decreased chlorophyll content and photosynthetic rate, in turn leading to reduction of rice yield. Our findings shed light on the genetic basis of tiller angle and provide a potential gene resource for the improvement of plant architecture and rice yield.

The grain filling of inferior spikelets is much less complete than that of superior spikelets in rice cultivars with large panicles and numerous spikelets and is promoted by moderate soil drying (MD) post-anthesis. A growing body of evidence has shown that microRNAs function in regulating grain development. However, little is known about the mechanism of microRNA control of grain filling of inferior spikelets in response to MD. In this study, grain filling of inferior spikelets was promoted by MD treatment in Nipponbare. Small-RNA profiling at the most active grain-filling stage was conducted in inferior spikelets under control (CK) and MD treatment. Of 521 known and 128 novel miRNAs, 38 known and 9 novel miRNAs were differentially expressed between the CK and MD treatments. Target genes of differentially expressed miRNAs were involved in multiple developmental and signaling pathways associated with catalytic activity, carbohydrate metabolism, and other functions. Both miR1861 and miR397 were upregulated by MD, leading to a decrease in OsSBDCP1 and OsLAC, two negative regulators of SSIIIa activity and BR signaling, respectively. In contrast, miR1432 abundance was reduced by MD, resulting in upregulation of OsACOT and thus an elevated content of both ABA and IAA. These results suggest that both starch synthesis and phytohormone biosynthesis are regulated by differentially expressed miRNAs in inferior spikelets in response to MD treatment. Our results suggest the molecular mechanisms by which miRNAs regulate grain filling in inferior spikelets of rice under moderate soil drying, providing potential application in agriculture to increase rice yields by genetic approaches.

RING finger E3 ligases play an important role in regulating plant growth and development by mediating substrate degradation. In this study, we identified TaGW2L, encoding a Grain width and weight2 (GW2)-like RING finger E3 ligase, as a novel positive regulator of heading date in wheat (Triticum aestivum L.). TaGW2L exhibited high amino acid sequence similarities with TaGW2 homoeologs, particularly in the conserved RING finger domain. Expression analysis indicated that TaGW2L was constitutively expressed in various wheat tissues. TaGW2L showed transactivation activity in yeast and could interact with the ubiquitin-conjugating enzymes E2s. An in vitro ubiquitination assay verified that TaGW2L possessed a similar E3 ligase activity to TaGW2. Overexpression of the TaGW2L-7A homoeolog in wheat led to a significantly earlier heading date under both natural conditions and long-day conditions. Transcriptome analysis revealed that multiple known genes positively regulating wheat heading were significantly upregulated in the TaGW2L-7A-overexpression plants compared with the wild-type control. Together, our findings shed light on the role of TaGW2L in wheat heading date and provide potential applications of TaGW2L for the adaptation improvement of crops.

Root system architecture is influenced by gravity. How the root senses gravity and directs its orientation, so-called gravitropism, is not only a fundamental question in plant biology but also theoretically important for genetic improvement of crop root architecture. However, the mechanism has not been elucidated in most crops. We characterized a rice agravitropism allele, wavy root 1 (war1), a loss-of-function allele in OsPIN2, which encodes an auxin efflux transporter. With loss of OsPIN2 function, war1 leads to altered root system architecture including wavy root, larger root distribution angle, and shallower root system due to the loss of gravitropic perception in root tips. In the war1 mutant, polar auxin transport was disrupted in the root tip, leading to abnormal auxin levels and disturbed auxin transport and distribution in columella cells. Amyloplast sedimentation, an important process in gravitropic sensing, was also decreased in root tip columella cells. The results indicated that OsPIN2 controls gravitropism by finely regulating auxin transport, distribution and levels, and amyloplast sedimentation in root tips. We identified a novel role of OsPIN2 in regulating ABA biosynthesis and response pathways. Loss of OsPIN2 function in the war1 resulted in increased sensitivity to ABA in seed germination, increased ABA level, changes in ABA-associated genes in roots, and decreased drought tolerance in the seedlings. These results suggest that the auxin transporter OsPIN2 not only modulates auxin transport to control root gravitropism, but also functions in ABA signaling to affect seed germination and root development, probably by mediating crosstalk between auxin and ABA pathways.

Multiple nitrate transporter (NRT) genes exist in the genome of bread wheat, and it is of great importance to identify the elite NRT genes for N-efficient wheat cultivar breeding. A candidate gene association study (CGAS) of six N use efficiency (NUE) related traits (grain N concentration (GNC), straw N concentration (SNC), grain yield (GY), grain N accumulation (GNA), shoot total N accumulation (STN) and N harvest index (NHI)) was performed based on SNPs in 46 NRT2 genes using a panel composed of 286 wheat cultivars. CGAS identified TaNRT2.1-6B as an elite NRT gene that is significantly associated with four (NHI, SNC, GNA and GY) of the six NUE-related traits simultaneously. TaNRT2.1-6B is located on the plasma membrane and acts as a dual-affinity NRT. The overexpression of TaNRT2.1-6B increased the N influx and root growth of wheat, whereas gene silence lines resulted in the opposite effects. The overexpression of TaNRT2.1-6B also improved GY and N accumulation of wheat under either limited or sufficient N conditions. The data provide the TaNRT2.1-6B gene and the two associated SNP markers as promising powerful tools for breeding wheat cultivars with high N uptake ability and NUE.

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

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

MicroRNAs (miRNAs) play essential roles in plant defense responses, although such roles have not been identified in cotton in response to the plant pathogenic fungus Verticillium dahliae. In this study, the functions of miR398b and its target genes in cotton-V. dahliae interaction were investigated. The transcript levels of miR398b were down-regulated by V. dahliae infection and miR398b overexpression in cotton made the plants more susceptible to V. dahliae. The results suggest that miR398b negatively regulates cotton resistance to V. dahliae. This may occur by miR398b repression of some CC-NBS-LRR genes via translational inhibition, interfering with defense responses and leading to cotton susceptibility to V. dahliae. Alternatively, miR398b may guide the cleavage of the mRNAs of GhCSD1, GhCSD2 and GhCCS, each of which functions in reactive oxygen species (ROS) regulation and homeostasis, thereby causing excessive ROS accumulation in miR398b-overexpressing plants in response to V. dahliae infection. This study suggests conserved and novel roles of miR398b in the cotton-V. dahliae interaction. These discoveries may be coupled with new strategies in cotton breeding programs to improve resistance to V. dahliae.

Fiber productivity and quality of cotton are severely affected by abiotic stresses. In this study, we identified the role of GhADF1, an actin depolymerizing factor, in cotton response to drought stress. GhADF1 expression in cotton could be induced by PEG6000. GhADF1-RNAi transgenic cotton showed increased tolerance to drought stress during seed germination and seedling development as well as at the reproductive stage. In contrast, overexpression of GhADF1 led to a drought-sensitive phenotype in transgenic plants. GhADF1-RNAi plants produced an enlarged root system with longer primary roots, more lateral roots, increased root dry biomass, and increased cell size. In leaves of GhADF1-RNAi cotton, proline content and activities of reactive oxygen species-scavenging enzymes were increased following drought stress compared with those in wild type. GhADF1-RNAi lines showed higher water-use efficiency than the wild type, accompanied by reduced leaf stomatal density and conductance. GhADF1-RNAi cotton produced higher fiber yield in the field under both normal and drought conditions. Transcriptomic analyses identified 124 differentially expressed genes in leaves of GhADF1-RNAi lines compared with the wild type following drought treatment. Upregulated genes included those encoding transcription factors, protein kinases, heat shock proteins, and other proteins known to be involved in stress responses. We conclude that GhADF1 reduces the expression of abiotic stress-associated genes in cotton response to drought stress and may be a promising candidate gene for crop improvement by genetic manipulation.

Maize (Zea mays L.) stalk rot is a devastating disease worldwide, causing severe yield losses. Although previous studies have focused on the genetic dissection of maize resistance to stalk rot, the mechanisms of resistance remain largely unknown. We used a comparative proteomics approach to identify candidate proteins associated with stalk rot resistance. Statistical analyses revealed 763 proteins differentially accumulated between Fusarium graminearum and mock-inoculated plants. Among them, the antioxidant protein ZmPrx5, which was up-accumulated in diseased plants, was selected for further study. ZmPrx5 transcripts were present in root, stalk, leaf, ear, and reproductive tissues. The expression of ZmPrx5 in three inbred lines increased significantly upon F. graminearum infection. ZmPrx5 was localized in the cytoplasm. Compared to control plants, maize plants overexpressing ZmPrx5 showed increased resistance to F. graminearum infection, and ZmPrx5 mutant plants were more susceptible than wild-type plants. Defense-associated pathways including plant-pathogen interactions, phenylalanine metabolism, and benzoxazinoid and flavonoid biosynthesis were suppressed in ZmPrx5 homozygous mutant plants compared with wild-type plants. We suggest that ZmPrx5 positively regulates resistance against stalk rot in maize, likely through defense-oriented transcriptome reprogramming. These results lay a foundation for further research on the roles of Prx5 subfamily proteins in resistance to plant fungal diseases, and provide a potential genetic resource for breeding disease-resistance maize lines.

As the second most abundant natural polymer, accounting for approximately 30% of the organic carbon in the biosphere, lignin plays an essential role in plant development. However, a high lignin content affects the nutritional quality of alfalfa (Medicago sativa L.), the most widely cultivated perennial legume forage crop. Histological analysis indicated that G-lignin and S-lignin were present in the stem, leaf, and petiole of alfalfa, and the deposition of lignin increased gradually in descending internodes. Neutral detergent fiber (NDF), acid detergent fiber (ADF), and acid detergent lignin (ADL) contents continually increased from the top to the bottom of the stem, and ADL content showed a similar trend in leaves. Alfalfa leaves and stems from five different nodes (1, 2, 4, 6, and 8) were used as materials to investigate molecular regulatory mechanisms in lignin synthesis by RNA sequencing. Respectively 8074 and 7752 differentially expressed genes (DEGs) were identified in leaves and stems, and 1694 DEGs were common to the two tissues. "Phenylpropanoid biosynthesis"? was the most enriched pathway in both leaves and stems, and 134 key regulatory genes in lignin synthesis were identified by a weighted gene co-expression network analysis. The NAC family transcription factor MsNST1 gene was highly expressed in old leaf and stem tissues. The deposition pattern of G- and S-lignin differed among M. truncatula wild-type, nst1 mutants, and overexpression lines, and the transcription levels of lignin synthesis genes such as HCT, F5H, and COMT in these three materials also differed. These results suggest that MsNST1 affects lignin synthesis in alfalfa. These findings provide a genetic basis and abundant gene resources for further study of the molecular mechanisms of lignin synthesis, laying a foundation for low-lignin alfalfa breeding research.

Germplasm conserved in gene banks is underutilized, owing mainly to the cost of characterization. Genomic prediction can be applied to predict the genetic merit of germplasm. Germplasm utilization could be greatly accelerated if prediction accuracy were sufficiently high with a training population of practical size. Large-scale resequencing projects in rice have generated high quality genome-wide variation information for many diverse accessions, making it possible to investigate the potential of genomic prediction in rice germplasm management and exploitation. We phenotyped six traits in nearly 2000 indica (XI) and japonica (GJ) accessions from the Rice 3K project and investigated different scenarios for forming training populations. A composite core training set was considered in two levels which targets used for prediction of subpopulations within subspecies or prediction across subspecies. Composite training sets incorporating 400 or 200 accessions from either subpopulation of XI or GJ showed satisfactory prediction accuracy. A composite training set of 600 XI and GJ accessions showed sufficiently high prediction accuracy for both XI and GJ subspecies. Comparable or even higher prediction accuracy was observed for the composite training set than for the corresponding homogeneous training sets comprising accessions only of specific subpopulations of XI or GJ (within-subspecies level) or pure XI or GJ accessions (across-subspecies level) that were included in the composite training set. Validation using an independent population of 281 rice cultivars supported the predictive ability of the composite training set. Reliability, which reflects the robustness of a training set, was markedly higher for the composite training set than for the corresponding homogeneous training sets. A core training set formed from diverse accessions could accurately predict the genetic merit of rice germplasm.

Heading date (flowering time) determines the adaptability of cultivars to different environments. We report the fine mapping and candidate gene analysis of qHD1b, a quantitative trait locus (QTL) responsible for early flowering that was derived from common wild rice (O. rufipogon) under both short-day and long-day conditions. The introgression line IL7391, which carried segments from common wild rice in a Zhonghui 8015 (ZH8015) background, exhibited early heading compared to the background and was crossed with ZH8015 to generate BC₅F_2:3 families for QTL analysis. This enabled the identification of two heading-date QTL, named qHD1b and qHD7, of which the first was selected for further research. High-resolution linkage analysis was performed in BC₅F_4:5 and BC₅F₆ populations, and the location of qHD1b was confined to a 112.7-kb interval containing 17 predicted genes. Five of these genes contained polymorphisms in the promoter or coding regions and were thus considered as candidates. Expression analysis revealed a positive association between LOC_Os01g11940 expression and early heading. This locus was annotated as OsFTL1, which encodes an ortholog of Arabidopsis Flowering Locus T and was the most likely candidate gene for qHD1b. Our study revealed that qHD1b acts as a floral activator that promotes flowering by up-regulating Ehd1, Hd3a, RFT1, OsMADS14, and OsMADS15 under both short-day and long-day conditions. Field experiments showed that qHD1b affected several yield-related agronomic traits including 1000-grain weight and grain length. qHD1b could be useful for marker-assisted selection and breeding of early-maturing cultivars.

Leaf development underlies crop growth and productivity and has been a major target of crop domestication and improvement. However, most genes controlling leaf development in barley remain unknown. We identified a dwarf and liguleless (dl) mutant derived by ethylmethane sulfonate mutagenesis. The dl mutant showed dramatic changes in shoot architecture compared with wild-type (Yangnongpi 5) plants. Besides lacking ligules, the dl mutant showed much shorter plant height (28"¯cm) than Yangnongpi 5 (78"¯cm). By map-based cloning, the dl gene was localized to a 56.58-kb genomic interval on the long arm of chromosome 7. A C-to-T single-nucleotide substitution was identified at exon position 790, and is a functional mutation resulting in a proline-to-serine substitution at the 264th amino acid residue of HORVU7Hr1G106960. Consequently, HORVU7Hr1G106960 was identified as the DL gene, encoding 269 amino acids and containing the Arabidopsis LSH1 and Oryza G1 (ALOG) domain. DL is highly similar to rice OsG1-LIKE 1/2 (OsG1L1/2) and sorghum AWN1/AWN1-10 at the amino acid level. Although the dl mutant allele showed no expression changes in selected tissues by real-time PCR, we propose HORVU7Hr1G106960 as a candidate gene conferring the dwarf and liguleless phenotype in barley.

Powdery mildew (PM), caused by the fungus Microsphaera diffusa, causes severe yield losses in soybean [Glycine max (L.) Merr.] under suitable environmental conditions. Identifying resistance genes and developing resistant cultivars may prevent soybean PM damage. In this study, analysis of F₁, F_2, and F_8:11 recombinant inbred line (RIL) populations derived from the cross between Zhonghuang 24 (ZH24) and Huaxia 3 (HX3) indicated that adult-plant resistance (APR) to powdery mildew in the soybean cultivar (cv.) ZH24 was controlled by a single dominant locus. A high-density genetic linkage map of the RIL population was used for fine mapping. The APR locus in ZH24 was mapped to a 281-kb genomic region on chromosome 16. Using 283 susceptible plants of another F₂ population, the candidate region was fine-mapped to a 32.8-kb genomic interval flanked by the markers InDel14 and Gm16_428. The interval harbored five genes, including four disease resistance (R)-like genes, according to the Williams 82.a2.v1 reference genome. Quantitative real-time PCR assays of candidate genes revealed that the expression levels of Glyma.16g214300 and Glyma.16g214500 were changed by M. diffusa infection and might be involved in disease defense. Rmd_B13 showed all-stage resistance (ASR) to PM in soybean cv. B13. An allelism test in the F₂ segregating population from the cross of ZH24 × B13 suggested that the APR locus Rmd_ZH24 and the ASR locus Rmd_B13 may be allelic or tightly linked. These results provide a reference marker-assisted selection in breeding programs.

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

Powdery mildew of wheat is a destructive disease seriously threatening yield and quality worldwide. Comprehensive dissection of new resistance-related loci/genes is necessary to control this disease. LS5082 is a Chinese wheat breeding line with resistance to powdery mildew. Genetic analysis, using the populations of LS5082 and three susceptible parents (Shannong 29, Shimai 22 and Huixianhong), indicated that a single dominant gene, tentatively designated PmLS5082, conferred seedling resistance to different Blumeria graminis f. sp. tritici (Bgt) isolates. Bulked segregant RNA-Seq was carried out to map PmLS5082 and to profile differentially expressed genes associated with PmLS5082. PmLS5082 was mapped to a 0.7 cM genetic interval on chromosome arm 2BL, which was aligned to a 0.7 Mb physical interval of 710.3-711.0 Mb. PmLS5082 differs from the known powdery mildew (Pm) resistance genes on chromosome arm 2BL based on their origin, chromosome positions and/or resistance spectrum, suggesting PmLS5082 is most likely a new Pm gene/allele. Through clusters of orthologous groups and kyoto encyclopedia of genes and genomes analyses, differentially expressed genes (DEGs) associated with PmLS5082 were profiled. Six DEGs in the PmLS5082 interval were confirmed to be associated with PmLS5082 via qPCR analysis, using an additional set of wheat samples and time-course analysis post-inoculation with Bgt isolate E09. Ten closely linked markers, including two kompetitive allele-specific PCR markers, were confirmed to be suitable for marker-assisted selection of PmLS5082 in different genetic backgrounds, thus can be used to detect PmLS5082 and pyramid it with other genes in breeding programs.

Sugarcane leaf blight (SLB), caused by Stagonospora tainanensis, is one of the most harmful fungal diseases, threatening the sugarcane industry and causing high losses of cane yield and sugar in susceptible cultivars. Using a two-way pseudo-testcross mapping strategy in combination with array genotyping, two high-density genetic maps were constructed for sugarcane cultivars YT93-159 and ROC22 with mean densities of respectively 3.0 and 3.5 cM per marker, and covering respectively 4485 and 2720 cM of genetic distance. The maps showed highly conserved colinearity with the genome of the ancestral species Saccharum officinarum, supporting the reliability of the linkage configurations of the maps. Quantitative trait loci (QTL) analysis of SLB resistance revealed six QTL (qSLB-1-qSLB-6). The major QTL qSLB-1 explaining 16.4% of phenotypic variance was assigned as the main QTL, and the total percentages of phenotypic variance explained in YT93-159 and ROC22 were 37.9% and 17.6%, respectively. Nine transcription factor and seven pathogen receptor genes lying in the qSLB-1 interval were highly expressed and are proposed as candidate causal genes for SLB resistance.

Erect milkvetch (Astragalus adsurgens) is a perennial legume forage crop with economic and ecological value in livestock grazing and soil-erosion control in arid and semiarid areas worldwide. Genomic information and molecular tools to support breeding and research in the species are limited. The objectives of this investigation were to map its genome using DNA markers and to identify quantitative trait loci (QTL) in the species. An F₁ mapping population of 250 plants was developed from a cross between two parents with differing flowering-related traits. A high-density genetic linkage map containing 4821 markers on eight linkage groups (LGs) with a total genetic length of 1395 cM and a mean interval of 0.29 cM between adjacent markers was constructed with SLAF-seq technology. Comparative genomic analyses revealed the highest genome sequence similarity (8.71%) between erect milkvetch and Medicago truncatula, followed by Glycine max (7.65%), Cicer arietinum (7.53%), and Lupinus angustifolius (5.21%). A total of 64 significant QTL for flowering-related traits on six LGs were detected, accounting for 9.38 to 19.1% of the associated phenotype variation. Five and 48 key candidate genes for floret number and inflorescence length were identified based on the Glycyrrhiza uralensis genome. These candidate genes were involved in ubiquitination/degradation, pollen development, cell division, cytokinin biosynthetic process, and plant flowering. These findings shed light on the regulation of flowering traits in erect milkvetch and provide genomic resources for future molecular breeding of the crop.

Developing wheat that acquires and uses phosphorus (P) more efficiently is a promising and low-cost solution for increasing grain yield and reducing P-related environmental impacts. The present study identified agronomic and physiological traits that contribute to genetic variation in the P acquisition, remobilization, and utilization efficiency of 11 wheat cultivars from southwest China grown in P-deficient purple lithomorphic soil (Olsen P = 4.7) with balanced (75 kg P ha^-1) and excess P (120 kg P ha^-1) supplies. On average, soil P deficiency (-P) reduced root P uptake (17.0%-60.8%), P remobilization (33.9%-52.8%), dry mass yield (11.5%-39.2%), and grain yield (17.7%-54.4%). Balanced P (+P) increased grain yield via increased plant biomass rather than increased HI. -P increased phosphorus uptake efficiency (PUpE, 4.5-fold), phosphorus utilization efficiency (PUtE, 1.25-fold), and phosphorus use efficiency (PUE, 5.4-fold) compared with those under +P, and PUtE explained most (58.1%-60.8%) of the genetic variation in PUE under both -P and +P. The high root P uptake of P-efficient cultivars under -P was regulated by root surface area and root length density in the 0-10 cm soil layer but not in the 10-20 and 20-40 cm soil layers, suggesting that a topsoil foraging strategy is a more economical approach than deeper root exploration for increasing P uptake. Root P uptake before anthesis and P remobilization after anthesis were critical for increasing the PUtE of wheat, given that P-efficient cultivars showed higher P_n (net photosynthetic rate) and sucrose levels than P-inefficient cultivars. P_n reduction by -P resulted from decreased G_s and C_i, and high evapotranspiration under +P increased shoot P% by increasing root P uptake. Genetic variation in the source-to-sink ratio was observed in consequence of a +P-induced allometric increase in sucrose in leaves and kernels. Owing to these beneficial effects, +P increased the kernel N and P yields of the 11 cultivars by 9.9%-52.4% and 12.3%-48.8%, respectively. The findings of this study could help improve wheat in future breeding efforts and P management by identifying desirable P-efficient phenotypes in P-deficient farming systems.

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

Nitrogen (N) fertilization increases rice yield, but inappropriate N fertilizer application increases N loss and the risk of environmental pollution. Short-term fertilizer postponing (FP) generally reduces N apparent surplus and increases rice yields, but the effects of long-term FP on N surplus and rice yields remain unknown. Our study was the first to investigate the impacts of long-term FP (11 years) on N apparent surplus and rice yields. FP effects in the short term (≤ 6 years) did not affect rice yields, whereas FP effects in the long term (>6 years) increased rice yields by 13.9% compared with conventional fertilization (CF). FP did not affect panicles per unit area, 1000-kernel weight, and filled-kernel rate, but spikelets per panicle increased over time due to spikelet formation stimulation. FP also reduced the N apparent surplus over time more strongly than CF owing to higher N accumulation and N utilization efficiency. FP effects in the long term also significantly increased soil organic matter, total N, and NH₄⁺-N content. Our results were supported by a pot experiment, showing that rice yields in soils with a history of FP were significantly higher than those for soils without a history of FP, indicating that FP increased rice yields more strongly in later years mainly because of soil quality improvement. Our findings suggest that long-term FP can reduce N loss while increasing rice yields by improving soil quality.

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

Biostimulators combined with pesticides can reduce the need for chemical crop protection to yield healthy wheat with high grain quality and nutritional value. The goal of this four-year field study was an assessment of the effects of seven levels of sulfonylurea herbicide, morpholine and triazole fungicides, and humic biostimulator protection on concentrations of 20 amino acids (AAs) and on yield parameters under diverse climatic conditions. Application of pesticides and biostimulators reduced amino acid concentrations. Sulfonylurea applied alone reduced AAs least. Chemical (herbicide + fungicide) protection or its combination with humic biostimulator were the most effective strategies for increasing yield, thousand-kernel weight, spike number, grain surface area, and wet gluten. Reduced dosages of fungicides showed effects on AA content and crop parameter values similar to those of the recommended dosages of fungicides and are in line with the European Commission's "From Farm to Fork"? strategy. Humic biostimulators as agents supporting pesticide protection should be optimized for wheat growth stage to achieve the most desirable wheat parameters and implemented in agricultural practice.

Grain size is one of the most important factors affecting rice grain quality and yield, and attracts great attention from molecular biologists and breeders. In this study, we engineered a CRISPR/Cas9 system targeting the miR396 recognition site of the rice GS2 gene, which encodes growth-regulating factor 4 (OsGRF4) and regulates multiple agronomic traits including grain size, grain quality, nitrogen use efficiency, abiotic stress response, and seed shattering. In contrast to most previous genome editing efforts in which indel mutations were chosen to obtain null mutants, a mutant named GS2^E carrying an in-frame 6-bp deletion and 1-bp substitution within the miR396-targeted sequence was identified. GS2^E plants showed increased expression of GS2 in consistent with impaired repression by miR396. As expected, the gain-of-function GS2^E mutant exhibited multiple beneficial traits including increased grain size and yield and bigger grain length/width ratio. Thousand grain weight and grain yield per plant of GS2^E plants were increased by 23.5% and 10.4%, respectively. These improved traits were passed to hybrids in a semi-dominant way, suggesting that the new GS2^E allele has great potential in rice improvement. Taken together, we report new GS2 germplasm and describe a novel gene-editing strategy that can be widely employed to improve grain size and yield in rice. This trait-improvement strategy could be applied to other genes containing miRNA target sites, in particular the conserved miR396-GRF/GIF module that governs plant growth, development and environmental response.

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