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Spikelet number per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop higher-yielding wheat varieties. A genetic linkage map constructed using the GenoBaits Wheat 16K Panel and the 660K SNP array contained 5991 polymorphic SNP markers spanning 2813.26 cM. A total of twelve QTL for SNS were detected in the recombinant inbred line (RIL) populationmsf× Chuannong 16 (MC), and two of them, i.e.,QSns.sau-MC-3D.1andQSns.sau-MC-7A, were stably expressed.QSns.sau-MC-3D.1had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison ofQSns.sau-MC-3D.1with previously reported SNS QTL suggested that it is likely a novel one. A kompetitive allele-specific PCR (KASP) marker, KASP-10, tightly linked toQSns.sau-MC-3D.1was developed to successfully validate its effect in three segregated populations and a natural population. Genetic analysis indicated thatWHEAT ORTHOLOG OFAPO1(WAPO1) was a candidate gene forQSns.sau-MC-7A. The combined additive effect ofQSns.sau-MC-3D.1andWAP01had a great additive effect increasing SNS by 7.10%. In addition, our results suggested that SNS is not affected by 1BL/1RS translocations in the MC RIL population. Correlation analysis between two major QTL and other agronomic traits showed thatQSns.sau-MC-3D.1was likely independent of these agronomic traits. However, the H2 haplotype ofWAPO1may affect effective tiller number and plant height. This indicated that the breeding potential ofQSns.sau-MC-3D.1is better than that ofWAPO1. The geographical distribution ofQSns.nsau-MC-3D.1showed thatQSns.sau-MC-3D.1positive allele frequency was dominant in most wheat-producing regions of China and it has been positively selected among modern cultivars released in China since the 1940s. Two genes,TraesCS3D03G0222600andTraesCS3D03G0216800, associated with SNS development were predicted in the physical interval ofQSns.sau-MC-3D.1. qRT-PCR results of the two genes showed that only the expression level ofTraesCS3D03G0216800was significantly different between msf and CN16. These results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of genes underlyingQSns.sau-MC-3D.1, and provide a basis for marker-assisted selection breeding.Author summaryIn this study, we identified two major QTL (QSns.sau-MC-3D.1andQSns.sau-MC-7A) in a RIL population.WAPO1was demonstrated to be the candidate gene forQSns.sau-MC-7A. QSns.sau-MC-3D.1was a novel and stably expressed QTL, and further confirmed in different genetic backgrounds. Our results further demonstrate thatQSns.sau-MC-3D.1has better breeding potential because of its no adverse effect on other agronomic traits thanWAPO1, and it has been positively selected during Chinese breeding programs since the 1940s. Taken together, the identification ofQSns.sau-MC-3D.1offers a promising resource to further increase wheat yields.

International audience; The leader–following consensus issue is investigated for multiagent systems under external disturbances and denial-of-service (DoS) attacks. DoS attacks are considered to be designed according to an unknown attack strategy and would block the communication network. First, a novel triggering mechanism is designed to save communication resources during normal communication periods by event-triggered strategy and to detect the end of attack periods by time-triggered strategy. Then, a set of estimators is constructed to predict the states of the agent itself and its neighbors when the attack occurs. The estimators do not contain the control signals, which only correct the prediction when the actual system states are received. As a result, a distributed switching controller is designed that includes event-triggered states during normal communication periods and predicted states during attack periods. Finally, the proposed secure control protocol is proven to ensure that the system states are eventually consensus and the Zeno behavior is not exhibited. Moreover, a simulation example is given to illustrate the effectiveness of the presented strategy.

Grain number per spikelet (GNS) is a key determinant of grain yield in wheat. A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from which the reference genome assembly of bread wheat was obtained. Both parents and the recombinant inbred lines were genotyped using the wheat 55K single nucleotide polymorphism (SNP) array. A high-density genetic map containing 21,197 SNPs was obtained. These markers covered each of the 21 chromosomes with a total linkage distance of 3792.71 cM. Locations of these markers in this linkage map were highly consistent with their physical locations in the genome assembly of Chinese Spring. The two parents and the whole RIL population were assessed for GNS in two consecutive years at two different locations. Based on multi-environment phenotype data and best liner unbiased prediction values, three quantitative trait loci (QTL) for GNS were identified. One of them located on chromosomes 2B and the other two on 2D. Phenotypic variation explained by these loci varied from 3.07% to 26.57%. One of these QTL, QGns.sicau-2D-2, was identified in each of all trials conducted. Based on the best linear unbiased prediction values, this locus explained 19.59%–26.57% of phenotypic variation. A KASP (Kompetitive Allele-Specific PCR) marker closely linked with this locus was generated and used to validate the effects of this locus in three different genetic backgrounds. The identified QTL and the KASP marker developed for it will be highly valuable in fine-mapping the locus and in exploiting it for marker-assisted selection in wheat breeding programs.

Crop nitrogen use efficiency (NUE) decreases as the N supply increases, leading to wasted resources. Genetic variations that alter root morphological traits may be useful for developing crops able to explore the deep soil strata to enhance their N acquisition and NUE. The objective of this study was to examine the relationship between root functional traits and NUE on the basis of a large set of wheat genotypes. A total of 126 genetically diverse wheat genotypes from major wheat-growing regions worldwide were grown for 2 months to compare root morphological traits, photosynthetic traits, biomass, N accumulation, and NUE under low N conditions. There were large genotypic variations in dry biomass accumulation, N accumulation, N concentration, and NUE in response to low N supply. An analysis of specific low N stress-induced phenotypic changes revealed the examined root morphological traits were closely associated with N accumulation, NUE, and biomass accumulation. A high root mass density (RMD) was conducive to improving NUE in response to the limited availability of N. Photosynthesis had little effect on NUE in wheat during the early stage under low N conditions. In wheat, compared with photosynthetic activities, root system development, especially in terms of RMD, has a greater effect on N acquisition and use for biomass production during the initial stage under low N conditions.

Controlled release fertilizer (CRF) has been shown to increase crop yield and N use efficiency (NUE) compared with traditional chemical fertilizer (TF). However, few studies examined the effects of CRF on CH4, N2O, and NO emissions simultaneously in alkaline paddy fields under rice–wheat rotation. In the present study, we conducted a 2-year field experiment to compare the effects of different CRF application strategies on these gas emissions with those of TF and explored the effects of CRF on global warming potential (GWP), crop yields, and greenhouse gas emission intensity (GHGI). Results showed that CRF can reduce 0.98–14.3%, 13.3–21.1%, and 8.22–16.3% of CH4, N2O, and NO emissions, respectively, in the studied alkaline paddy field. CRF reduce CH4 emission probably by regulating soil NH4+ concentration. CRF reduce N2O and NO emissions probably by regulating inorganic N content in the studied alkaline paddy soil. CRF had the same effect on annual crop yield as TF, especially when CRF was applied twice in each season and had the same N application rate as TF. Annual crop yields and the agronomic efficiency of N (AEN) increased by 8.24% and 21.6%, respectively. On the average of the two rice–wheat rotation cycles, GHGI significantly decreased by up to 14.1% after the application of CRF as relative to that after the application of TF (P

We identified and validated two stable grain filling rate (GFR) quantitative trait loci (QTL) in wheat that positively influenced several yield-related traits. Among them, QGfr.sicau-7D.1 was a novel GFR QTL. The grain filling rate (GFR) plays a crucial role in determining grain yield. To advance the current understanding of the genetic characteristics underlying the GFR in common wheat, three recombinant inbred line populations were used to map and validate GFR quantitative trait loci (QTL). Using a high-density genetic linkage map, 10 GFR QTL were detected. They were located on chromosomes 2D, 4A, 4B, 5B, 6D, 7A and 7D, explained 4.99–12.62% of the phenotypic variation. Two of them, QGfr.sicau-6D and QGfr.sicau-7D.1, were detected in all four environments tested and their genetic effect was validated by closely linked kompetitive allele specific PCR (KASP) markers in different genetic backgrounds. The effects of these two GFR QTL on other yield-related traits were also estimated. QGfr.sicau-6D had a significant positive influence (p

Barley shrunken endosperm mutants have been extensively reported. However, knowledge of the underlying molecular mechanisms of these mutants remains limited. Here, a pair of near isogenic lines (normal endosperm: Bowman and shrunken endosperm: sex1) was subjected to transcriptome analysis to identify mRNAs and lncRNAs related to endosperm development to further dissect its mechanism of molecular regulation. A total of 2123 (1140 up- and 983 down-regulated) unique differentially expressed genes (DEGs) were detected. Functional analyses showed that these DEGs were mainly involved in starch and sucrose metabolism, biosynthesis of secondary metabolites, and plant hormone signal transduction. A total of 343 unique target genes were identified for 57 differentially expressed lncRNAs (DE lncRNAs). These DE lncRNAs were mainly involved in glycerophospholipid metabolism, starch and sucrose metabolism, hormone signal transduction, and stress response. In addition, key lncRNAs were identified by constructing a co-expression network of the target genes of DE lncRNAs. Transcriptome results suggested that mRNA and lncRNA played a critical role in endosperm development. The shrunken endosperm in barley seems to be closely related to plant hormone signal transduction, starch and sucrose metabolism, and cell apoptosis. This study provides a foundation for fine mapping, elucidates the molecular mechanism of shrunken endosperm mutants, and also provides a reference for further studies of lncRNAs during the grain development of plants.

Increasing soil petroleum hydrocarbons (PHs) pollution have caused world-wide concerns. The removal of PHs from soils mainly involves physical, chemical, biological processes and their combinations. To date, most reviews in this field based on research articles, but limited papers focused on the integration of remediation technologies from the perspective of patents. In this study, 20-years Chinese patents related to the remediation of soil PHs were comprehensively analyzed. It showed an increasing number of patent applications and the patents' quantity were positively correlated with Chinese GDP over the years, suggesting the more the economy developed the more environmental problems and corresponding solutions emerged. In addition, chemical technologies were mostly used in a combination to achieve faster and better effects, while the physical technologies were often used alone due to high costs. In all PHs remediation techniques, bacteria-based bioremediation was the most used from 2000 to 2019. Bacillus spp. and Pseudomonas spp. were the most used bacteria for PHs treatment because these taxa were widely harboring functions such as biosurfactant production and hydrocarbon degradation. The future research on joint technologies combining microbial and physicochemical ones for better remediation effect and application are highly encouraged.

Biological nitrification inhibitors are exudates from plant roots that can inhibit nitrification, and have advantages over traditional synthetic nitrification inhibitors. However, our understanding of the effects of biological nitrification inhibitors on nitrogen (N) loss and fertilizer N recovery efficiency in staple food crops is limited. In this study, acidic and calcareous soils were selected, and rice growth pot experiments were conducted to investigate the effects of the biological nitrification inhibitor, methyl 3-(4-hydroxyphenyl) propionate (MHPP) and/or a urease inhibitor (N-[n-butyl], thiophosphoric triamide [NBPT]) on NH

As an essential plant micronutrient, copper (Cu) is required as a component of several enzymes, but it can be highly toxic to plants when present in excess quantities. Nitrogen (N) application can help to alleviate the phytotoxic effects of heavy metals, including Cu, and different N forms significantly affect the uptake and accumulation of heavy metals in plants. The aim of this study was to determine the effects of different N forms, i.e., ammonium (NH4+) and nitrate (NO3−), on Cu detoxification in wheat seedlings. The inhibition of seedling growth under excess Cu was more obvious in wheat plants supplied with NO3− than in those supplied with NH4+. This growth inhibition was directly induced by excess Cu accumulation and reduced absorption of other mineral nutrients by the plants. Compared with seedlings treated with NO3−, those treated with NH4+ showed a decrease in Cu-induced toxicity as a result of increased antioxidant capacity in the leaves and a lower redox potential in the rhizosphere. Furthermore, treatment with NH4+ decreased the loss of mineral nutrients in wheat seedlings exposed to excess Cu. In conclusion, compared with supplying NO3−, supplying NH4+ to wheat seedlings under Cu stress improved their ability to maintain their nutritional and redox balance and increased their antioxidant capacity, thereby preventing a decline in photosynthesis. According to our results, NH4+ is more effective than NO3− in reducing Cu phytotoxicity in wheat seedlings.

With the aim to solve the leader-following consensus problem for a class of strict-feedback multi-agent systems with unknown disturbances and input saturation under a directed topology, this paper proposes a distributed event-triggered control approach based on disturbance observer. First, this approach designs a disturbance observer to estimate unknown disturbances, and then combining the dynamic surface control with the adaptive backstepping approach, the control input is obtained. Second, a relative threshold event-triggered control strategy is adopted to solve the problem of limited communication resources. Using the saturation compensation system, a mismatch between the controller signal and the actuator signal is compensated. Besides, using the Lyapunov stability theory, it can be proved that all signals of the closed-loop system are semiglobally uniformly ultimately bounded. Finally, simulation is conducted to evaluate the performance of the proposed approach, and the simulation results prove the effectiveness of the proposed control approach.

Both nitrogen (N) and nitric oxide (NO) postpone plant flowering. However, we still don't know whether N and NO trigger the same signaling pathways leading to flowering delay. Our previous study found that ferredoxin NADP+ oxidoreductase (FNR1) and the blue-light receptor cryptochrome 1 (CRY1) are involved in nitrogen-regulated flowering-time control. However, NO-induced late-flowering does not require FNR1 or CRY1. Sucrose supply counteracts the flowering delay induced by NO. However high-N-induced late-flowering could not be reversed by 5% sucrose supplementation. The high nitrogen condition decreased the amplitudes of all transcripts of the circadian clock. While NO increased the amplitudes of circadian transcripts of CRY1, LHY (LATE ELONGATED HYPOCOTYL), CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) and TOC1 (TIMING OF CAB EXPRESSION 1), but decreased the amplitudes of circadian transcripts of CO (CONSTANS) and GI (GIGANTEA). 5% sucrose supplementation reversed the declines in amplitudes of circadian transcripts of CO and GI after the NO treatment. NO induced S-nitrosation modification on oscillators CO and GI, but not on the other oscillators of the circadian clock. Sucrose supply interestingly reduced S-nitrosation levels of GI and CO proteins. Thus N and NO rely on overlapping but distinct signaling pathways on plant flowering.

Plants can optimize the allocation of phosphorus (P) among their foliar P fractions to increase the P utilization efficiency (PUE). Identifying the genetic relationships between foliar P fractionation and PUE could provide opportunities to improve the P efficiency of barley (Hordeum vulgare L.). The differences in the concentrations and proportions of inorganic P, ester P, nucleic acid P and insoluble P between a wild barley cultivar CN4027 and a commercial cultivar Baudin were studied, and their quantitative trait loci (QTLs) at normal P (NP) and low P (LP) fertilisations were mapped. The PUE that was determined in the previous study was used to analyze the relationship between PUE and foliar P fractionation in this research. Both cultivars of barley could increase their metabolic P fractions as an LP stress tolerance strategy to ensure their continued metabolic activities in response to LP stress. Cultivar CN4027 showed higher nucleic acid P concentration (NPC), nucleic acid P proportion (NPP) and insoluble P proportion (IPP) than cultivar Baudin under LP stress. This abundant organic P (Po) pool of CN4027 ensured the normal functioning of its metabolic pathways under LP stress. The close relationships between the foliar P fractionation and PUE could be explained by two QTL clusters, Cl-3H.02 and Cl-5H.01. The QTL cluster Cl-3H.02 is flanked by the markers bPb3256099-bPb3255630 on chromosome 3H and controls the ester P concentration (EPC), ester P proportion (EPP), insoluble P concentration (IPC) and IPP. The QTL cluster Cl-3H.02 might have great potential for the future genetic improvement of barley PUE and may offer clues for the genetic relationships between the foliar P fractionation and PUE.

The 5-leaf-stage rape seedlings were more insensitive to Pi starvation than that of the 3-leaf-stage plants, which may be attributed to the higher expression levels of ethylene signaling and sugar-metabolism genes in more mature seedlings. Traditional suppression subtractive hybridization (SSH) and RNA-Seq usually screen out thousands of differentially expressed genes. However, identification of the most important regulators has not been performed to date. Here, we employed two methods, namely, a two-round SSH and two-factor transcriptome analysis derived from the two-factor ANOVA that is commonly used in the statistics, to identify development-associated inorganic phosphate (Pi) starvation-induced genes in Brassica napus. Several of these genes are related to ethylene signaling (such as EIN3, ACO3, ACS8, ERF1A, and ERF2) or sugar metabolism (such as ACC2, GH3, LHCB1.4, XTH4, and SUS2). Although sucrose and ethylene may counteract each other at the biosynthetic level, they may also work synergistically on Pi-starvation-induced gene expression (such as PT1, PT2, RNS1, ACP5, AT4, and IPS1) and root acid phosphatase activation. Furthermore, three new transcription factors that are responsive to Pi starvation were identified: the zinc-finger MYND domain-containing protein 15 (MYND), a Magonashi family protein (MAGO), and a B-box zinc-finger family salt-tolerance protein. This study indicates that the two methods are highly efficient for functional gene screening in non-model organisms.

Therefore, applying NH4+-N tp PHW-SA caused greater tolerance to Cd toxicity by higher biomass production, photosynthetic capacity, Ca and Cu accumulation, better root development and lower translocation factor of Cd as well as Cd concetration in organelle fraction. The Cd stress inhibited the growth performance of wheat seedlings, the mineral nutrient accumulation, and nitrogen uptake and distribution, and different forms of nitrogen have different protective effects on wheat. In PHW-SA, ANCd treatment caused lower reduction in biomass accumulation, photosynthesis, isotope stable N content, Ca and Cu accumulation, root development inhibition, tissue Cd concentration, and transfer factor, which even led to lower concentrations of Cd in Fco than those in Fcw and Fs in comparison with NNCd treatment. On the other hand, the converse growth performance was recorded in J-11 under ANCd treatment. Meanwhile, the nitrogen absorption preference in PHW-SA was altered along with the enhanced absorption efficiency of nitrogen. Therefore, applying NH4+-N to PHW-SA caused greater tolerance to Cd toxicity by higher biomass production, photosynthetic capacity, Ca and Cu accumulation, better root development and lower translocation factor of Cd as well as Cd concetration in organelle fraction..

Nitrogen management measures (NMMs) such as the application of urease inhibitors (UIs), synthetic nitrification inhibitors (SNIs), and biochar (BC) are commonly used in mitigating nitrogen (N) loss and increasing fertilizer recovery efficiency (FRE) in agriculture. Calcareous soil under rice cropping is characterized by high nitrification potential, N loss risk, and low FRE. Application of SNIs may stimulate NH

Increasing wheat yield is essential in solving the global food shortage. The spikelet number per spike (SNS) is a primary factor that determines the kernel number per spike which has a great effect on wheat yield. Modern wheat breeding methods reduce the genetic diversity among cultivars, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace Ailanmai wild emmer wheat recombinant inbred line (RIL) population was used to construct a high-density genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. The linkage map revealed that 94.83% (6204) of the mapped markers had consistent genetic and physical chromosomal locations. Fourteen quantitative trait loci (QTL) for SNS, explaining 4.23-27.26% of the phenotypic variation, were identified. QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were detected as the major and novel QTL with a large cumulative effect that increased SNS by 17.47%. Some development-related genes within the physical intervals of QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were predicted to participate in spikelet growth, thereby affecting SNS. Genetic associations between SNS and other agronomic traits such as a significant and positive correlation between SNS and thousand kernel weight (TKW) were detected and analyzed. QTL analysis was also performed for other spike-related traits, including spike length (SL), kernel number per spike (KNS), kernel number per spikelet (KNL), and spike density (SD). QSns.sau-AM-2B.3 was co-located with QSl.sau-AM-2B in the interval between AX-111626925 and AX-111588559. Similarly, QKns.sau-AM-5B.1 was co-related with QKnl.sau-AM-5B.2 in the region between AX-108760512 and AX-110180251. This study demonstrates the feasibility of wheat 55K SNP array in genetic mapping of tetraploid wheat population and shows the potential application of wheat related species in wheat improvement programs.

Nitrogen (N), phosphorus (P), and potassium (K) are three essential macro-elements for plant growth and development. Used to improve yield in agricultural production, the excessive use of chemical fertilizers often leads to increased production costs and ecological environmental pollution. Vitamins C and E are antioxidants that play an important role in alleviating abiotic stress. However, there are few studies on alleviating oxidative stress caused by macro-element deficiency. Here, we used Arabidopsis vitamin E synthesis-deficient mutant vte4 and vitamin C synthesis-deficient mutant vtc1 on which exogenous vitamin E and vitamin C, respectively, were applied at the bolting stage. In the deficiency of macro-elements, the Arabidopsis chlorophyll content decreased, malondialdehyde (MDA) content and relative electric conductivity increased, and reactive oxygen species (ROS) accumulated. The mutants vtc1 and vte4 are more severely stressed than the wild-type plants. Adding exogenous vitamin E was found to better alleviate stress than adding vitamin C. Vitamin C barely affected and vitamin E significantly inhibited the synthesis of ethylene (ETH) and jasmonic acid (JA) genes, thereby reducing the accumulation of ETH and JA that alleviated the senescence caused by macro-element deficiency at the later stage of bolting in Arabidopsis. A deficiency of macro-elements also reduced the yield and germination rate of the seeds, which were more apparent in vtc1 and vte4, and adding exogenous vitamin C and vitamin E, respectively, could restore them. This study reported, for the first time, that vitamin E is better than vitamin C in delaying seedling senescence caused by macro-element deficiency in Arabidopsis.

Nitrate reductase (NR) is one of the key enzymes for plant nitrogen assimilation and root architecture remodeling. However, crosstalk between NR-mediated signaling and auxin-mediated root development in nitrogen-status responses has not been investigated in details before. In this study, root phenotype and auxin distribution in nia1/nia2 (nitrate reductase) double mutant and chl1-5 (nitrate transporter NRT1.1) mutant under different nitrogen availabilities were compared. The nia1/nia2 mutant showed very low expression levels of auxin biosynthetic/signaling genes and was insensitive to nitrogen changes. While the chl1-5 mutant showed a high NR activity with a high level of auxin in the meristematic zone and a weaker response to nitrogen changes, when compared with the wild-type plants. We firstly found that NR activity was roughly positive-correlated with the root auxin level, and there is a crosstalk between nitrate signaling and auxin signaling. The putative signaling pathways downstream of NR have been discussed.

Eight major and stably expressed QTL for flag leaf morphology across eleven environments were identified and validated using newly developed KASP markers in seven biparental populations with different genetic backgrounds. Flag leaf morphology is a determinant trait influencing plant architecture and yield potential in wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population with a 55 K SNP-based constructed genetic map was used to map quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), area (FLA), angle (FLANG), opening angle (FLOA), and bend angle (FLBA) in eleven environments. Eight major QTL were detected in 11 environments with 5.73–54.38% of explained phenotypic variation. These QTL were successfully verified using the newly developed Kompetitive Allele Specific PCR (KASP) markers in six biparental populations with different genetic backgrounds. Among these 8 major QTL, two co-located intervals were identified. Significant interactions for both FLL- and FLW-related QTL were detected. Comparison analysis showed that QFll.sau-SY-2B and QFla.sau-SY-2B are likely new loci. Significant relationships between flag leaf- and yield-related traits were observed and discussed. Several genes associated with leaf development including the ortholog of maize ZmRAVL1, a B3-domain transcription factor involved in regulation of leaf angle, were predicted in physical intervals harboring these major QTL on reference genomes of bread wheat ‘Chinese spring’, T. turgidum, and Aegilops tauschii. Taken together, these results broaden our understanding on genetic basis of flag leaf morphology and provide clues for fine mapping and marker-assisted breeding wheat with optimized plant architecture for promising loci.

MADS-box genes interact with

MADS-box genes interact with TB1 to regulate plant organ morphogenesis. In rice, OsMADS57 interacts with OsTB1 to control OsD14 transcription. In this study, we aimed to determine the relationships among these genes in barley. We identified a natural mutant of HvTB1 (HvTB1x) formed by a C→A transition at position 230, which resulted in a premature stop codon. We cloned the HvMADS57 and HvD14 genes and studied their expression in the tb1 mutant. The results showed that HvMADS57 is a MIKCc-type MADS-box gene, and the expression levels of both HvMADS57 and HvD14 were significantly reduced in the tb1 mutant when compared to those in the wildtype gene. These results indicate that, HvMADS57 regulates plant growth and development by interacting with HvTB1 to suppress the transcription of HvD14 in barley which is similar to the relationships among the orthologs of these genes in rice.

Emerging evidence demonstrates that lncRNAs participate in various developmental processes in plants via post-transcription regulation. However, few lncRNAs have been identified as regulators of tiller development in wheat (Triticum aestivum L.). In this study, high-throughput ribosomal depleted RNA sequencing was performed on the tillering nodes of two pairs of near-isogenic lines that differed only in the tillering trait. We identified 5399 lncRNA transcripts using bioinformational analyses. KEGG pathway analysis revealed 74 common differentially expressed lncRNAs substantially enriched in photosynthesis-related, phenylpropanoid biosynthesis, phosphatidylinositol signaling, brassinosteroid biosynthesis, zeatin biosynthesis, and carotenoid biosynthesis pathways. Detailed functional annotations of target genes were used to identify 27 tillering-associated lncRNAs. Among these, 10 were in photosynthesis-related pathways; 15 were in secondary metabolite pathways; and 8 were in plant hormone pathways, with 6 enriched in two kinds of pathways. These findings contribute to identifying tillering-associated lncRNAs in wheat and enable further investigation into the functions and roles of key candidate lncRNAs, and more experimental evidence was also needed if breeders wanted to utilize these candidate lncRNAs in wheat crop yield improvement in the future.

Additional file 2: Fig. S1. Manhattan plots and quantile-quantile (Q-Q) plots for 15 seedling traits under application of phosphorus (AP) and non-application of phosphorus (NP).

Nitrogen management measures (NMMs) such as the application of urease inhibitors (UIs), synthetic nitrification inhibitors (SNIs), and biochar (BC) are commonly used in mitigating nitrogen (N) loss and increasing fertilizer recovery efficiency (FRE) in agriculture. Calcareous soil under rice cropping is characterized by high nitrification potential, N loss risk, and low FRE. Application of SNIs may stimulate NH3 volatilization in high pH soils and the effects of SNIs on FRE are not always positive. BNIs have many advantages over SNIs. Whether combined application of BNI, UI, and BC that can result in a synergistic effect of improving FRE and decreasing N loss in a calcareous soil under rice cropping worth investigating. In this study, we conducted pot experiments to investigate the effects of single and co-application of BNI (methyl 3-(4-hydroxyphenyl) propionate or MHPP, 500 mg kg−1 soil), UI (N-(n-butyl), thiophosphoric triamide or NBPT, 2% of urea-N), or BC (wheat straw, 0.5% (w/w)) with chemical fertilizer on NH3 volatilization, N2O emission, N leaching, crop N uptake, and FRE in a calcareous soil under rice cropping. Our results demonstrated that those NMMs could mitigate NH3 volatilization by 12.5%–26.5%, N2O emission by 62.7%–73.5%, and N leaching loss by 17.5%–49.0%. However, BNI might have a risk of increasing NH3 (5.98%) volatilization loss. Among those NMMs, double inhibitors (BNI plus UI) yielded a synergistic effect that could mitigate N loss to the maximum extent and effectively improve FRE by 25.4%. The mechanisms of the above effects could be partly ascribed to the niche differentiation between the abundance of AOA and AOB and the changed community structure of AOB, which could further influence nitrification and N fate. Our results demonstrated that co-application of BNI and UI with urea is an effective strategy in reducing N loss and improving FRE in a calcareous soil under rice cropping.

Fluorescence in situ hybridization (FISH) has been widely used to analyze the physical mapping of chromosomes and study the chromosome rearrangements during evolution. The conventional FISH technique is time-consuming and labor-intensive as it involves many experimental steps including (1) PCR amplification of the target sequence, (2) recovery of the amplified product, (3) plasmid extraction, (4) fluorescence labeling, as well as (5) denaturing of chromosomes and probes. Here we report an effective method for the design of oligonucleotide probes and the development of a new oligonucleotide probe for non-denaturing FISH in barley. The probe Oligo-442A01 with 6133 copies in barley genome could be mapped to the subtelomeres of barley. However, there were significant differences in signal positions and strengths between Oligo-442A01 and the contrast probe Oligo-HvT01.1, especially on chromosome 3H. These oligonucleotide probes combinations (AGG)5 and Oligo-442A01, (CTT)5 and Oligo-HvT01.1 could effectively differentiate the barley chromosomes.

The translocation of 4AL/5AL in Triticum, which occurred before the differentiation of T. urartu and einkorn, is an important chromosomal rearrangement. Recently, the first identification of breakpoint sequence on 4AL for this translocation provides the opportunity to analyze the variation and diversity of breakpoints in Triticum. In this study, the breakpoint regions of 52 accessions from 21 species were isolated and further characterized. The sequences were divided into 12 types based on their lengths, which ranged from 2009 to 2552 bp. Cluster analysis showed that they were further divided into three groups. Interesting evolutionary relationships among a few of the species were observed and discussed. Multiple sequence alignment of the 52 sequences made it possible to detect 13 insertion and deletion length polymorphisms (InDels) and 101 single nucleotide polymorphisms (SNPs). Furthermore, several species- or accession-specific SNPs or InDels were also identified. Based on BLAST analysis of the conserved sequences, the breakpoint was narrowed down to a 125 bp fragment. Taken together, the results obtained in this study enrich our understanding of chromosomal breakpoints and will be useful for the identification of other breakpoints in wheat.

Background Phosphorus deficiency is a major limiting factors for affecting crop production globally. To understand the genetic variation of phosphorus-deficiency-tolerance, a total of 15 seedling traits were evaluated among 707 Chinese wheat landraces under application of phosphorus (AP) and non-application of phosphorus (NP). A total of 18,594 single-nucleotide polymorphisms and 38,678 diversity arrays technology sequencing markers were used to detect marker-trait associations under AP and NP. Results Top ten genotypes with extremely tolerance and bottommost ten genotypes with extremely sensitivity were selected from 707 Chinese wheat landraces for future breeding and genetic analysis. A total of 55 significant markers (81 marker-trait associations) for 13 traits by both CMLM and SUPER method. These were distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 4B, 5A, 5B, 6A, 6B, 6D, 7A and 7B. Considering the linkage disequilibrium decay distance, 25 and 12 quantitative trait loci (QTL) were detected under AP and NP, respectively (9 QTL were specific to NP). Conclusions The extremely tolerant landraces could be used for breeding phosphorus-deficiency-tolerant cultivars. The QTL could be useful in wheat breeding through marker-assisted selection. Our findings provide new insight into the genetic analysis of P-deficiency-tolerance, and will be helpful for breeding P-deficiency-tolerant cultivars.