Search

Additional file 1: Fig. S1. Spearman correlation coefficients between different samples

Background: Wheat is an important cereal crop and improving wheat production is essential for meeting the food demand from the growing population worldwide. Flag leaf width (FLW) is an important trait affecting plant architecture and contributing to grain yield. To detect loci conferring FLW, we assessed a population of recombinant inbred lines (RILs) from a cross of EGA Wylie/Sumai 3 in different environments.Results: A total of six QTL were detected from the population. Two of them located on chromosome 2B and the other four located on chromosomes 2D, 4B, 7A, and 7B, respectively. The percentage of phenotypic variation (PEV) explained by these loci ranged from 14.6% to 33.8%, with LOD scores varying from 3.01 to 7.81. Of them, the locus located on chromosome arm 7AS is likely novel. Significant effects of this locus were detected in multiple trials conducted and the PEV explained by this QTL varied from 14.6% to 19.8% among the different trials. An orthologous analysis based on rice and Arabidopsis identified 3 putative genes underlying this potentially novel locus.Conclusion: This study identified a stable potentially novel QTL in multiple environments and predicted three candidate genes of it, which laid the foundation for further fine-mapping and cloning the gene(s) underlying QFlw.WS-7A with the contribution to grain yield.

Backgrounds: Grain protein concentration (GPC), grain starch concentration (GSC), and wet gluten concentration (WGC) are complex traits that determine nutrient concentration, end-use quality, and yield in wheat. To identify the elite and stable loci or genomic regions conferring high GPC, GSC, and WGC, a genome-wide association study (GWAS) based on a mixed linear model (MLM) was performed using 55K single nucleotide polymorphism (SNP) array in a panel of 236 wheat accessions, including 160 commercial varieties and 76 landraces, derived from Sichuan Province, China. The panel was evaluated for GPC, GSC, and WGC at four different fields. Results: Phenotypic analysis showed variation in GPC, GSC, and WGC among the different genotypes and environments. GWAS identified 12 quantitative trait loci (QTL) (-log10(P) > 2.5) associated with these three quality traits in at least two environments and located on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 5D, and 7D; the phenotypic variation explained (PVE) by these QTL ranged from 4.2% to 10.7%. Among these, three, seven, and two QTL are associated with GPC, GSC, and WGC, respectively; five QTL (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were defined potentially novel Compared with the previously reported QTLs/genes by linkage or association mapping, 5 QTLs (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were potentially novel. Furthermore, 21 presumptive candidate genes, which are involved in the metabolism or transportation of all kinds of carbohydrates, photosynthesis, programmed cell death, the balance of abscisic acid and ethylene, within these potentially novel genomic regions were predicted. Conclusions: This study provided new genetic resources and valuable genetic information of nutritional quality to broaden the genetic background and laid the molecular foundation for marker-assisted selection in wheat quality breeding.

Background Flowering is an important inflection point in the transformation from vegetative to reproductive growth, and premature bolting severely decreases crop yield and quality. Results In this study, a stable early-bolting mutant, ebm3, was identified in an ethyl methanesulfonate (EMS)-mutagenized population of a Chinese cabbage doubled haploid (DH) line ‘FT’. Compared with ‘FT’, ebm3 showed early bolting under natural cultivation in autumn, and curled leaves. Genetic analysis showed that the early-bolting phenotype was controlled by a single recessive nuclear gene. Modified MutMap sequencing, genotyping analyses and allelism test provide strong evidence that BrEBM3 (BraA04g017190.3 C), encoding the histone methyltransferase CURLY LEAF (CLF), was the strongly candidate gene of the emb3. A C to T base substitution in the 14th exon of BrEBM3 resulted in an amino acid change (S to F) and the early-bolting phenotype of emb3. The mutation occurred in the SET domain (Suppressor of protein-effect variegation 3–9, Enhancer-of-zeste, Trithorax), which catalyzes site- and state-specific lysine methylation in histones. Tissue-specific expression analysis showed that BrEBM3 was highly expressed in the flower and bud. Promoter activity assay confirmed that BrEBM3 promoter was active in inflorescences. Subcellular localization analysis revealed that BrEBM3 localized in the nucleus. Transcriptomic studies supported that BrEBM3 mutation might repress H3K27me3 deposition and activate expression of the AGAMOUS (AG) and AGAMOUS-like (AGL) loci, resulting in early flowering. Conclusions Our study revealed that an EMS-induced early-bolting mutant ebm3 in Chinese cabbage was caused by a nonsynonymous mutation in BraA04g017190.3 C, encoding the histone methyltransferase CLF. These results improve our knowledge of the genetic and genomic resources of bolting and flowering, and may be beneficial to the genetic improvement of Chinese cabbage.

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an economical crop with excellent edible, nutritional, and medicinal values. However, the production of Tartary buckwheat is very low and it is urgent to breed high-yield varieties for satisfying the increasing market demand. Heterotrimeric G-protein signaling involves in the regulation of agronomical traits and fruit development in several plant species. In this study, fifteen genes involved in G-protein signaling were characterized in Tartary buckwheat and their potential roles in fruit development were revealed by expression analysis. The exon-intron organization and conserved motif of Tartary buckwheat G-protein signaling genes were similar to those in other dicot plants. All these genes were ubiquitously and differently expressed in five tissues. The expression patterns of Tartary buckwheat G-protein signaling genes in fruit suggested they may play important roles in the fruit at early development stage, which was supported by meta-analysis of G-protein signaling genes' expression in the fruits from different species. Furthermore, we found the expression of G-protein signaling genes in fruit showed high correlation with 178 transcription factors, which indicated a transcriptional regulatory loop moderating G-protein signaling genes' expression during fruit development. This paper provides new insights into the physiological functions of G-protein signaling in fruit.

Background: Brassica napus is one of the most important sources of vegetable oil for human nutrition and biofuel. It is an allotetraploid formed about 7500 years ago by hybridization between B. rapa and B. oleracea. Results from earlier studies show that the allopolyploidization process was accompanied by rapid and intensive changes and abundant homoeologous exchanges between the subgenomes have been accumulated during its short history of evolution. Results: By comparing differences between 19 artificially synthesized and 30 natural genotypes, we assessed possible changes in gene ratio, diversity and functional groups during the evolution and domestication of this species. This comparison revealed that gene ratio and diversity between the two subgenomes have hardly changed. However, large numbers of genes have been lost and many new genes gained. Compared with the artificial genotypes, the natural ones contain much lower proportions of genes conferring resistance and tolerance to biotic and abiotic stresses but much higher proportions of genes associated with seeds development and metabolic processes. The diploid donor for the A subgenome of B. napus contributed more genes involved in agronomic traits and the C subgenome donor contributed more genes related to cellular development and metabolic process. Conclusions: Our results show that genes conditioning resistance and tolerance to both biotic and abiotic stresses have suffered stronger selection during the evolution and domestication of B. napus, and that changes in different aspects including gene content and genome size in the allotetraploid are not random but dictated by its two diploid donors.

With the increasing application of nanomaterials, evaluation of the phytotoxicity of nanoparticles has attracted considerable interest. Buckwheat is an economically pseudocereal crop, which is a potential model for investigating the response of plants to hazardous materials. In this study, the response of buckwheat to graphene oxide (GO) was investigated by integrating physiological and transcriptome analysis. GO can penetrate into buckwheat root and stem, and high concentrations of GO inhibited seedlings growth. High concentration of GO improved ROS production and regulated the activities and gene expression of oxidative enzymes, which implying GO may affect plant growth via regulating ROS detoxification. Root and stem exhibit distinct transcriptomic responses to GO, and the GO-responsive genes in stem are more enriched in cell cycle and epigenetic regulation. GO inhibited plant hormone biosynthesis and signaling by analyzing the expression data. Additionally, 97 small secreted peptides (SSPs) encoding genes were found to be involved in GO response. The gene expression of 111 transcription factor (TFs) and 43 receptor-like protein kinases (RLKs) were regulated by GO, and their expression showed high correlation with SSPs. Finally, the TFs-SSPs-RLKs signaling networks in regulating GO response were proposed. This study provides insights into the molecular responses of plants to GO.

Small secreted peptides (SSPs) regulate nitrogen (N) response and signaling in plants. Although much progress has been made in understanding the functions of SSPs in N response, very little information is available regarding non-model plants. Tartary buckwheat (Fagopyrum tataricum), a dicotyledonous crop, has a good adaptability to low N (LN) stress; however, little is known regarding the associated mechanisms underlying this adaptation. In this study, 932 putative SSPs were genome-wide characterized in TB genome. Of these SSPs, 233 SSPs were annotated as established SSPs, such as CLE, RALF, PSK, and CEP peptides. The gene expression of 675 putative SSPs was detected in five tissues and 258 SSPs were tissue-specific expressed genes. To analyze the responses of TB SSPs to LN, the dynamic expression analysis of TB roots under LN stress was conducted by RNA-seq. The expression of 378 putative TB SSP genes was detected with diverse expression patterns under LN stress, and some important LN-responsive SSPs were identified. Co-expression analysis suggested SSPs may regulate the adaptability of TB under LN conditions by modulating the expression of the genes involved in N transport and assimilation and IAA signaling. Furthermore, 53 LN stress-responsive RLKs encoding genes were identified and they were predicted as potential SSP receptors. This study expands the repertoire of SSPs in plants and provides useful information for further investigation of the functions of Tartary buckwheat SSPs in LN stress responses.

The phenomenon of overcompensation has been reported in various plant species although it has been treated by some as isolated incidents with only limited values. Reviewing reports on the extensive studies of defoliation in maize showed that different genotypes respond differently to defoliation, varying from phenomenal increase to significant loss in grain yield. The different responses of maize in kernel yield among genotypes to defoliation are confirmed in our experiments conducted in both China and Australia. Defoliated plants are likely to use less water during vegetative growth and that they also have better ability to extract water from the soil. We also found that defoliation dramatically delayed plant senescence under dry conditions, facilitating the production of high quality silage by widening the harvest window. As overcompensation occurs only in some genotypes, we believe that exploiting defoliation as a management practice directly for crop production can be risky. However, the fact that significant yield increase following defoliation does occur and that large genetic variation does exist meet the requirements for a successful breeding program. The detection of sizable quantitative trait locus (QTL) in the model plant species provides further evidence indicating the feasibility of exploiting this phenomenon through breeding. The stunning magnitudes of desirable responses reported in the literature suggest that overcompensation could become the most valuable breeding target in at least some species and its impact on crop production could be huge even if only a proportion of the reported variations could be captured.

Stripe rust, which is caused by the biotrophic fungus Puccinia striiformis f. sp. tritici (Pst), is one of the most challenging fungal diseases affecting wheat (Triticum aestivum L.), because specific virulent races often overcome host resistance genes. There is a continuous demand for new host resistance genes that are effective against such races. Chinese wheat landrace, which is the primary gene pool of the common wheat, is a valuable source of novel stripe rust resistance genes for wheat breeding. Chinese wheat landrace ‘Hejiangyizai’ (HY) is highly resistant to a wide spectrum of Chinese Pst races in both seedling and adult-plant stages. Genetic analysis has indicated that a single dominant gene in HY confers resistance to stripe rust, which has been temporarily designated as YrHY. Segregation of the F2 population and its F2:3 families derived from the cross between HY and Taichung 29 was used for bulked segregant analysis using simple sequence repeats (SSRs), resistance gene analog polymorphisms (RGAPs), sequence-related amplified polymorphisms (SRAPs), and target region amplified polymorphisms (TRAPs). Linkage analysis indicated that six SSR, eight RGAP, two TRAP, and six SRAP polymorphic markers were linked to the stripe rust resistance gene YrHY. The two closest flanking SSR markers were Xbarc92 and Xcfd66, with genetic distances of 4.3 and 8.5 cM, respectively. YrHY was physically mapped to chromosome 7DS using a set of Chinese spring nullisomic-tetrasomic lines. Comprehensive analyses of the seedling and adult reaction patterns of HY tested whit Chinese PST race CYR32, allelic test, and pedigree relationship indicated that YrHY differed from Yr18, Yr33, YrY201, YrY212, and YrWV on chromosome 7D. These results demonstrated that the YrHY may be a novel stripe rust resistance gene.

A wide range of differences between the subgenomes, termed as subgenome asymmetry or SA, has been reported in various polyploids and different species seem to have different responses to polyploidization. We compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences in neither gene ratio nor relative diversity between the subgenomes were detected between these two types of polyploid genotypes although they differ in times exposed to evolutional selection. As expected, the estimated ratio of retained genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes due likely to the presence of variable genome components (VGC). Clearly, the presence of VGC means that exaggerated differences between a donor and a subgenome in a polyploid are inevitable when random genotypes were used to represent species of either a polyploid or its donors. SA was also detected in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. Considering that significant changes during and following polyploidization have been detected in previous studies, our results suggest that the influence of VGC needs to be considered in evaluating SA and that diploid donors may define changes in polyploid evolution.

Leaf color mutants are not only ideal resources for studying the physiological mechanisms of plant photosynthesis, but they are also selection markers for hybrid production. In this study, the chlorosis mutant ‘564Y’ and its wild-type counterpart ‘564’ were used to explore physiological characteristics and gene expression in pak choi. Compared with those of wild type, the dry weight and fresh weight of ‘564Y’ were significantly reduced, but the hypocotyl length of ‘564Y’ was longer. Pigment analysis showed that the chlorophyll a and carotenoid contents of ‘564Y’ were lower than those of wild type. However, there was no significant difference in chlorophyll b content between these two varieties. The photosynthetic capacity of ‘564Y’ was lower than that of ‘564’, and the photosynthetic electron transfer ability and light energy conversion efficiency were weaker in the former. Transmission electron microscopy showed that the chloroplast structure of ‘564Y’ was not compact, the thylakoid structure was irregular, and the number of matrix, grana, and stacking layers was decreased. Transcriptome analysis revealed 2958 differentially expressed genes (DEGs), and 78 gene ontology terms and 35 Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched. Among the DEGs, nine genes were associated with the chlorophyll synthesis pathway (Bra031690, Bra012595, Bra005677, Bra022628, Bra026410, Bra032155, Bra039206, Bra029875, and Bra012511) and one gene was associated with photosynthesis (Bra038011). Among these genes, 3 were identified as related to auxin metabolism too (Bra032155, Bra039206, and Bra029875). Their differential expression in the ‘564Y’ mutant and wild-type plant was confirmed by qRT-PCR. These results lay the foundation for future genetic and functional genomic studies in pak choi.

Homoploid hybrid speciation has been reported in a wide range of species since the exploitation of genome sequences in evolutionary studies. However, the interference of ancestral subdivision has not been adequately considered in many such investigations. Using the D lineage in wheat as an example, we showed clearly that ancestral subdivision has led to false detection of homoploid hybridization signals. We develop a novel statistical framework by examining the changes in shared ancestral variations and infer on the likelihood of speciation due to genuine homoploid hybridization or ancestral subdivisions. Applying this to wheat data, we found that homoploid hybridization was not involved in the origin of the D lineage contrary to the now widely held belief. This example indicates that the significance of homoploid hybrid speciation is likely exaggerated. The underlying methodology developed in this study should be valuable for clarifying whether homoploid hybridization has contributed to the speciation of many other species.

Background Stripe rust (also called yellow rust) is a common and serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici. The narrow genetic basis of modern wheat cultivars and rapid evolution of the rust pathogen have been responsible for periodic and devastating epidemics of wheat rust diseases. In this study, we conducted a genome-wide association study with 44,059 single nucleotide polymorphism markers to identify loci associated with resistance to stripe rust in 244 Sichuan wheat accessions, including 79 landraces and 165 cultivars, in six environments. Results In all the field assessments, 24 accessions displayed stable high resistance to stripe rust. Significant correlations among environments were observed for both infection (IT) and disease severity (DS), and high heritability levels were found for both IT and DS. Using mixed linear models, 12 quantitative trait loci (QTLs) significantly associated with IT and/or DS were identified. Two QTLs were mapped on chromosomes 5AS and 5AL and were distant from previously identified stripe rust resistance genes or QTL regions, indicating that they may be novel resistance loci. Conclusions Our results revealed that resistance alleles to stripe rust were accumulated in Sichuan wheat germplasm, implying direct or indirect selection for improved stripe rust resistance in elite wheat breeding programs. The identified stable QTLs or favorable alleles could be important chromosome regions in Sichuan wheat that controlled the resistance to stripe rust. These markers can be used molecular marker-assisted breeding of Sichuan wheat cultivars, and will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust. Electronic supplementary material The online version of this article (10.1186/s12870-019-1764-4) contains supplementary material, which is available to authorized users.

Leaf color mutants are valuable resources for studying regulatory mechanisms of photosynthetic pigment metabolism. In this study, a chlorophyll-deficient golden leaf mutant lcm1 of Chinese cabbage was identified from its wild-type “FT” by ethyl methanesulfonate (EMS) mutagenesis. The phenotype of the golden leaf mutant lcm1 was that the leaves remained golden throughout development. Pigment measurements showed that the chlorophyll content of the mutant lcm1 was less than that of the wild-type “FT”. There were no obvious grana lamellae observed in the chloroplast microstructure of the mutant lcm1. Genetic analysis revealed that the mutant lcm1 phenotype was controlled by a single recessive nuclear gene, lcm1 (BrChlH). The MutMap method and Kompetitive Allele Specific PCR genotyping were used to predict that Bra006208 encoding a Mg-chelatase H subunit, the candidate gene for the mutant lcm1. The 4249-bp lcm1 gene had five exons and a single nucleotide substitution (G to A) in the third exon that resulted in an amino acid substitution (A to V). This SNP2523351 occurred in the highly conserved CobN-Mg_chel domain of the LCM1 (BrCHLH) protein. This study suggests that lcm1 gene plays an important role in the function of CHLH and provides a solid foundation for further studies on the development of plant leaf color.

Spearmanâ s correlations coefficients of response to stripe rust evaluated in four environments and BLUE_ALL. (DOCX 20â kb)

Temperatures during the wheat growth seasons in three environments. The plant growth season was from October to the following May. The lowest temperature in CZ18 was lowest among all three environments and lower than 0 °C from December to following February. CZ17 = Chongzhou 2017; MY17 = Mianyang 2017; CZ18 = Chongzhou 2018 (PDF 74 kb)

The genome specific comparisons of molecular diversity between subpopulation 1 and subpopulation 2 landraces. (DOCX 9540â kb)

Cold stress is an important environmental factor restricting the cultivation of melons in winter and spring. Exogenous trehalose (Tre) can improve the stress tolerance of crops. However, the mechanistic role of Tre in regulating crop cold tolerance is not completely clear and whether hydrogen peroxide (H2O2) and nitric oxide (NO) act as signalling molecules in Tre regulation melon cold tolerance remains unknown. Thus, this study was conducted to analyse the cold tolerance of cold-tolerant (IVF571) and cold-sensitive (IVF004) melon varieties and their H2O2 and NO levels. Then, the roles of exogenous Tre in regulating the cold tolerance of melons and the interaction of H2O2 and NO in Tre-regulated cold tolerance were investigated. Results showed that the damage to membrane lipid peroxidation in IVF571 plants was significantly slighter than that in IVF004 plants, and the levels of H2O2 and NO in IVF571 plants were significantly higher than those in IVF004 plants under cold stress. Exogenous Tre was more effective than sucrose and glucose in significantly increasing the maximal quantum yield of PSII photochemistry, reducing the relative electrical conductivity in melon leaves under cold stress by increasing the superoxide dismutase (SOD) activity under normal conditions and enhancing SOD, glutathione reductase and ascorbate peroxidase activities and GSH/GSSG ratio under cold stress. Exogenous Tre could induce the increase in H2O2 and NO levels. The removal of endogenous H2O2 with dimethylthiourea weakened the role of exogenous Tre, whereas eliminating NO with 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide almost abolished the effects of exogenous Tre and H2O2. In summary, the higher cold tolerance of IVF571 seedlings than that of IVF004 seedlings might be related to the increase in H2O2 and NO levels triggered by cold stress. Tre might have a unique effect on the regulation of cold-induced oxidative stress in melon. Tre could elevate endogenous H2O2 and NO levels, which stimulated the stress response system of melon. Consequently, when melon plants were exposed to cold stress, antioxidant enzyme activities improved, and the damage to membrane lipid peroxidation was reduced. In this process, H2O2 and NO participated in the roles of Tre, and NO might be located downstream of H2O2.

Cold stress inhibits plant growth and ultimately affects yield formation. Exogenous 5- aminolevulinic acid (ALA) can improve tomato cold tolerance and promote plant growth. It significantly up-regulated glutamate decarboxylase gene (SlGAD4) expression, which was involved in gamma-aminobutyric acid (GABA) synthesis. Whether the GABA was involved in ALA-regulated tomato cold tolerance and plant growth was unclear. Thus, this study aimed to explore the effects of exogenous ALA and GABA on endogenous ALA and GABA synthesis. The roles of ALA and GABA on regulating the antioxidation and cell morphological changes related to plant growth in tomato leaves were further explored. And the internal relationship between ALA and GABA in increasing tomato cold tolerance was also determined. Results showed that cold stress increased the glutamate (Glu) and GABA contents and reduced the ALA content. The exogenous ALA- or GABA-treated plants demonstrated decreased Glu content and increased GABA or ALA contents. Exogenous ALA or GABA treatment promoted the expansion of upper epidermal (UEP) and palisade parenchymal (PA) cells and up-regulated the xyloglucan endotransglucosylase/hydrolases gene (SlXTH23) expression in tomato leaves. Exogenous ALA or GABA significantly alleviated cold-induced tomato membrane lipid peroxidation and enhanced C-repeat binding factors gene (SlCBF2) expression and superoxide dismutase (SOD), catalase (CAT), APX and GR activities. Inhibiting endogenous GABA with 3-mercaptopropionic (3-mp) dramatically decreased the size of UEP and PA cells and reduced SOD and CAT activities. It also aggravated the membrane peroxidation damage, which notably weakened the alleviated effects of exogenous ALA. Inhibiting endogenous ALA with gabaculine (gaba) partly inhibited the alleviated effects of exogenous GABA. These findings indicated that spray with exogenous ALA or GABA could increase endogenous ALA and GABA levels in tomato leaves. In addition, endogenous GABA and ALA could be mutually converted through Glu. Exogenous ALA and GABA promoted cell expansion, stimulated the antioxidant system and might enhance tomato cold tolerance via endogenous GABA signal and the C-repeat binding factor regulation pathway, thereby alleviating cold inhibited plant growth. In conclusion, GABA crosstalk with ALA improved tomato cold stress tolerance and promoted plant growth by regulating antioxidants and cell expansion.

Cold adversely affects tomato (Solanum lycopersicum) growth and yield during winter and early spring in northern China. Trehalose (Tre) is a growth regulator that is widely used to enhance plant stress tolerance. However, there are few reports on the mechanistic role of Tre in regulating tomato cold tolerance or the interactions between hydrogen peroxide (H2O2) and nitric oxide (NO) in Tre-induced cold stress tolerance in plants. Here, we explored the role of Tre in tomato cold tolerance and evaluated whether H2O2 and NO were involved in this regulation. Tre pretreatment significantly upregulated superoxide dismutase (Cu/Zn SOD) and glutathione reductase (GR1) transcription and increased catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR) activities under normal temperatures. Under cold stress, Tre pretreatment dramatically elevated Cu/Zn SOD and CAT1 transcription and increased SOD and CAT activities. Tre pretreatment reduced membrane lipid peroxidation and alleviated plant growth inhibition caused by cold stress conditions. Under normal temperatures, Tre pretreatment upregulated the expression of respiratory burst oxidase homolog1 (RBOH1), nitrate reductase (NR), and nitric oxide synthase (NOS) and elevated H2O2 and NO levels. Treating tomato leaves with H2O2 and NO scavengers [dimethylthiourea (DMTU) and 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO), respectively] significantly diminished Tre-mediated alleviation of membrane lipid peroxidation. The effect of H2O2 on reducing cold stress-induced damage in tomato was essentially abolished by cPTIO treatment. These results indicated that exogenous Tre enhanced cold stress tolerance in tomato by regulating the antioxidant defense system. Tre may act as an exogenous inducer of H2O2 and NO that regulate antioxidase gene expression and activities to promote plant responses to cold stress, enhance cold stress tolerance, and reduce membrane lipid peroxidation and cellular injury. NO may act downstream of H2O2 to mediate Tre-regulated tomato oxidative stress tolerance under cold stress.

Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker–trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance.

Cyclic nucleotide-gated channels (CNGCs) are a class of nonselective cationic channels that are widely found in animals and plants. Plant CNGCs participate in numerous biological functions that vary from development to stress tolerance. Most CNGC genes have been identified in plant genomes, but no such comprehensive study has yet been conducted on Chinese cabbage. In this study, thirty BrCNGC genes were identified, divided into five groups, and used for evolutionary analysis. We assigned names of all individual CNGC members on the basis of phylogenetic relationship with A. thaliana CNGCs. All BrCNGC genes were randomly distributed on chromosomes, and the A08 chromosome did not carry any CNGC gene. The CNGC genes of Chinese cabbage and A. thaliana from the same group displayed similar conserved motifs and gene structures. Especially the closer the homology, the higher the similarity. Quantitative expression analysis showed that most of the CNGC genes were expressed under four stresses, indicating that they play a key role in the stress response of Chinese cabbage. Expression patterns of 12 BrCNGC in the roots, stems, leaves, flowers, and siliques showed that BrCNGC8 and BrCNGC16 were specifically expressed only in flowers but not in other parts. This study lays a theoretical foundation for future research on the function of the CNGC gene family in Chinese cabbage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-019-1647-2) contains supplementary material, which is available to authorized users.

Flavor quality in cucumber is affected by different rootstocks, but the molecular mechanism is largely unclean. To clarify the differences of sugar and aromatic compounds, cucumber (cucumis sativus) fruits from plants of self-grafted (SG) or grafted onto figleaf gourd (Cucurbita ficifolia; G1) or 'Weisheng No.1' rootstock (Cucurbita moschata ⅹCucurbita moschata hybrids; G2) were performed the transcriptome analysis. We obtained 1013 and 920 differentially expressed genes (DEGs) from G1 and G2 compared to SG respectively, in which 453 genes were co-expressed. Functional annotations showed many DEGs were involved in glycolysis/gluconeogenesis metabolism, fructose metabolism and α-Linolenic acid metabolisms, 20 DEGs were selected from the 3 pathways to validate sequencing accuracy by quantitative real-time PCR. The gene relative expression levels were concurrent with RNA-seq results and sugar and aromatic compounds content phenotypes. Moreover, some vital transcript factors and transport proteins were analyzed. These findings indicate that different rootstocks could induce significantly changes in the physiological profiling and transcripts of sugar- and aromatic flavor-related genes. This study provides a novel insight into the molecular mechanisms of fruit quality regulated by candidate genes.

The glutathione-S-transferase (GST) family of proteins is ancient and versatile, and plays an important role in combating exogenous pathogens, endogenous toxicants, and various abiotic stresses. Although the GST family has been studied in many crops, few studies have been reported in Chinese cabbage (Brassica rapa ssp. Pekinensis). In the present work, genome-wide analysis of the GST family in Chinese cabbage was carried out, and the expression and functions of genes under different conditions were investigated. A total of 88 GST genes were identified and divided into seven subfamilies according to their evolutionary relationships. Tandem duplication of genes was revealed as the main mechanism of expansion in this family. Transcriptome analysis under high and low temperatures and abiotic stress conditions revealed that most GST genes respond to environmental changes to varying degrees, particularly under herbicide and cadmium stress conditions. Our findings provide a basis for analysing the functions of GST family members in Chinese cabbage, especially in response to various abiotic stresses.

This study explored the genetic constitutions of several wheat- A. cristatum translocation lines and determined the effects of A. cristatum 6P chromosome segments on fertile tiller number in wheat. Progress in wheat breeding is hampered by a relatively narrow range of genetic variation. To overcome this hurdle, wild relatives of common wheat with superior agronomic traits are often used as donors of desirable genes in wheat-breeding programs. One of the successfully utilized wheat wild relatives is Agropyron cristatum (L.) Gaertn (2n = 4x = 28; genomes PPPP). We previously reported that WAT31-13 was a wheat-A. cristatum 5A-6P reciprocal translocation line with higher fertile tiller number and grain number per spike compared to common wheat. However, WAT31-13 was genetically unstable. In this study, we analyzed the 43 genetically stable progenies from WAT31-13 using genomic in situ hybridization, dual-color fluorescence in situ hybridization, and molecular markers. We classified them into three translocation types (TrS, TrL and TrA) and seven subtypes, and also pinpointed the translocation breakpoint. The genotypic data, combined with the phenotypes of each translocation type, enabled us to physically map agronomic traits to specific A. cristatum 6P chromosome arms or segments. Our results indicated that A. cristatum chromosome 6P played an important role in regulating fertile tiller number, and that positive and negative regulators of fertile tiller number existed on the A. cristatum chromosome arm 6PS and 6PL, respectively. By exploring the relationship between fertile tiller number and A. cristatum chromosome segment, this study presented a number of feasible approaches for creation, analysis, and utilization of wheat-alien chromosome translocation lines in genetic improvement of wheat.

Stripe rust (Yr), caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is a devastating foliar disease of wheat in China. Chinese wheat landraces originating from the middle and lower reaches of the Yangtze River are potential stripe-rust resistance resources. To identify APR genes for stripe-rust resistance, a panel of 188 accessions derived from the middle and lower reaches of the Yangtze River were inoculated with a mixture of Chinese P. striiformis f. sp. tritici races and resistance evaluated under field conditions in five environments at adult-plant stages. Seventy-three accessions showed degrees of stable resistance. Combining phenotypic datasets from multiple field experiments with high-quality Diversity Arrays Technology and simple sequence repeat markers, we detected 21 marker-trait associations spanning 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3B, 4A, 5A, 5B, 6B, and 6D, respectively. Single QTLs explained 9.67% to 16.14% of the observed phenotypic variation. Nine QTLs co-localized with previously reported Yr genes or genomic regions. The remaining QTLs were potential novel loci associated with adult-stage stripe-rust resistance. Two novel QTLs, QYr.sicau-3B.2 and QYr.sicau-5B.3, located on chromosomes 3B and 5B significantly explained 16.14% and 11.16% of the phenotypic variation, respectively. Haplotype analysis revealed that accessions carrying APR variants or their combinations showed enhanced degrees of resistance. The potentially novel loci or genomic regions associated with adult-stage resistance may be useful to improve stripe-rust resistance in current wheat cultivars and for future isolation of stripe-rust resistance genes.

Three eggplant cultivars were inoculated with Verticillium dahliae Kleb. to assess their resistance to Verticillium wilt. Solanum tor was resistant, “Liyuanziqie ” was tolerant, and “ Xi’anlvqie” susceptible. The disease incidence and disease index of Verticillium wilt and the amount of V. dahliae in rhizospheric soil, variation of microbial composition, the allelopathy of root exudates to mycelium growth of V. dahliae and the chemical substances of root exudates from eggplant cultivars with different resistance to Verticillium wilt were investigated in this experiment. The results showed that the root exudates of resistant type could not only affect the growth and development of V. dahliae, but also influence V. dahliae indirectly through regulating soil microbial community composition. This may be one of the reasons for the increase of disease resistance. However, the susceptible type exhibited an opposite trend. It was inferred that the resistant type contained some particular components, such as acohd, amide, pyranoid, fluorene, while the susceptible one comprised more types of components, that is, ketone, phenol, ester and phenolic acid. Key words: Allelopathy, allelochemical, root exudates, eggplant, Verticillium dahliae, Verticillium wilt, microbial composition.

Yellow or stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating foliar disease that affects common wheat (Triticum aestivum L.) around the world. In China, common wheat landraces are potential sources of disease and abiotic stress resistance genes for wheat improvement. Yilongtuomai (YL), a wheat landrace from Yilong County, Sichuan Province, shows high levels of resistance against most Chinese Pst races. In this study, the resistance of YL to stripe rust disease was examined in detail. Parent strains, YL and Taichung 29, a variety susceptible to Pst race CYR32, and their F1, F2, and F2:3 offspring, were inoculated with CYR32 during the seedling stage in the field or adult-plant stage in the greenhouse. Results indicated that resistance to CYR32 in YL is conferred by a single dominant gene, designated YrYL The segregating F2 population (352 plants), was analyzed in terms of its resistance locus using simple sequence repeats (SSRs), resistance gene analog polymorphisms (RGAPs), and sequence-related amplified polymorphism (SRAP). A linkage group of 6 SSRs, 2 RGAPs, and 1 SRAP was constructed for the YrYL gene. Using the identified SSRs associated with physical mapping of RGAP using Chinese Spring nullisomic-tetrasomic stocks, the YrYL gene was localized to the short arm of chromosome 7D. The gene was flanked by 1 SSR marker, Xbarc92, and 1 RGAP marker, CLRRfor/Ptokin4, at genetic distances of 5.35 and 9.86 cM, respectively. The YrYL gene was compared to other stripe rust resistance genes reported on chromosome 7D by evaluating its reaction patterns to CYR32 and its pedigree relationship. Our results suggest that the YrYL gene is a new stripe rust resistance gene.

2Agriculture Technology Generalize Station of Dong’anshan Town, Anshan City, LiaoNing Province, 114041, China. Accepted 3 August, 2012 14 eggplant cultivars were inoculated by Verticillium dahliae to screen their resistance against verticillium wilt. The resistances were shown as the disease incidence and disease index, and eggplant cultivars were classified into resistant type (R), moderate resistant type (MR), tolerant type (T), moderate susceptible (MS) and susceptible type (S), according to the final disease index. To find out the correlated physiological and biochemical indexes for evaluating the resistance of eggplant to verticillium wilt, the activities of defense-related enzymes, and the contents of some biochemical substances of leaves were investigated. The results show that the activities of polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL) were significantly positively correlated with resistance (P