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Background Polyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution. Scope In addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered. Conclusions Contrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed. [ABSTRACT FROM AUTHOR]

Fusarium crown rot (FCR), caused by various Fusarium species, is a chronic disease of cereals in many semi-arid regions worldwide. To clarify what effects drought-stress may have on FCR development, visual assessment, histological analysis and quantitative PCR were used to analyse the infection process of F. pseudograminearum in barley. This study observed for the first time that the severity of FCR symptom reflects the quantity of pathogens in infected tissues of barley under both drought-stressed and well-watered conditions. Drought-stress prolongs the initial infection phase but enhances the proliferation and spread of Fusarium pathogens after the initial infection phase. Under drought-stressed conditions, the invading hyphae were frequently observed to re-emerge from stomata and invade again the surrounding epidermis cells. Under the well-watered conditions, however, very few hyphae re-emerged from stomata and most infection was caused by hyphae intracellularly grown. It was also observed that drought-stress increased the length and density of trichomes dramatically especially in the susceptible genotypes, and that the length and density of trichomes were positively related to fungal biomass of F. pseudograminearum in plants. [ABSTRACT FROM AUTHOR]

Ten pairs of near-isogenic lines (NILs) were developed for a major quantitative trait locus conferring Fusarium crown rot (FCR) resistance in barley. The locus locates on the long arm of chromosome 4H and the presence of the resistance allele reduced FCR severity by between 32.8 and 63.4 % with an average of 43.9 % across these NILs. Histological and quantitative PCR analyses all confirmed that the rates of Fusarium infection and disease development were much slower in the resistant isolines compared with those in the susceptible isolines. The contrasting phenotypes in FCR severity between the isolines for each of these NIL pairs would facilitate efforts in cloning and functional analyses of genes conferring resistance to this disease. [ABSTRACT FROM AUTHOR]

Fusarium crown rot ( FCR) is becoming a major disease in many parts of the cereal-growing regions worldwide. Significant QTL conferring FCR resistance have been reported on 13 of the 21 possible hexaploid wheat chromosomes in wheat and on three of the seven chromosomes in barley. Available results show that host resistance to FCR is not pathogen species-specific, that resistance QTL have strong additive effect and that both plant height and growth rate affect FCR severity. Further, different loci seem to be responsible for resistances to FCR and Fusarium head blight although both diseases can be caused by the same Fusarium pathogens. Although marker-assisted selection for FCR resistance has been initiated, the available markers are all derived from QTL mapping, which provides only limited resolution. Further work has to be conducted in developing diagnostic markers before significant progress can be made in deploying marker-assisted selection as a routine tool to accelerate and improve FCR in breeding programmes. [ABSTRACT FROM AUTHOR]

Based on visual assessment of disease severity, previous studies reported that tall genotypes tend to be more severely affected by Fusarium crown rot ( FCR) in wheat and barley. To clarify whether tall and dwarf genotypes have different susceptibility to FCR or whether it takes longer for Fusarium pathogens to infect dwarf genotypes, histological analyses were conducted with two pairs of near isogenic lines ( NILs) for a semi-dwarfing gene in barley. This analysis showed that F. pseudograminearum hyphae were detected earlier and proliferated more rapidly during the time-course of FCR development in the tall isolines. Histological analysis showed that cell densities of the dwarf isolines were significantly higher than those of the tall isolines due to reduced lengths and widths of cells, and FCR severity was strongly correlated with cell density. An analysis with real-time quantitative polymerase chain reaction detected a higher amount of F. pseudograminearum in the tall isolines at each of the time points assessed during FCR development. These results support the hypothesis that the increased cell density associated with dwarf genes could act as a physical barrier to the spread of FCR in cereals. [ABSTRACT FROM AUTHOR]

A meta-analysis of quantitative trait loci (QTL) associated with tolerance to abiotic stresses in barley was carried out using results from 35 different experiments. 'MetaQTL' software was used to project QTL positions on a reference map. Three hundred and thirty-seven QTL for traits associated with tolerance to abiotic stresses were included in this analysis which identified 79 metaQTL (MQTL) including 26 for drought, 11 for low temperature, 22 for salinity, 17 for water-logging, and 3 for mineral toxicity and deficiency. The distribution of MQTL was similar to that of the initial QTL. Many of these MQTL were located on chromosomes 2H (mainly for water-logging and drought) and 5H (mainly for salinity and low temperature). It inferred that chromosomes 2H and 5H were important for researches on barley abiotic tolerance, and the genes associated with abiotic stresses were concentrated relatively. As expected from trait correlations, 22.8 % of these MQTL displayed overlapping CIs. These overlapping regions were mainly on chromosomes 1H, 2H and 4H. The results indicated that the tolerance to diverse abiotic stresses were associated with each other in barley. Additionally, 67 candidate genes responsive to abiotic stresses were co-located with the abiotic-stress MQTL. Of them, a total of 55 had different conserved motifs. It inferred that the tolerance to abiotic stresses was contributed by multi-genes with diverse functions, though there might be some important genes associated with the tolerance to abiotic stresses in barley. Additionally, of these candidate genes, scsnp02622, scsnp01644 and scsnp19641 could be better for further studies of abiotic stresses tolerance. [ABSTRACT FROM AUTHOR]

The vasopressin V 2 receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target for water balance disorders such as polycystic kidney disease. Traditionally, the discovery of novel agents for the vasopressin V 2 receptor has been guided by evaluating their receptor affinity, largely ignoring the binding kinetics. However, the latter is receiving increasing attention in the drug research community and has been proved to be a more complete descriptor of the dynamic process of ligand-receptor interaction. Herein we aim to revisit the molecular basis of ligand-vasopressin V 2 receptor interaction from the less-investigated kinetic perspective. A homogenous time-resolved fluorescence resonance energy transfer (TR-FRET) assay was set up and optimized, which enabled accurate kinetic profiling of unlabeled vasopressin V 2 receptor ligands. Receptor occupancy profiles of two representative antagonists with distinct target residence time were simulated. Their functional effects were further explored in cAMP assays. Our results showed that the antagonist with longer receptor residence time (lixivaptan) displayed sustained target occupancy than the antagonist with shorter receptor residence time (mozavaptan). In accordance, lixivaptan displayed insurmountable antagonism and wash-resistant inhibitory effect on the cellular cAMP level, while not so for mozavaptan. Together, our data provide evidence that binding kinetics, next to their affinity, offers additional information for the dynamic process of ligand-receptor interaction. Hopefully, this study may lead to more kinetics-directed medicinal chemistry efforts and aid the design and discovery of different-in-class of vasopressin V 2 receptor ligands for clinical applications. [ABSTRACT FROM AUTHOR]

Key message: This study reported the identification and validation of novel QTL conferring coleoptile length in barley and predicted candidate genes underlying the largest effect QTL based on orthologous analysis and comparison of the whole genome assemblies for both parental genotypes of the mapping population. Coleoptile length (CL) is one of the most important agronomic traits in cereal crops due to its direct influence on the optimal depth for seed sowing which facilitates better seedling establishment. Varieties with longer coleoptiles are preferred in drought-prone areas where less moisture maintains at the top layer of the soil. Compared to wheat, genetic study on coleoptile length is limited in barley. Here, we reported a study on detecting the genomic regions associated with CL in barley by assessing a population consisting of 201 recombinant inbred lines. Four putative QTL conferring CL were consistently identified on chromosomes 1H, 5H, 6H, and 7H in each of the trials conducted. Of these QTL, the two located on chromosomes 5H and 6H (designated as Qcl.caf-5H and Qcl.caf-6H) are likely novel and Qcl.caf-5H showed the most significant effect explaining up to 30.9% of phenotypic variance with a LOD value of 15.1. To further validate the effect of this putative QTL, five pairs of near isogenic lines (NILs) were then developed and assessed. Analysis of the NILs showed an average difference of 21.0% in CL between the two isolines. Notably, none of the other assessed morphological characteristics showed consistent differences between the two isolines for each pair of the NILs. Candidate genes underlying the Qcl.caf-5H locus were also predicted by employing orthologous analysis and comparing the genome assemblies for both parental genotypes of the mapping population in the present study. Taken together, these findings expand our understanding on genetic basis of CL and will be indicative for further gene cloning and functional analysis underly this locus in barley. [ABSTRACT FROM AUTHOR]

Key message: Shared changes in transcriptomes caused by Fusarium crown rot infection and drought stress were investigated based on a single pair of near-isogenic lines developed for a major locus conferring tolerance to both stresses. Fusarium crown rot (FCR) is a devastating disease in many areas of cereal production worldwide. It is well-known that drought stress enhances FCR severity but possible molecular relationship between these two stresses remains unclear. To investigate their relationships, we generated several pairs of near isogenic lines (NILs) targeting a locus conferring FCR resistance on chromosome 2D in bread wheat. One pair of these NILs showing significant differences between the two isolines for both FCR resistance and drought tolerance was used to investigate transcriptomic changes in responsive to these two stresses. Our results showed that the two isolines likely deployed different strategies in dealing with the stresses, and significant differences in expressed gene networks exist between the two time points of drought stresses evaluated in this study. Nevertheless, results from analysing Gene Ontology terms and transcription factors revealed that similar regulatory frameworks were activated in coping with these two stresses. Based on the position of the targeted locus, changes in expression following FCR infection and drought stresses, and the presence of non-synonymous variants between the two isolines, several candidate genes conferring resistance or tolerance to these two types of stresses were identified. The NILs generated, the large number of DEGs with single-nucleotide polymorphisms detected between the two isolines, and the candidate genes identified would be invaluable in fine mapping and cloning the gene(s) underlying the targeted locus. [ABSTRACT FROM AUTHOR]

Key message: A co-located novel QTL for TFS, FPs, FMs, FFS, FFPs, KWS, and KWPs with potential of improving wheat yield was identified and validated. Spike-related traits, including fertile florets per spike (FFS), kernel weight per spike (KWS), total florets per spike (TFS), florets per spikelet (FPs), florets in the middle spikelet (FMs), fertile florets per spikelet (FFPs), and kernel weight per spikelet (KWPs), are key traits in improving wheat yield. In the present study, quantitative trait loci (QTL) for these traits evaluated under various environments were detected in a recombinant inbred line population (msf/Chuannong 16) mainly genotyped using the 16 K SNP array. Ultimately, we identified 60 QTL, but only QFFS.sau-MC-1A for FFS was a major and stably expressed QTL. It was located on chromosome arm 1AS, where loci for TFS, FPs, FMs, FFS, FFPs, KWS, and KWPs were also simultaneously co-mapped. The effect of QFFS.sau-MC-1A was further validated in three independent segregating populations using a Kompetitive Allele-Specific PCR marker. For the co-located QTL, QFFS.sau-MC-1A, the presence of a positive allele from msf was associate with increases for all traits: + 12.29% TFS, + 10.15% FPs, + 13.97% FMs, + 17.12% FFS, + 14.75% FFPs, + 22.17% KWS, and + 19.42% KWPs. Furthermore, pleiotropy analysis showed that the positive allele at QFFS.sau-MC-1A simultaneously increased the spike length, spikelet number per spike, and thousand-kernel weight. QFFS.sau-MC-1A represents a novel QTL for marker-assisted selection with the potential for improving wheat yield. Four genes, TraesCS1A03G0012700, TraesCS1A03G0015700, TraesCS1A03G0016000, and TraesCS1A03G0016300, which may affect spike development, were predicted in the physical interval harboring QFFS.sau-MC-1A. Our results will help in further fine mapping QFFS.sau-MC-1A and be useful for improving wheat yield. [ABSTRACT FROM AUTHOR]

Key message: A novel and stably expressed QTL QSNS.sicau-SSY-7A for spikelet number per spike in wheat without negative effects on thousand-kernel weight was identified and validated in different genetic backgrounds. Spikelet number per spike (SNS) is an important determinant of yield in wheat. In the present study, we combined bulked segregant analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array to rapidly identify genomic regions associated with SNS from a recombinant inbred line (RIL) population derived from a cross between the wheat lines S849-8 and SY95-71. A genetic map was constructed using Kompetitive Allele Specific PCR markers in the SNP-enriched region on the long arm of chromosome 7A. A major and stably expressed QTL, QSNS.sicau-SSY-7A, was detected in multiple environments. It was located in a 1.6 cM interval on chromosome arm 7AL flanked by the markers AX-109983514 and AX-109820548. This QTL explained 6.86–15.72% of the phenotypic variance, with LOD values ranging from 3.66 to 8.66. Several genes associated with plant growth and development were identified in the interval where QSNS.sicau-SSY-7A was located on the ‘Chinese Spring’ wheat and wild emmer reference genomes. Furthermore, the effects of QSNS.sicau-SSY-7A and WHEAT ORTHOLOG OFAPO1(WAPO1) on SNS were analyzed. Interestingly, QSNS.sicau-SSY-7A significantly increased SNS without negative effects on thousand-kernel weight, anthesis date and plant height, demonstrating its great potential for breeding aimed at improving grain yield. Taken together, these results indicate that QSNS.sicau-SSY-7A is a promising locus for yield improvement, and its linkage markers are helpful for fine mapping and molecular breeding. [ABSTRACT FROM AUTHOR]

Key message: This study reported validation and fine mapping of a Fusarium crown rot resistant locus on chromosome arm 6HL in barley using near isogenic lines, transcriptome sequences, and a large near isogenic line-derived population. Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, is a chronic and serious disease affecting cereal production in semi-arid regions globally. The increasing prevalence of this disease in recent years is attributed to the widespread adoption of minimum tillage and stubble retention practices. In the study reported here, we generated eight pairs of near isogenic lines (NILs) targeting a putative QTL (Qcrs.caf-6H) conferring FCR resistance in barley. Assessing the NILs confirmed the large effect of this locus. Aimed to develop markers that can be reliably used in incorporating this resistant allele into breeding programs and identify candidate genes, transcriptomic analyses were conducted against three of the NIL pairs and a large NIL-derived population consisting of 1085 F7 recombinant inbred lines generated. By analyzing the transcriptomic data and the fine mapping population, Qcrs.caf-6H was delineated into an interval of 0.9 cM covering a physical distance of ~ 547 kb. Six markers co-segregating with this locus were developed. Based on differential gene expression and SNP variations between the two isolines among the three NIL pairs, candidate genes underlying the resistance at this locus were detected. These results would improve the efficiency of incorporating the targeted locus into barley breeding programs and facilitate the cloning of causal gene(s) responsible for the resistance. [ABSTRACT FROM AUTHOR]

Crop productivity is highly dependent on successful seed germination and seedling establishment. This study evaluated two mapping populations, Batavia/Ernie (double haploid) and Synthetic/Opata (recombinant inbred lines), for early vigor under water stress and normal growing conditions. Significant gene, environment (water), and gene by environment interaction effects were observed. Broad sense heritability was 29 and 40% for the Batavia/Ernie and Synthetic/Opata populations, respectively. Quantitative trait loci (QTL) were analyzed based on single and multienvironment models. The two mapping populations differed in the number and locations of QTLs except qNev.uwa.4AL was identified in both populations under the non-stress condition, while qSev.uwa.3BL was specifically expressed under the stress condition in the Synthetic/Opata population. QTL by environment interaction (QEI) enabled identification of nine QTLs, including those identified by the single environment approach. Phenotypic variation expression (PVE) of QEIs ranged from 4.8 to 14.9% across the populations. Larger proportion of PVE of QEIs was explained by the additive components. Favorable alleles for three of the QTLs identified in the Synthetic/Opata population were derived from Synthetic, while Batavia contributed favorable alleles to a QTL on the long arm of chromosome 1D in the Batavia/Ernie population. QTL detected under water stress (qSev.uwa.3BL) co-located with the DREB 1 gene, which was mapped between markers Xmwg818 and Xfbb117 (58.1-77.6 cM). QTLs with high proportion of additive components can be validated for marker assisted gene pyramiding and selection. [ABSTRACT FROM AUTHOR]

Methods allowing quick generation cycles are available for various crop species but are limited to spring genotypes. However, winter types predominate in many crops including wheat and barley. Different from spring ones, winter genotypes need to be treated in low temperature for extended periods to accelerate flowering. Combined with known factors that reduce generation cycles for spring wheat and barley, the generation cycle effects of vernalizing seedlings from young embryos of winter types at 10°C of several crop species were studied. Here, we described how to obtain up to seven generations of winter barley, six generations for winter wheat or five generations for both winter oat and triticale genotypes per annum. This procedure should find wide applications in breeding and other biological studies. [ABSTRACT FROM AUTHOR]

The adoption of reduced height ( Rht) genes has dramatically enhanced yield potential of cereal crops. The semi-dwarfing gene uzu in barley is widely used in East Asia. Its value as an Rht gene in the warm and dry environments in Australia was evaluated in this study. In addition to plant height, this gene showed significant effects on a wide range of characteristics. It reduced the overall plant height by an average of 33.7 % with the most significant reduction occurred on the internode below the peduncle. The gene reduces spike length by 31.6 % and grain weight by 18.8 %. It increases grain number per spike by 5.6 % and grain density by 51.8 %. Seedling assays suggested that the effects of this gene became more significant with increased temperature. It reduced coleoptile and seedling length by 19.4 % and 15.1 %, respectively at 7 °C. The reduction increased to 61 % and 46.7 %, respectively, at 25 °C. These results indicated that the uzu gene could have limited values in some high temperature and drought prone environments. [ABSTRACT FROM AUTHOR]

Background: Carbohydrate accumulation of photosynthetic organs, mainly leaves, are the primary sources of grain yield in cereals. The flag leaf plays a vital role in seed development, which is probably the most neglected morphological characteristic during traditional selection processes. Results: In this experiment, four flag leaf morphological traits and seven yield-related traits were investigated in a DH population derived from a cross between a wild barley and an Australian malting barley cultivar. Flag leaf thickness (FLT) showed significantly positive correlations with grain size. Four QTL, located on chromosomes 1H, 2H, 3H, and 5H, respectively, were identified for FLT. Among them, a major QTL was located on chromosome 3H with a LOD value of 18.4 and determined 32% of the phenotypic variation. This QTL showed close links but not pleiotropism to the previously reported semi-dwarf gene sdw1 from the cultivated barley. This QTL was not reported before and the thick leaf allele from the wild barley could provide a useful source for improving grain yield through breeding. Conclusions: Our results also provided valuable evidence that source traits and sink traits in barley are tightly connected and suggest further improvement of barley yield potential with enhanced and balanced source and sink relationships by exploiting potentialities of the wild barley resources. Moreover, this study will provide a novel sight on understanding the evolution and development of leaf morphology in barley and improving barley production by rewilding for lost superior traits during plant evolution. [ABSTRACT FROM AUTHOR]

Key message: In this first genetic study on assessing leaf thickness directly in cereals, major and environmentally stable QTL were detected in barley and candidate genes underlying a major locus were identified. Leaf thickness (LT) is an important characteristic affecting leaf functions which have been intensively studied. However, as LT has a small dimension in many plant species and technically difficult to measure, previous studies on this characteristic are often based on indirect estimations. In the first study of detecting QTL controlling LT by directly measuring the characteristic in barley, large and stable loci were detected from both field and glasshouse trials conducted in different cropping seasons by assessing a population of 201 recombinant inbred lines. Four loci (locating on chromosome arms 2H, 3H, 5H and 6H, respectively) were consistently detected for flag leaf thickness (FLT) in each of these trials. The one on 6H had the largest effect, with a maximum LOD 9.8 explaining up to 20.9% of phenotypic variance. FLT does not only show strong interactions with flag leaf width and flag leaf area but has also strong correlations with fertile tiller number, spike row types, kernel number per spike and heading date. Though with reduced efficiency, these loci were also detectable from assessing second last leaf of fully grown plants or even from assessing the third leaves of seedlings. Taking advantage of the high-quality genome assemblies for both parents of the mapping population used in this study, three candidate genes underlying the 6H QTL were predicted based on orthologous analysis. These results do not only broaden our understanding on genetic basis of LT and its relationship with other traits in cereal crops but also form the bases for cloning and functional analysis of genes regulating LT in barley. [ABSTRACT FROM AUTHOR]

Fusarium crown rot (FCR) is one of the most damaging cereal diseases in semi-arid regions worldwide. Genetic studies on FCR resistance have mainly focused on disease symptoms measured by the browning of either leaf sheaths in seedlings or stems of mature plants. Two major QTLs conferring FCR resistance in barley, Qcsr.cpi-1H and Qcrs.cpi-4H, were previously identified in the growth room. They could explain up to 33.4 and 45.3% of phenotypic variance, respectively. This is the first study where the possible effects of FCR-resistant loci identified in the previous studies based on seedling assay are tested for their abilities to reduce grain yield loss. Near isogenic lines (NILs) and backcross (BC) lines targeting these two loci were assessed in the 2017 and 2018 crop seasons. Results from the NILs showed that the presence of a resistance allele at either the 1HL or 4HL locus reduced grain yield loss by an average of 12.0% and 10.7%, respectively. Grain yields of the top BC lines containing resistance alleles at both loci were 34.4% higher than the average of the commercial varieties under FCR inoculation. These lines will be highly valuable in breeding barley varieties with enhanced resistance to FCR. [ABSTRACT FROM AUTHOR]

Multiple species of Fusarium can infect wheat and barley plants at various stages of development. Fusarium head blight (FHB) refers to the infection of spikes and developing kernels by these pathogens, and crown rot (FCR) infers to infection of the root, crown, and basal stem by Fusarium pathogens. Interestingly, most of the host genes conferring resistance to these two diseases are different in both wheat and barley, and plants' susceptibility to these two diseases are oppositely affected by both plant height and reduced water availability. Available results do not support the hypothesis that reduced height genes have different effects on biotrophic and necrotrophic diseases. Rather, differences in temperature and humidity in microenvironments surrounding the infected tissues and the difference in the physical barriers originating from the difference in cell density seem to be important factors affecting the development of these two diseases. The fact that genes conferring resistance to Type I and Type II of FHB are different indicates that it could be feasible to identify and exploit genes showing resistance at the three distinct stages of FCR infection for breeding varieties with further enhanced resistance. The strong association between FCR severity and drought stress suggests that it should be possible to exploit some of the genes underlying drought tolerance in improving resistance to FCR. [ABSTRACT FROM AUTHOR]

Due to its accuracy, sensitivity and high throughput, real time quantitative PCR (RT-qPCR) has been widely used in analysing gene expression. The quality of data from such analyses is affected by the quality of reference genes used. Expression stabilities for nine candidate reference genes widely used in soybean were evaluated under different stresses in this study. Our results showed that EF1A and ACT11 were the best under salinity stress, TUB4, TUA5 and EF1A were the best under drought stress, ACT11 and UKN2 were the best under dark treatment, and EF1B and UKN2 were the best under virus infection. EF1B and UKN2 were the top two genes which can be reliably used in all of the stress conditions assessed. [ABSTRACT FROM AUTHOR]

Callose is a β-l,3-glucan with diverse roles in the viral pathogenesis of plants. It is widely believed that the deposition of callose and hypersensitive reaction (HR) are critical defence responses of host plants against viral infection. However, the sequence of these two events and their resistance mechanisms are unclear. By exploiting a point inoculation approach combined with aniline blue staining, immuno-electron microscopy and external sphincters staining with tannic acid, we systematically investigated the possible roles of callose deposition during viral infection in soybean. In the incompatible combination, callose deposition at the plasmodesmata (PD) was clearly visible at the sites of inoculation but viral RNA of coat protein (CP-RNA) was not detected by RT-PCR in the leaf above the inoculated one (the upper leaf). In the compatible combination, however, callose deposition at PD was not detected at the site of infection but the viral CP-RNA was detected by RT-PCR in the upper leaf. We also found that in the incompatible combination the fluorescence due to callose formation at the inoculation point disappeared following the injection of 2-deoxy- d-glucose (DDG, an inhibitor of callose synthesis). At same time, in the incompatible combination, necrosis was observed and the viral CP-RNA was detected by RT-PCR in the upper leaf and HR characteristics were evident at the inoculation sites. These results show that, during the defensive response of soybean to viral infection, callose deposition at PD is mainly responsible for restricting the movement of the virus between cells and it occurs prior to the HR response. [ABSTRACT FROM AUTHOR]

Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences were not detected between these two types of polyploid genotypes, although they differ in times exposed to evolutionary selection. The estimated ratio of shared genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes than those for the natural genotypes, which is expected as it is now well-known that many genes in a species are not shared among all individuals. As the exact diploid parent for a given subgenome is unknown, the estimated ratios of shared genes for the natural genotypes would also include difference among individual genotypes of the diploid donor species. Further, we detected the presence of SA in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. These results indicate that SA may, to a large degree, reflect differences between its diploid donors or that changes occurred during polyploid evolution are defined by their donor genomes. [ABSTRACT FROM AUTHOR]

Trichomes are differentiated epidermal cells and can be found on above ground organs of nearly all land plants. Results from previous studies show that trichomes play important roles against a wide range of both biotic and abiotic stresses. By examining differences between parental genotypes of available populations, we identified a population of recombinant inbred lines showing clear segregation for trichome density and length. Assessing the F8 lines of the population growing in the field detected a major locus on chromosome arm 4BL. This locus was detected based the assessments of either fully expanded third leaves or flag leaves after anthesis. Based on the position of the QTL, an SSR marker was used to identify heterozygous plants at this locus from F5 lines derived from the same cross for the F8 population. Three pairs of near isogenic lines targeting this locus were obtained from these heterozygous plants. Difference in trichome length between the two lines with opposite alleles for each of these NIL pairs were similar to that between the two parental genotypes for the mapping populations, confirming that this single locus is mainly responsible for the trichome characteristics measured in this study. The allele with long and dense trichome is dominant as this characteristic was shown by the heterozygous individuals at this marker locus. Apart from the targeted locus, NIL pairs have highly homogeneous genetic backgrounds. Thus, the NILs could be invaluable in understanding the relationship between trichome density and resistance or tolerance to various biotic and abiotic stresses. [ABSTRACT FROM AUTHOR]

Key message: We identified 1.844 million barley pan-genome sequence anchors from 12,306 genotypes using genetic mapping and machine learning. There is increasing evidence that genes from a given crop genotype are far to cover all genes in that species; thus, building more comprehensive pan-genomes is of great importance in genetic research and breeding. Obtaining a thousand-genotype scale pan-genome using deep-sequencing data is currently impractical for species like barley which has a huge and highly repetitive genome. To this end, we attempted to identify barley pan-genome sequence anchors from a large quantity of genotype-by-sequencing (GBS) datasets by combining genetic mapping and machine learning algorithms. Based on the GBS sequences from 11,166 domesticated and 1140 wild barley genotypes, we identified 1.844 million pan-genome sequence anchors. Of them, 532,253 were identified as presence/absence variation (PAV) tags. Through aligning these PAV tags to the genome of hulless barley genotype Zangqing320, our analysis resulted in a validation of 83.6% of them from the domesticated genotypes and 88.6% from the wild barley genotypes. Association analyses against flowering time, plant height and kernel size showed that the relative importance of the PAV and non-PAV tags varied for different traits. The pan-genome sequence anchors based on GBS tags can facilitate the construction of a comprehensive pan-genome and greatly assist various genetic studies including identification of structural variation, genetic mapping and breeding in barley. [ABSTRACT FROM AUTHOR]

Leaf rust, caused by Puccinia triticina, is one of the most destructive fungal diseases in wheat production worldwide. The hypersensitive reaction (HR) is an important defence response against P. triticina infection. In this study, the physiological races 165 and 260 of P. triticina were combined with a line derived from the bread wheat cultivar Thatcher with the leaf rust resistance locus Lr26 to form compatible and incompatible combinations, respectively. Based on an RNA‐Seq database of the interaction systems, a new wheat cysteine‐rich receptor‐like kinase gene, TaCRK2, is specifically induced and up‐regulated in the incompatible combination. We identified that TaCRK2 was regulated in a Ca2+‐dependent manner. Knockdown of TaCRK2 by virus‐induced gene silencing and RNAi leads to a dramatic increase in HR area and the number of haustorial mother cells at the single infection site. In addition, urediniospores, a P. triticina‐specific pathogenic marker in compatible combinations, were observed on leaf surfaces of silenced plants at approximately 15 days after inoculation in the incompatible combination. Moreover, transcription levels of TaPR1, TaPR2, and TaPR5 were obviously reduced in TaCRK2‐silenced plants. TaCRK2 overexpression in Nicotiana benthamiana induced strong HR‐like cell death. Finally, transient expression of green fluorescent protein fused with TaCRK2 in N. benthamiana indicated that TaCRK2 localizes in the endoplasmic reticulum. Thus, TaCRK2 plays an important role in the resistance to P. triticina infection and has a positive regulation effect on the HR cell death process induced by P. triticina. [ABSTRACT FROM AUTHOR]

Summary: Wild barley (Hordeum spontaneum) is the progenitor of cultivated barley (Hordeum vulgare) and provides a rich source of genetic variations for barley improvement. Currently, the genome sequences of wild barley and its differences with cultivated barley remain unclear. In this study, we report a high‐quality draft assembly of wild barley accession (AWCS276; henceforth named as WB1), which consists of 4.28 Gb genome and 36 395 high‐confidence protein‐coding genes. BUSCO analysis revealed that the assembly included full lengths of 95.3% of the 956 single‐copy plant genes, illustrating that the gene‐containing regions have been well assembled. By comparing with the genome of the cultivated genotype Morex, it is inferred that the WB1 genome contains more genes involved in resistance and tolerance to biotic and abiotic stresses. The presence of the numerous WB1‐specific genes indicates that, in addition to enhance allele diversity for genes already existing in the cultigen, exploiting the wild barley taxon in breeding should also allow the incorporation of novel genes. Furthermore, high levels of genetic variation in the pericentromeric regions were detected in chromosomes 3H and 5H between the wild and cultivated genotypes, which may be the results of domestication. This H. spontaneum draft genome assembly will help to accelerate wild barley research and be an invaluable resource for barley improvement and comparative genomics research. [ABSTRACT FROM AUTHOR]

Elevated circulating free fatty acid (FFA) level is closely linked to the pathogenesis of insulin resistance and type 2 diabetes mellitus. Activation of the adenosine A 1 receptor (A 1 R) inhibits lipolysis in adipocytes and hence reduces the concentration of FFA, which represents a potential target for the development of antilipolytic agents. We aimed to assess the binding affinity as well as target binding kinetics of A 1 R agonists and further delineate a possible relationship with their antilipolytic effect in adipocytes. Radioligand binding assays were performed to determine the affinity and kinetics of three representative A 1 R agonists, namely CPA, LUF6944 and LUF6941, on the rat A 1 R. Functional responses to these agonists were examined in both a recombinant cell system and physiologically relevant rat adipocytes. The three A 1 R agonists displayed similar affinity while divergent target binding kinetics on the rat A 1 R. Irrespective of equilibrium binding affinity, temporal analysis of receptor signaling demonstrated persistent functional responses for the long residence time agonist, despite removal of excess agonist, in both a recombinant cell system and in rat adipocytes. By contrast, such effect was less pronounced or even lost for agonists with medium or short receptor residence time, respectively. Our results indicate that ligand receptor binding kinetics rather than their affinity or potency play an essential role in regulating cellular responses. The long residence time A 1 R agonist produces a sustained wash-resistant antilipolytic effect in rat adipocytes and thus may represent a potential antilipolytic alternative for further investigation. [ABSTRACT FROM AUTHOR]

Key message: A major, likely novel stripe rust resistance QTL for all-stage resistance on chromosome arm 1BL identified in a 1.76-cM interval using a saturated linkage map was validated in four populations with different genetic backgrounds. Stripe rust is a globally important disease of wheat. Identification and utilization of new resistance genes are essential for breeding resistant cultivars. Wheat line 20828 has exhibited high levels of stripe rust resistance for over a decade. However, the genetics of stripe rust resistance in this line has not been studied. A set of 199 recombinant inbred lines (RILs) were developed from a cross between 20828 and a susceptible cultivar Chuannong 16. The RIL population was genotyped with the Wheat55K SNP (single nucleotide polymorphism) array and SSR (simple sequence repeat) markers and evaluated in four environments with current predominant Puccinia striiformis f. sp. tritici t races including CYR32, CYR33 and CYR34. Four stable QTL were located on chromosomes 1B (2 QTL), 4A and 6A. Among them, the major QTL, QYr.sicau-1B.1 (LOD = 23–28, PVE = 16–39%), was localized to a 1.76-cM interval flanked by SSR markers Xwmc216 and Xwmc156 on chromosome 1BL. Eight resistance genes were previously identified in the physical interval of QYr.sicau-1B.1. Compared with previous studies, QYr.sicau-1B.1 is a new gene for resistant to stripe rust. It was further verified by analysis of the closely linked SSR markers Xwmc216 and Xwmc156 in four other populations with different genetic backgrounds. QYr.sicau-1B.1 reduced the stripe rust disease index by up to 82.8%. Three minor stable QTL (located on chromosomes 1B, 4A and 6A, respectively) also added to the resistance level of QYr.sicau-1B.1. Our results provide valuable information for further fine mapping and cloning as well as molecular-assisted breeding with QYr.sicau-1B.1. [ABSTRACT FROM AUTHOR]

Background: It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications. Results: In this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones. Conclusions: We demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication. [ABSTRACT FROM AUTHOR]

Key message: This study demonstrates the feasibility of developing co-segregating markers and identifying candidate genes for Fusarium crown rot resistance in barley based on the generation and exploitation of a near-isogenic line-derived large population.Abstract: Fusarium crown rot (FCR) is a chronic and severe disease in cereals in semi-arid regions worldwide. Previous studies showed that FCR assessment could be affected by many factors including plant height, growth rate as well as drought stress. Thus, accurate assessment, which is essential for detailed mapping of any locus conferring FCR resistance, is difficult. Targeting one of the resistance loci reported earlier, we developed a near-isogenic line-derived population consisting of 1820 F9 lines. By analysing this population, the Qcrs.cpi-4H locus was mapped to an interval of 0.09 cM covering a physical distance of about 637 kb and 13 markers co-segregating with the targeted locus were developed. Candidate genes underlying the resistance locus were identified by analysing the expression and sequence variation of genes in the targeted interval. The accurate localization and the development of co-segregating markers should facilitate the incorporation of this large-effect QTL into breeding programmes as well as the cloning of gene(s) underlying the locus. [ABSTRACT FROM AUTHOR]

Key message: A high-density genetic map constructed with a wheat 55 K SNP array was highly consistent with the physical map of this species and it facilitated the identification of a novel major QTL for productive tiller number.Abstract: Productive tiller number (PTN) plays a key role in wheat grain yield. In this study, a recombinant inbred line population with 199 lines derived from a cross between ‘20828’ and ‘Chuannong16’ was used to construct a high-density genetic map using wheat 55 K single nucleotide polymorphism (SNP) array. The constructed genetic map contains 12,109 SNP markers spanning 3021.04 cM across the 21 wheat chromosomes. The orders of the genetic and physical positions of these markers are generally in agreement, and they also match well with those based on the 660 K SNP array from which the one used in this study was derived. The ratios of SNPs located in each of the wheat deletion bins were similar among the wheat 9 K, 55 K, 90 K, 660 K and 820 K SNP arrays. Based on the constructed maps, a novel major quantitative trait locus QPtn.sau-4B for PTN was detected across multi-environments in a 0.55 cM interval on 4B and it explained 17.23-45.46% of the phenotypic variance. Twenty common genes in the physical interval between the flanking markers were identified on chromosome 4B of ‘Chinese Spring’ and wild emmer. These results indicate that wheat 55 K SNP array could be an ideal tool in primary mapping of target genes and the identification of QPtn.sau-4B laid a foundation for the following fine mapping and cloning work. [ABSTRACT FROM AUTHOR]

Barley (Hordeum vulgare L)mayalter its root morphology to improve Pacquisition efficiency under low-P (LP) stress. This research studied the variations in adventitious and lateral root morphological traits of barley and mapped their quantitative trait loci (QTLs) under LP and high P (HP). The recombinant inbred lines were derived from the F1 population of a cross between CN4027 and Baudin. Two experiments aimed to identify QTLs related to adventitious and lateral root morphological traits under LP and HP. The length, surface area and volume of adventitious and lateral roots were measured. Under HP, Baudin had larger root morphology, especially lateral root morphology, than CN4027. LP stress induced lateral root growth but inhibited adventitious root growth. Nineteen QTLs for root morphological traits were detected. These QTLs clustered within four regions (Cl-2H, Cl-3H, Cl-4H and Cl-7H) on chromosomes 2H, 3H, 4H and 7H, with corresponding contributions of 12.0-42.9%. Some QTLs are linked with the QTLs for P efficiency detected previously, demonstrating the role of root morphological traits in P efficiency. The Cl-2H region was identified in the interval bPb3927665-bPb3265744 on chromosome 2H and had major effects on lateral root growth, especially under LP. Lateral root length and surface area increased when alleles from Baudin were present at the QTLs in Cl-2H. This study demonstrated the patterns of growth among root types and the role of lateral roots in barley's adaption to LP stress. The QTL clusters, especially Cl-2H, may offer clues for fine mapping and map-based cloning. [ABSTRACT FROM AUTHOR]

Key message: Sequence comparison between spelt and common wheat reveals that the former has huge potential in enriching the genetic variation of the latter.Abstract: Genetic variation is the foundation of crop improvement. By comparing genome sequences of a Triticum spelta accession and one of its derived hexaploid lines with the sequences of the international reference genotype Chinese Spring, we detected variants more than tenfold higher than those present among common wheat (T. aestivum L) genotypes. Furthermore, different from the typical ‘V-shaped’ pattern of variant distribution often observed along wheat chromosomes, the sequence variation detected in this study was more evenly distributed along the 3B chromosome. This was also the case between T. spelta and the wild emmer genome. Genetic analysis showed that T. spelta and common wheat formed discrete groups. These results showed that, although it is believed that the spelt and common wheat are evolutionarily closely related and belong to the same species, a significant sequence divergence exists between them. Thus, the values of T. spelta in enriching the genetic variation of common wheat can be huge. [ABSTRACT FROM AUTHOR]

Key message: This study demonstrates how identification of genes underpinning disease-resistance QTL based on differential expression and SNPs can be improved by performing transcriptomic analysis on multiple near isogenic lines.Abstract: Transcriptomic analysis has been widely used to understand the genetic basis of a trait of interest by comparing genotypes with contrasting phenotypes. However, these approaches identify such large sets of differentially expressed genes that it proves difficult to isolate which genes underpin the phenotype of interest. This study tests whether using multiple near isogenic lines (NILs) can improve the resolution of RNA-seq-based approaches to identify genes underpinning disease-resistance QTL. A set of NILs for a major effect Fusarium crown rot-resistance QTL in barley on the 4HL chromosome arm were analysed under Fusarium crown rot using RNA-seq. Differential gene expression and single nucleotide polymorphism detection analyses reduced the number of putative candidates from thousands within individual NIL pairs to only one hundred and two genes, which were differentially expressed or contained SNPs in common across NIL pairs and occurred on 4HL. Our findings support the value of performing RNA-seq analysis using multiple NILs to remove genetic background effects. The enrichment analyses indicated conserved differences in the response to infection between resistant and sensitive isolines suggesting that sensitive isolines are impaired in systemic defence response to Fusarium pseudograminearum. [ABSTRACT FROM AUTHOR]

Fusarium pseudograminearum is an important pathogen of wheat and barley, particularly in semi-arid environments. Previous genome assemblies for this organism were based entirely on short read data and are highly fragmented. In this work, a genetic map of F. pseudograminearum has been constructed for the first time based on a mapping population of 178 individuals. The genetic map, together with long read scaffolding of a short read-based genome assembly, was used to give a near-complete assembly of the four F. pseudograminearum chromosomes. Large regions of synteny between F. pseudograminearum and F. graminearum, the related pathogen that is the primary causal agent of cereal head blight disease, were previously proposed in the core conserved genome, but the construction of a genetic map to order and orient contigs is critical to the validation of synteny and the placing of species-specific regions. Indeed, our comparative analyses of the genomes of these two related pathogens suggest that rearrangements in the F. pseudograminearum genome have occurred in the chromosome ends. One of these rearrangements includes the transposition of an entire gene cluster involved in the detoxification of the benzoxazolinone (BOA) class of plant phytoalexins. This work provides an important genomic and genetic resource for F. pseudograminearum, which is less well characterized than F. graminearum. In addition, this study provides new insights into a better understanding of the sexual reproduction process in F. pseudograminearum, which informs us of the potential of this pathogen to evolve. [ABSTRACT FROM AUTHOR]

Fusarium crown rot (FCR) has become one of the most damaging cereal diseases in semi-arid regions worldwide. Targeting three large-effect QTL (located on the chromosome arm 3BL, 5DS and 2DL, respectively), we investigated the feasibility of enhancing FCR resistance by gene pyramiding. Significant effects were detected for each of the three QTL in both populations assessed. Lines with any combination of two resistant alleles gave significantly better resistance than those with a single resistant allele only and those without any allele, and lines possessing all three resistant alleles showed the best resistance. These results demonstrated that gene pyramiding can be an effective approach in improving FCR resistance. Those lines with resistant alleles from all three QTL could be valuable genetic stocks for breeding programs. [ABSTRACT FROM AUTHOR]

Anthocyanin-rich barley can have great potential in promoting human health and in developing nutraceuticals and functional foods. As different anthocyanin compounds have different antioxidant activities, breeding cultivars with pre-designed anthocyanin compositions could be highly desirable. Working toward this possibility, we assessed and reported for the first time the genetic control of individual anthocyanin compounds in barley. Of the ten anthocyanins assessed, two, peonidin-3-glucoside (P3G) and cyanidin-3-glucoside (C3G), were major components in the purple pericarp barley genotype RUSSIA68. Quantitative trait locus (QTL) mapping showed that both anthocyanin compounds were the interactive products of two loci, one located on chromosome arm 2HL and the other on 7HS. However, the two different anthocyanin components seem to be controlled by different interactions between the two loci. The effects of the 7HS locus on P3G and C3G were difficult to detect without removing the effect of the 2HL locus. At least one copy of the 2HL alleles from the purple pericarp parent was required for the synthesis of P3G. This does not seem to be the case for the production of C3G which was produced in each of all the different allele combinations between the two loci. Typical maternal effect was also observed in the inheritance of purple pericarp grains in barley. The varied values of different compounds, coupled with their different genetic controls, highlight the need for targeting individual anthocyanins in crop breeding and food processing. [ABSTRACT FROM AUTHOR]

During their interactions with plants, fungal pathogens employ large numbers of pathogenesis-associated molecules including secreted effectors and enzymes that can degrade various defence compounds. However, in many cases, in planta targets of pathogen-produced enzymes remain unknown. We identified a gene in the wheat pathogen Fusarium graminearum , encoding a putative enzyme that shows 84% sequence identity to FoTom1, a tomatinase produced by the tomato pathogen Fusarium oxysporum f. sp. lycopersici. In F. oxysporum f. sp. lycopersici , FoTom1 is a virulence factor involved in the degradation of tomato defence compound tomatine, a saponin compound. Given that wheat is unknown to produce tomatine, we tested the ability of F. graminearum to degrade tomatine and found that F. graminearum was unable to degrade tomatine in culture. However, FgTom1 degraded tomatine in vitro when heterologously expressed. To determine the possible function of FgTom1 in pathogen virulence, we generated FgTom1 knockout mutants (ΔTom1). ΔTom1 mutants were not different from wild type when grown in culture but showed significant reduction in pathogen virulence in root rot and head blight assays. In an attempt to identify possible in planta targets of FgTom1, the metabolomes of wheat heads infected with wildtype pathogen and ΔTom1 were compared and several peaks differentially abundant between treatments identified. Although the exact identity of these peaks is currently unknown, this result suggested that FgTom1 may have in planta targets in wheat, possibly tomatine-like saponin compounds. Overall, our results presented here show that FgTom1 is a new virulence factor in F. graminearum . [ABSTRACT FROM AUTHOR]

Plants produce a variety of secondary metabolites to defend themselves from pathogen attack, while pathogens have evolved to overcome plant defences by producing enzymes that degrade or modify these defence compounds. However, many compounds targeted by pathogen enzymes currently remain enigmatic. Identifying host compounds targeted by pathogen enzymes would enable us to understand the potential importance of such compounds in plant defence and modify them to make them insensitive to pathogen enzymes., Here, a proof of concept metabolomics-based method was developed to discover plant defence compounds modified by pathogens using two pathogen enzymes with known targets in wheat and tomato. Plant extracts treated with purified pathogen enzymes were subjected to LC-MS, and the relative abundance of metabolites before and after treatment were comparatively analysed., Using two enzymes from different pathogens the in planta targets could be found by combining relatively simple enzymology with the power of untargeted metabolomics. Key to the method is dataset simplification based on natural isotope occurrence and statistical filtering, which can be scripted., The method presented here will aid in our understanding of plant-pathogen interactions and may lead to the development of new plant protection strategies. [ABSTRACT FROM AUTHOR]

A fast generation cycling system ( FGCS) was developed in oat and triticale, allowing the production of pure line populations of the crops within 1-year timeframe. Twelve oat and 12 triticale cultivars were tested using the FGCS, and most of them completed a generation cycle within 48-61 days under the system achieving up to seven generations a year. This system involves growing plants under stressed conditions to promote reproduction and in vitro culture of immature embryos bypassing full seed maturation. The developed system could be widely adopted in breeding and genetic studies of crops for producing desired segregating pure line populations, which could significantly shorten the breeding cycles. [ABSTRACT FROM AUTHOR]

ADP-glucose pyrophosphorylase (AGP), which consists of two large subunits (AGP-L) and two small subunits (AGP-S), controls the rate-limiting step in the starch biosynthetic pathway. In this study, a full-length open reading frame (ORF) of AGP-L gene (named as Agp2) in wheat and a series of Agp2 gene sequences in wheat relatives were isolated. The coding region of Agp2 contained 15 exons and 14 introns including a full-length ORF of 1566 nucleotides, and the deduced protein contained 522 amino acids (57.8 kDa). Generally, the phylogenetic tree of Agp2 indicated that sequences from A- and D-genome donor species were most similar to each other and sequences from B-genome donor species contained more variation. Starch accumulation and Agp2 expression in wheat grains reached their peak at 21 and 15 days post anthesis (DPA), respectively. [ABSTRACT FROM AUTHOR]

Key message: SNP-based QTL mapping provided useful information for novel loci that can be used in breeding programs to control tillering and improve yield in wheat via marker-assisted selection. Abstract: Tillering is one of the most important agronomic traits affecting biomass and grain yield potential in wheat. Wheat lines with very limited tillering capacity are more productive than free-tillering lines under severe drought conditions. In this study, three recombinant inbred line (RIL) populations were generated and used, having H461, a low-tillering genotype, as a common parent. A linkage map containing 7808 single nucleotide polymorphism loci was constructed on the basis of H461/CN16 RIL population. Three QTL controlling low tillering were identified on Chromosome (Chr.) 2D ( Qltn.sicau- 2D), Chr. 2B ( Qltn.sicau- 2B), and Chr. 5A ( Qltn.sicau- 5A). Qltn.sicau- 2D, Qltn.sicau- 2B, and Qltn.sicau- 5A explained up to 19.1, 14.6, and 9.6 % of the phenotypic variance, respectively. Comparing with previous findings, Qltn.sicau- 2D and Qltn.sicau- 2B should thus be novel tillering QTL. The effects of these QTL were further validated in two additional RIL populations. Significant effects of Qltn.sicau- 2D were detected across all growth stages in different genetic backgrounds, making it an ideal target for breeding programs as well as for further characterization of the gene(s) underlying this locus. [ABSTRACT FROM AUTHOR]

Introduction: Salinity is one of the major abiotic stresses affecting crop production via adverse effects of osmotic stress, specific ion toxicity, and stress-related nutritional disorders. Detrimental effects of salinity are also often exacerbated by low oxygen availability when plants are grown under waterlogged conditions. Developing salinity-tolerant varieties is critical to overcome these problems, and molecular marker assisted selection can make breeding programs more effective. Methods: In this study, a double haploid (DH) population consisting of 175 lines, derived from a cross between a Chinese barley variety Yangsimai 1 (YSM1) and an Australian malting barley variety Gairdner, was used to construct a high density molecular map which contained more than 8,000 Diversity Arrays Technology (DArT) markers and single nucleotide polymorphism (SNP) markers. Salinity tolerance of parental and DH lines was evaluated under drained (SalinityD) and waterlogged (SalinityW) conditions at two different sowing times. Results: Three quantitative trait loci (QTL) located on chromosome 1H, single QTL located on chromosomes 1H, 2H, 4H, 5H and 7H, were identified to be responsible for salinity tolerance under different environments. Waterlogging stress, daylight length and temperature showed significant effects on barley salinity tolerance. The QTL for salinity tolerance mapped on chromosomes 4H and 7H, QSlwd.YG.4H, QSlwd.YG.7H and QSlww.YG.7H were only identified in winter trials, while the QTL on chromosome 2H QSlsd.YG.2H and QSlsw.YG.2H were only detected in summer trials. Genes associated with flowering time were found to pose significant effects on the salinity QTL mapped on chromosomes 2H and 5H in summer trials. Given the fact that the QTL for salinity tolerance QSlsd.YG.1H and QSlww.YG.1H-1 reported here have never been considered in the literature, this warrants further investigation and evaluation for suitability to be used in breeding programs. [ABSTRACT FROM AUTHOR]

Mung bean (Vigna radiate (L.) Wilczek) is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina paired-end sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0%) and 23,235 (47.7%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5%) could be classified into gene ontology categories, 18,316 (37.6%) into Swiss-Prot categories and 10,918 (22.4%) into KOG database categories (E-value < 1.0E-5). A total of 6,585 (8.3%) were mapped onto 244 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. Among the unigenes, 10,053 sequences contained a unique simple sequence repeat (SSR), and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST). A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%), GAA/TTC (12.6%), AAAT/ATTT (6.8%), AAAAT/ATTTT (6.2%) and AAAAAT/ATTTTT (1.9%). A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species. [ABSTRACT FROM AUTHOR]

Fusarium crown rot (FCR) is a serious disease in wheat and barley in semiarid regions worldwide. The feasibility of enhancing FCR resistance by gene pyramiding was investigated by generating and assessing two populations segregating for three large-effect QTL located on the long arms of chromosomes 1H, 3H and 4H, respectively. Significant effects were detected for each of the three QTL in both of the populations assessed. Lines with any combination of two resistant alleles from the three QTL gave, on average, significantly better resistance than those with a single resistant allele only, and lines with resistant alleles from all three of the QTL gave the least FCR symptom. However, wide variations in FCR severity were detected for lines belonging to each of the groups with different numbers of resistant alleles. Significant effects of plant height on FCR were detected in both populations, and a significant association between heading date and FCR severity was detected in one of the two populations assessed. Results from the current study also showed that the effects of a given allele of resistance decreased with the increase in the number of resistant alleles an individual group possessed. Overall, results from this study demonstrate that gene pyramiding can be an effective approach in improving FCR resistance and those lines with resistant alleles from all of the three QTL could be valuable for breeding programs. [ABSTRACT FROM AUTHOR]

Fusarium pathogens cause two major diseases in cereals, Fusarium crown rot (FCR) and head blight (FHB). A large-effect locus conferring resistance to FCR disease was previously located to chromosome arm 3BL (designated as Qcrs-3B) and several independent sets of near isogenic lines (NILs) have been developed for this locus. In this study, five sets of the NILs were used to examine transcriptional changes associated with the Qcrs-3B locus and to identify genes linked to the resistance locus as a step towards the isolation of the causative gene(s). Of the differentially expressed genes (DEGs) detected between the NILs, 12.7% was located on the single chromosome 3B. Of the expressed genes containing SNP (SNP-EGs) detected, 23.5% was mapped to this chromosome. Several of the DEGs and SNP-EGs are known to be involved in host-pathogen interactions, and a large number of the DEGs were among those detected for FHB in previous studies. Of the DEGs detected, 22 were mapped in the Qcrs-3B interval and they included eight which were detected in the resistant isolines only. The enrichment of DEG, and not necessarily those containing SNPs between the resistant and susceptible isolines, around the Qcrs-3B locus is suggestive of local regulation of this region by the resistance allele. Functions for 13 of these DEGs are known. Of the SNP-EGs, 28 were mapped in the Qcrs-3B interval and biological functions for 16 of them are known. These results provide insights into responses regulated by the 3BL locus and identify a tractable number of target genes for fine mapping and functional testing to identify the causative gene(s) at this QTL. [ABSTRACT FROM AUTHOR]

Abstract: Despite numerous studies on shrunken endosperm mutants caused by either maternal tissues (seg) or kernel per se (sex) in barley, the molecular mechanism for all of the eight seg mutants (seg1–seg8) and some sex mutants is yet to be uncovered. In this study, we determined the amylose content, characterized granule-binding proteins, analyzed the expression of key genes involved in starch synthesis, and examined starch granule structure of both normal (Bowman and Morex) and shrunken endosperm (seg1, seg3, seg4a, seg4b, seg5, seg6, seg7, and sex1) barley accessions. Our results showed that amylose contents of shrunken endosperm mutants ranged from 8.9% (seg4a) to 25.8% (seg1). SDS-PAGE analysis revealed that 87kDa proteins corresponding to the starch branching enzyme II (SBEII) and starch synthase II (SSII) were not present in seg1, seg3, seg6, and seg7 mutants. Real-time quantitative PCR (RT-qPCR) analysis indicated that waxy expression levels of seg1, seg3, seg6, and seg7 mutants decreased in varying degrees to lower levels until 27days after anthesis (DAA) after reaching the peak at 15–21DAA, which differed from the pattern of normal barley accessions. Further characterization of waxy alleles revealed 7 non-synonymous single nucleotide polymorphisms (SNPs) in the coding sequences and 16 SNPs and 8 indels in the promoter sequences of the mutants. Results from starch granule by scanning electron microscopy (SEM) indicated that, in comparison with normal barley accessions, seg4a, seg4b, and sex1 had fewer starch granules per grain; seg3 and seg6 had less small B-type granules; some large A-type granules in seg7 had a hollow surface. These results improve our understanding about effects of seg and sex mutants on starch biosynthesis and granule structure during endosperm development and provide information for identification of key genes responsible for these shrunken endosperm mutants. [Copyright &y& Elsevier]

Fusarium crown rot (FCR) is one of the most damaging cereal diseases in semi-arid regions worldwide. The genetics of FCR resistance in the bread wheat (Triticum eastivum L.) variety EGA Wylie, the most resistant commercial variety available, was studied by QTL mapping. Three populations of recombinant inbred lines were developed with this elite variety as the resistant parent. Four QTL conferring FCR resistance were detected and resistance alleles of all of them were derived from the resistant parent EGA Wylie. One of these loci was located on the short arm of chromosome 5D (designated as Qcrs.cpi-5D). This QTL explains up to 31.1% of the phenotypic variance with an LOD value of 9.6. The second locus was located on the long arm of chromosome 2D (designated as Qcrs.cpi-2D) and explained up to 20.2% of the phenotypic variance with an LOD value of 4.5. Significant effects of both Qcrs.cpi-5D and Qcrs.cpi-2D were detected in each of the three populations assessed. Another two QTL (designated as Qcrs.cpi-4B.1 and Qcrs.cpi-4B.2, respectively) were located on the short arm of chromosome 4B. These two QTL explained up to 16.9% and 18.8% of phenotypic variance, respectively. However, significant effects of Qcrs.cpi-4B.1 and Qcrs.cpi-4B.2 were not detected when the effects of plant height was accounted for by covariance analysis. The elite characteristics of this commercial variety should facilitate the incorporation of the resistance loci it contains into breeding programs. [ABSTRACT FROM AUTHOR]

Structural changes of chromosomes are a primary mechanism of genome rearrangement over the course of evolution and detailed knowledge of such changes in a given species and its close relatives should increase the efficiency and precision of chromosome engineering in crop improvement. We have identified sequences bordering each of the main translocation and inversion breakpoints on chromosomes 4A, 5A and 7B of the modern bread wheat genome. The locations of these breakpoints allow, for the first time, a detailed description of the evolutionary origins of these chromosomes at the gene level. Results from this study also demonstrate that, although the strategy of exploiting sorted chromosome arms has dramatically simplified the efforts of wheat genome sequencing, simultaneous analysis of sequences from homoeologous and non-homoeologous chromosomes is essential in understanding the origins of DNA sequences in polyploid species. [ABSTRACT FROM AUTHOR]