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 3/17   本期作者:麦萌




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1 Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing

The availability of information on the genetic diversity and population structure in wheat (          Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F3:6) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon’s information index (          I) = 0.494, diversity index (          h) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity (          I = 0.348,           h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.

2 Plant and Floret Growth at Distinct Developmental Stages During the Stem Elongation Phase in Wheat

Floret development is critical for grain setting in wheat (          Triticum aestivum), but more than 50% of grain yield potential (based on the maximum number of floret primordia) is lost during the stem elongation phase (SEP, from the terminal spikelet stage to anthesis). Dynamic plant (e.g., leaf area, plant height) and floret (e.g., anther and ovary size) growth and its connection with grain yield traits (e.g., grain number and width) are not clearly understood. In this study, for the first time, we dissected the SEP into seven stages to investigate plant (first experiment) and floret (second experiment) growth in greenhouse- and field-grown wheat. In the first experiment, the values of various plant growth trait indices at different stages were generally consistent between field and greenhouse and were independent of the environment. However, at specific stages, some traits significantly differed between the two environments. In the second experiment, phenotypic and genotypic similarity analysis revealed that grain number and size corresponded closely to ovary size at anthesis, suggesting that ovary size is strongly associated with grain number and size. Moreover, principal component analysis (PCA) showed that the top six principal components PCs explained 99.13, 98.61, 98.41, 98.35, and 97.93% of the total phenotypic variation at the green anther, yellow anther, tipping, heading, and anthesis stages, respectively. The cumulative variance explained by the first PC decreased with floret growth, with the highest value detected at the green anther stage (88.8%) and the lowest at the anthesis (50.09%). Finally, ovary size at anthesis was greater in wheat accessions with early release years than in accessions with late release years, and anther/ovary size shared closer connections with grain number/size traits at the late vs. early stages of floral development. Our findings shed light on the dynamic changes in plant and floret growth-related traits in wheat and the effects of the environment on these traits.

3 Utilization of a Wheat55K SNP Array for Mapping of Major QTL for Temporal Expression of the Tiller Number

Maximum tiller number and productive tiller number are important traits for wheat grain yield, but research involving the temporal expression of tiller number at different quantitative trait loci (QTL) levels is limited. In the present study, a population set of 371 recombined inbred lines derived from a cross between Chuan-Nong18 and T1208 was used to construct a high-density genetic map using a Wheat55K SNP Array and to perform dynamic QTL analysis of the tiller number at four growth stages. A high-density genetic map containing 11,583 SNP markers and 59 SSR markers that spanned 4,513.95 cM and was distributed across 21 wheat chromosomes was constructed. A total of 28 single environmental QTL were identified in the recombined inbred lines population, and among these, seven QTL were stable and used for multi-environmental and dynamic analysis. These QTL were mapped to chromosomes 2D, 4A, 4D, 5A, 5D, and 7D, respectively. Each QTL explained 1.63–21.22% of the observed phenotypic variation, with an additive effect from -20.51 to 11.59. Dynamic analysis showed that           cqTN-2D.2can be detected at four growth stages of tillering, explaining 4.92–17.16% of the observed phenotypic variations and spanning 13.71 Mb (          AX-109283238-AX-110544009: 82189047-95895626) according to the physical location of the flanking markers. The effects of the stable QTL were validated in the recombined inbred lines population, and the beneficial alleles could be utilized in future marker-assisted selection. Several candidate genes for MTN and PTN were predicted. The results provide a better understanding of the QTL selectively expressing the control of tiller number and will facilitate future map-based cloning. 9.17% SNP markers showed best hits to the Chinese Spring contigs. It was indicated that Wheat55K Array was efficient and valid to construct a high-density wheat genetic map.

4 The Role of Hydrogen Peroxide in Mediating the Mechanical Wounding-Induced Freezing Tolerance in Wheat

Systemic wound response (SWR), a well-characterized systemic signaling response, plays crucial roles in plant defense responses. Progress in understanding of the SWR in abiotic stress has also been aided by the researchers. However, the function of SWR in freezing stress remains elusive. In this study, we showed that local mild mechanical wounding enhanced freezing tolerance in newly occurred systemic leaves of wheat plants (          Triticum aestivum L.). Wounding significantly increased the maximal photochemical efficiency of photosystem II, net photosynthetic rate, and the activities of the antioxidant enzymes under freezing stress. Wounding also alleviated freezing-induced chlorophyll decomposition, electrolyte leakage, water lose, and membrane peroxidation. In addition, wounding-induced freezing stress mitigation was closely associated with the ratio between reduced glutathione (GSH) and oxidized glutathione (GSSG), and the ratio between ascorbate (AsA) and dehydroascorbate (DHA), as well as the contents of total soluble sugars and free amino acids. Importantly, pharmacological study showed that wounding-induced freezing tolerance was substantially arrested by pretreatment of wheat leaves with the scavenger of hydrogen peroxide (H2O2) or the inhibitor of NADPH oxidase (RBOH). These results support the hypothesis that local mechanical wounding-induced SWR in newly occurred leaves is largely attributed to RBOH-dependent H2O2production, which may subsequently induce freezing tolerance in wheat plants. This mechanism may have a potential application to reduce the yield losses of wheat under late spring freezing conditions.

5 Identification and Characterization of Wheat Yellow Striate Virus, a Novel Leafhopper-Transmitted Nucleorhabdovirus Infecting Wheat

A new wheat viral disease was found in China. Bullet-shaped viral particles within the nucleus of the infected wheat leave cells, which possessed 180–210 nm length and 35–40 nm width, were observed under transmission electron microscopy. A putative wheat-infecting rhabdovirus vectored by the leafhopper           Psammotettix alienus was identified and tentatively named wheat yellow striate virus (WYSV). The full-length nucleotide sequence of WYSV was determined using transcriptome sequencing and RACE analysis of both wheat samples and leafhoppers           P. alienus. The negative-sense RNA genome of WYSV contains 14,486 nucleotides (nt) and seven open reading frames (ORFs) encode deduced proteins in the order N-P-P3-M-P6-G-L on the antisense strand. In addition, WYSV genome has a 76-nt 3′ leader RNA and a 258-nt 5′ trailer, and the ORFs are separated by conserved intergenic sequences. The entire genome sequence shares 58.1 and 57.7% nucleotide sequence identity with two strains of rice yellow stunt virus (RYSV-A and RYSV-B) genomes, respectively. The highest amino acid sequence identity was 63.8% between the L proteins of the WYSV and RYSV-B, but the lowest was 29.5% between the P6 proteins of these viruses. Phylogenetic analysis firmly established WYSV as a new member of the genus           Nucleorhabdovirus. Collectively, this study provided evidence that WYSV is likely the first nucleorhabdovirus described infecting wheat via leafhopper           P. alienus transmission.

6 Genetic dissection of interactions between wheat flour starch and its components in two populations using two QTL mapping methods

Starch content and its components are important for determining wheat end-use quality and yield. However, little information is available about their interactions at the QTL/gene level in more than one population using different QTL mapping methods. Therefore, to dissect these interactions, two mapping populations from two locations over 2 years were used. The QTLs for the populations were analyzed by unconditional and conditional QTL mapping by two different analysis methods. In the two populations, there were a total of 24 unconditional additive QTLs detected for flour amylose (FAMS), flour amylopectin (FAMP), flour total starch (FTSC), and the ratio of FAMS to FAMP using ICIMapping4.1 methods, but 26 unconditional QTLs were found using QTLNetwork2.0 methods. Of these QTLs, 10 stable major additive QTLs were identified in more than one environment, mainly distributed on chromosomes 3B, 4A, 5A, and 7D. The maximum percentage of phenotypic variance explained (PVE) reached 54.31%. Two new unconditional major additive QTLs on chromosome 3B (          Qftsc3B and           Qfamp3B) were found. A total of 23 and 19 conditional additive QTLs were identified in the two populations using two different methods, respectively. Of which, eight and six stable major conditional QTLs were detected on chromosomes 3B, 4A, and 7D, respectively. New repressed QTLs were identified, such as           Qftsc/          fams5B-1 and           Qftsc/fams5B-2. There were 20 epistatic unconditional and 15 conditional QTLs detected. In all, important QTLs on chromosomes 3B, 4A, and 7A were found in both populations. However, the number of important QTLs in the special recombinant inbred line (RIL) population was higher than that in the double haploid (DH) population, especially on chromosomes 7D and 5B. Moreover, the QTLs on chromosomes 4A, 7A, and 7D were close to the Wx-1 loci in the RIL population. These indicated better results can be obtained by a special population to target traits than by a common population. The important QTLs on key chromosomes can always be detected no matter what kinds of populations are used, such as the QTLs on chromosome 4A. In addition, QTL clusters were found on chromosomes 4A, 3B, 7A, 7D, and 5A in the two populations, indicating these chromosome regions were very important for starch biosynthesis.

7 Zinc-biofortified seeds improved seedling growth under zinc deficiency and drought stress in durum wheat


High zinc (Zn) concentration of seeds has beneficial effects both on seed vigor and human nutrition. This study investigated the effect of Zn biofortification on growth of young durum wheat (          Triticum durum cv. Yelken) seedlings under varied Zn and water supply. The seeds differing in Zn concentrations were obtained by spraying ZnSO4 to durum wheat plants at different rates under field conditions. Three groups of seeds were obtained with the following Zn concentrations: 9, 20, and 50 mg Zn kg−1. The seeds differing in Zn were tested for germination rate, seedling height, shoot dry matter production, and shoot Zn concentration under limited and well irrigated conditions in a Zn-deficient soil with and without Zn application. In an additional experiment carried out in solution culture, root and shoot growth and superoxide dismutase activity (SOD) of seedlings were studied under low and adequate Zn supply. Low seed Zn concentration resulted in significant decreases in seedling height both in Zn-deficient and sufficient soil, but more clearly under water-limited soil condition. Decrease in seed germination due to low seed Zn was also more evident under limited water supply. Increasing seed Zn concentration significantly restored impairments in seedling development. Drought-induced decrease in seedling growth at a given seed Zn concentration was much higher when soil was Zn-deficient. Increasing seed Zn concentration also significantly improved SOD activity in seedlings grown under low Zn supply, but not under adequate Zn supply. The results suggest that using Zn-biofortified seeds assures better seed vigor and seedling growth, particularly when Zn and water are limited in the growth medium. The role of a higher antioxidative potential (          i.e., higher SOD activity) is discussed as a possible major factor in better germination and development of seedlings resulting from Zn-biofortified seeds.

8 QTL mapping for seedling morphology under drought stress in wheat cross synthetic (W7984)/Opata

Drought stress ‘particularly at seedling stage’ causes morpho-physiological differences in wheat which are crucial for its survival and adaptability. In the present study, 209 recombinant inbred lines (RILs) from synthetic wheat (W7984)× ‘Opata’ (also known as SynOpRIL) population were investigated under well-watered and water-limited conditions to identify quantitative trait loci (QTL) for morphological traits at seedling stage. Analysis of variance revealed significant differences (P < 0.01) among RILs, and water treatments for all traits with moderate to high broad sense heritability. Pearson's coefficient of correlation revealed positive correlation among all traits except dry root weight that showed poor correlation with fresh shoot weight (FSW) under water-limited conditions. A high-density linkage map was constructed with 2639 genotyping-by-sequencing markers and covering 5047 cM with an average marker density of 2 markers/cM. Composite interval mapping identified 16 QTL distributed over nine chromosomes, of which six were identified under well-watered and 10 in water-limited conditions. These QTL explained from 4 to 59% of the phenotypic variance. Six QTL were identified on chromosome 7B; three for shoot length under water-limited conditions (QSL.nust-7B) at 64, 104 and 221 cM, two for fresh root weight (QFRW.nust-7B) at 124 and 128 cM, and one for root length (QRL.nust-7B) at 122 cM positions. QFSW.nust-7B appeared to be the most significant QTL explaining 59% of the phenotypic variance and also associated with FSW at well-watered conditions. These QTL could serve as target regions for candidate gene discovery and marker-assisted selection in wheat breeding.

9 The wheat multidomain cystatin TaMDC1 displays antifungal, antibacterial, and insecticidal activities in planta

Cystatins are the polypeptides with cysteine proteinase inhibitory activities. Plant cystatins or phytocystatins are known to contribute to plant resistance against insect pests. Recently, increasing data proved that some of the phytocystatins also have antifungal activities in vitro. Here, we functionally characterized a wheat multidomain cystatin, TaMDC1, using in planta assays. Expression of           TaMDC1 in wheat seedlings is up-regulated in response to methyl jasmonate and salicylic acid, indicating that TaMDC1 is involved in biotic stress responses mediated by these plant hormones. The           TaMDC1 cDNA was integrated in tomato genome and expressed under cauliflower mosaic virus 35S promoter. Four transgenic plants that show high level of the transgene expression were selected by RNA gel blot and immunoblot analysis and utilized to assess biotic stress resistance against the bacterial pathogen           Pseudomonas syringae, the fungal pathogens           Botrytis cinerea and           Alternaria alternata, and the insect pest Colorado potato beetle (CPB,           Leptinotarsa decemlineata). Detached leaf inoculation assays revealed that the tomato plants expressing TaMDC1 showed high levels of resistance against           P. syringae and           A. alternata, and elevated tolerance against           B. cinerea. Sustenance of           L. decemlineata larvae to the transgenic plants demonstrated inhibition of CPB larvae growth. Inhibitory activity of TaMDC1 against selected pathogens was also demonstrated by in vitro assays with total protein extracted from transgenic tomato plants. Taken together, the presented data suggest that TaMDC1 is involved in a broad spectrum biotic stress resistance in planta.

10 Identification and validation of a major chromosome region for high grain number per spike under meiotic stage water stress in wheat (        Triticum aestivum L.)

Grain number is a major trait for wheat yield under dryland farming. An International Triticeae Mapping Initiative (ITMI) mapping population comprising 105 recombinant inbred lines (RIL) developed from a cross between a Synthetic hexaploid wheat (          Triticum aestivum) ‘W7984’ and a spring wheat variety ‘Opata M85’ was used to identify quantitative trait loci (QTL) associated with grain number per spike under two treatment conditions, normal watering and water stress during meiosis. Two major QTL for grain number per spike on the main stem           Q.          Gnu.          uwa-5A-1and           Q.          Gnu.          uwa-5A-2 with phenotypic variations of 25.71% and 24.93%, respectively, were detected on the long arm of chromosome 5A when plants were exposed to water stress during meiosis. One QTL (          Q.          Gnu.          uwa-2A) with a LOD score of 2.8 was detected on the long arm of chromosome 2A under normal watering condition. The alleles associated with higher grain number per spike under different treatment conditions came from the Synthetic W7984 parent. Two populations developed from crosses Synthetic W7984 × Lang and Synthetic W7984 × Westonia were used to validate the identified QTL under water stress during meiosis. SSR markers Xbarc230 and Xbarc319 linked with the identified QTL on chromosome 5AL were validated in the two F2:4 segregating populations. These closely linked SSR markers could potentially be utilized in marker-assisted selection to reduce yield loss in regions where water stress during meiosis occurs frequently. The identified QTL can be incorporated into elite lines / cultivars to improve wheat grain yield.

11 The impacts of phosphorus deficiency on the photosynthetic electron transport chain

Phosphorus (P) is an essential macronutrient, and P deficiency limits plant productivity. Recent work showed that P deficiency affects electron transport to photosystem I (PSI), but the underlying mechanisms are unknown. Here, we present a comprehensive biological model describing how P deficiency disrupts the photosynthetic machinery and the electron transport chain through a series of sequential events in barley (Hordeum vulgare). Phosphorus deficiency reduces the orthophosphate (Pi) concentration in the chloroplast stroma to levels that inhibit ATP synthase activity. Consequently, protons accumulate in the thylakoids and cause lumen acidification, which inhibits linear electron flow. Limited plastoquinol (PQH2) oxidation retards electron transport to the cytochrome (Cyt) b6f complex, yet the electron transfer rate of PSI is increased under steady-state growth light and is limited under high light conditions. Under P deficiency, the enhanced electron flow through PSI increases the levels of NADPH, whereas ATP production remains restricted and hence reduces CO2 fixation. In parallel, lumen acidification activates the qE component of the non-photochemical quenching (NPQ) mechanism and prevents over-excitation of photosystem II (PSII) and damage to the leaf tissue. Consequently, plants can be severely affected by P deficiency for weeks without displaying any visual leaf symptoms. All of the processes in the photosynthetic machinery influenced by P deficiency appear to be fully reversible and can be restored in less than 60 min after resupply of Pi to the leaf tissue.

12 Differential Expression Profiling of Microspores During the Early Stages of Isolated Microspore Culture Using the Responsive Barley Cultivar Gobernadora

In barley, it is possible to induce embryogenesis in the haploid and uninucleate microspore to obtain a diploid plant that is perfectly homozygous. To change developmental fates in this fashion, microspores need to engage in cellular de-differentiation, interrupting the pollen formation, and restore totipotency prior to engaging in embryogenesis. In this work, we used the barley cultivar Gobernadora to characterize the transcriptome of microspores prior to (day 0) and immediately after (days 2 and 5) the application of a stress pretreatment. A deep RNA-seq analysis revealed that microspores at these three time points exhibit a transcriptome of ~14k genes, ~90% of which were shared. An expression analysis identified a total of 3,382 differentially expressed genes (DEGs); of these, 2,155 and 2,281 DEGs were respectively identified when contrasting expression at days 0 and 2 and at days 2 and 5. These define 8 expression profiles in which DEGs share a common up- or down-regulation at these time points. Up-regulation of numerous glutathione S-transferase and heat shock protein genes as well as down-regulation of ribosomal subunit protein genes was observed between days 0 and 2. The transition from microspores to developing embryos (days 2 vs 5) was marked by the induction of transcription factor genes known to play important roles in early embryogenesis, numerous genes involved in hormone biosynthesis and plant hormonal signal transduction in addition to genes involved in secondary metabolism. This work sheds light on transcriptional changes accompanying an important developmental shift and provides candidate biomarkers for embryogenesis in barley.

13 Targeted resequencing reveals genomic signatures of barley domestication

DOI: 10.1111/nph.15077

  • Barley (              Hordeum vulgare) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear.

  • To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci.

  • We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes were descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts.

  • These findings provided the first molecular evidence implicating multiple wild or protodomesticated lineages in the process of barley domestication initiated in the Levantine and Zagros clusters of the origin of agriculture.

14 Transcriptome Analysis of a Premature Leaf Senescence Mutant of Common Wheat (        Triticum aestivum L.)

Leaf senescence is an important agronomic trait that affects both crop yield and quality. In this study, we characterized a premature leaf senescence mutant of wheat (          Triticum aestivum L.) obtained by ethylmethane sulfonate (EMS) mutagenesis, named           m68. Genetic analysis showed that the leaf senescence phenotype of           m68 is controlled by a single recessive nuclear gene. We compared the transcriptome of wheat leaves between the wild type (WT) and the           m68 mutant at four time points. Differentially expressed gene (DEG) analysis revealed many genes that were closely related to senescence genes. Gene Ontology (GO) enrichment analysis suggested that transcription factors and protein transport genes might function in the beginning of leaf senescence, while genes that were associated with chlorophyll and carbon metabolism might function in the later stage. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the genes that are involved in plant hormone signal transduction were significantly enriched. Through expression pattern clustering of DEGs, we identified 1012 genes that were induced during senescence, and we found that the           WRKY family and zinc finger transcription factors might be more important than other transcription factors in the early stage of leaf senescence. These results will not only support further gene cloning and functional analysis of           m68, but also facilitate the study of leaf senescence in wheat.

15 Transcriptome Analysis Identifies a 140 kb Region of Chromosome 3B Containing Genes Specific to Fusarium Head Blight Resistance in Wheat

Fusarium head blight (FHB), mainly caused by           Fusarium graminearum, is one of the most destructive fungal diseases of wheat (          Triticum aestivum L.). Because of the quantitative nature of FHB resistance, its mechanism is poorly understood. We conducted a comparative transcriptome analysis to identify genes that are differentially expressed in FHB-resistant and FHB-susceptible wheat lines grown under field conditions for various periods after           F. graminearum infection and determined the chromosomal distribution of the differentially expressed genes (DEGs). For each line, the expression in the spike (which exhibits symptoms in the infected plants) was compared with that in the flag leaves (which do not exhibit symptoms in the infected plants). We identified an island of 53 constitutive DEGs in a 140 kb region with high homology to the           FhbL693b region on chromosome 3B. Of these genes, 13 were assigned to specific chloroplast-related pathways. Furthermore, one gene encoded inositol monophosphate (IMPa) and two genes encoded ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Our findings suggest that the temporary susceptibility in locally infected spikes results from the cross-talk between RuBisCO and IMPa, which blocks secondary signaling pathways mediated by salicylic acid and induces a systemic acquired resistance in the distant leaf tissue.

16 Effects of water deficit on breadmaking quality and storage protein compositions in bread wheat (Triticum aestivum L.)

DOI: 10.1002/jsfa.8968

Water deficiency produced a shorten grain-filling period and a decrease in grain number, grain weight and grain yield, a reduced starch granule; increased protein content and glutenin macropolymer contents, resulting in superior dough properties and breadmaking quality. Reversed-phase ultra-performance liquid chromatography analysis showed that the total gliadin and glutenin content as well as the accumulation of individual composition were significantly increased by water deficiency. Two-dimensional gel electrophoresis detected 144 individual storage protein spots with significant accumulation changes in developing grains under water deficit. The comparative proteomics analysis revealed that water deficiency resulted in significant upregulation of 12 gliadins, 12 HMW-GSs, and 46 LMW-GSs. Quantitative real-time polymerase chain reaction analysis revealed that the expression of two storage protein biosynthesis related transcription factors           Dof and           Spa was upregulated by water deficiency.




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