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Sanghuangporus sanghuang (SS) is a rare medicinal polypore fungus that grows solely on Morus trees. In this study, seven grains (oats, barley, millet, rice, buckwheat, corn, and coix seed) were used as solid substrates for SS fermentation and characterized in their nutrition, functional composition, and antioxidant activities. After fermentation, the nutrient compositions of crude protein (F1,41 = 111.1, P F1,41 = 595.7, P F1,41 = 51.4, P F1,41 = 227.3, P ΔT-AOC/ABTS+/DPPH/DNAp, that was correlated to part of changes in polyphenol, carotenoid, triterpenoids, and flavonoid contents. In summary, oats have the greatest potential for use as a fermentation substrate for health food development.

Agricultural straws (AS) may serve as potential base-substances in the production of Agaricus bisporus. Six AS that occur across China were investigated in a two-stage composting experiment; lignocellulose components, AS morphology, and the effects of different AS on mushroom yields from 2015–2017 were examined. In addition, microbial biodiversity and their impact on substrate degradation were studied using 16S gene sequenc based on six different AS on the 3rd (I.F), 6th (I.S), and 10th (I.T) day of Phase I, and Phase II (II). Results showed that the six different AS exhibited differences in the progression of degradation under the same compost condition; the wheat straw, rice straw, and cotton straw induced a significantly higher mushroom yield than did the others (P < 0.05); Thermobispora, Thermopolyspora, and Vulgatibacter genera may play an important role in the different AS degradations. According to our experiments, we can adjust formulations and compost methods to obtain high-yield mushroom compost based on different AS in the future.

Agricultural straws (AS) may serve as potential base-substances in the production of Agaricus bisporus. Six AS that occur across China were investigated in a two-stage composting experiment; lignocellulose components, AS morphology, and the effects of different AS on mushroom yields from 2015–2017 were examined. In addition, microbial biodiversity and their impact on substrate degradation were studied using 16S gene sequenc based on six different AS on the 3rd (I.F), 6th (I.S), and 10th (I.T) day of Phase I, and Phase II (II). Results showed that the six different AS exhibited differences in the progression of degradation under the same compost condition; the wheat straw, rice straw, and cotton straw induced a significantly higher mushroom yield than did the others (P < 0.05); Thermobispora, Thermopolyspora, and Vulgatibacter genera may play an important role in the different AS degradations. According to our experiments, we can adjust formulations and compost methods to obtain high-yield mushroom compost based on different AS in the future.

The Agaricus genus represents the most popular edible mushroom in the world. Wheat straw often is used as the substrate for mushroom cultivation following pretreatment to degrade the lignocellulosic biomass in agricultural waste. In this study, we investigated the changes in bacterial and fungal microflora of wheat straw substrate during different phases of composting. We collected samples of the raw material (M1), phase I aerobic fermentation (F1, F2, F3), and phase II after-fermentation (AF1) for high-throughput 16S rRNA and internal transcribed spacer (ITS) sequencing to analyze the microbial diversity in the substrate during composting. Our data revealed that among the five stages, 365 operational taxonomic units (OTUs) were shared, with Firmicutes, Proteobacteria, and Actinobacteria being the predominant bacterial phyla. In addition, Thermobispora, Thermopolyspora, Ruminiclostridium, Thermobacillus, and Bacillus were the predominant genera in F3 and AF1, with the species Thermobispora bispora and Pseudoxanthomonas taiwanensis being predominant in F2. Both principal component analysis (PCA) and nonmetric multidimensional scaling (NMDS) plots showed that the bacterial communities of five stages could be distinguished from each other based on their composting time. The Shannon and Simpson indexes of F2 were lower than M1 (P < 0.05), and the clustering dendrogram showed that the bacterial communities in AF1 were similar to F3, with Micromonosporaceae, Streptosporaceae, Thermomonosporaceae, and Vulgatibacteraceae representing the differential bacterial families by linear discriminant analysis with effect size (LEfSe) analysis. The analysis of fungal communities showed that 384 OTUs were common among the five stages, with 1054 and 454 OTUs unique to M1 and AF1, respectively. Ascomycota and Basidiomycota were the two predominant phyla in all stages, and Chytridiomycota was predominant in F2, F3, and AF1 stages. PCA and NMDS plots showed that the clusters of F2 and AF1 were more dispersed than the other stages. No differences were observed in alpha diversity between the stages, and samples of F1, F2, and F3 were closer to AF1 in the clustering dendrogram. By LEfSe analysis, Mycothermus thermophilus, Gonapodya polymorpha, and Phaeophleospora_eugeniae were identified as the predominant fungal species in AF1.

In this study, the complete mitochondrial genome of Sanghuangporus vaninii Zhehuang-1 was determined. Genomic DNA samples individually collected from a population in southeastern China (Qiandaohu, ...

BackgroundLight plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. ResultsA total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. ConclusionsOur study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.

Additional file 3: Enriched GO terms of 193 differentially expressed transcripts in CSSL50-1 and Asominori. Enriched GO terms of 193 differentially expressed transcripts detected by Significant Analysis Microarray software (fold change > = 2, q value < = 5%). (DOC 300 KB)

Additional file of Transcriptome analysis of grain-filling caryopses reveals involvement of multiple regulatory pathways in chalky grain formation in rice

Additional file 4: Functional classification of 623 differentially expressed genes between CSSL50-1 and Asominori. Functional classification of 623 differentially expressed genes between CSSL50-1 and Asominori as detected by one-way ANOVA (P value

Additional file 5: Sequence of primers used for RT-PCR. A list of primers used for RT-PCR and the sequence information. (DOC 78 KB)

Rice straw is an important raw material for preparing Agaricus bisporus compost in China, and the size mushroom yield is largely determined by the quality of compost, which in turn is dependent on the microbial processes occurring during composting and the microbial populations inhabiting the mature compost. In this study, we compared the traditional composting method used in China with an aerated tunnel-based composting system through Phase I of the process. Phospholipid fatty acid (PLFA) analysis, used to monitor changes in the respective microbial populations, demonstrated a significant difference in the structure of the microbial communities and bacterial biomass associated with the two compost types. Chemical analysis of the degraded rice straw (RS) revealed that hemicellulose and silicate levels decreased more strongly in the aerated compared than in traditional non-aerated compost. Transmission electron microscopy (TEM), used to assess histological changes occurring in the stem tissue and cell walls of RS subjected to the two composting methods, showed that the aeration treatment resulted in more pronounced effects on stem structure. Composting using the aerated method also facilitated faster mycelial growth rates and higher yields of mushroom fruit bodies. Our data indicated that aeration-assisted composting of RS leads to improved degradation and assimilation of breakdown products by A. bisporus, and suggest that introduction of the process on a commercial scale in China has huge potential.

Rice (Oryza sativa L.) is one of the most important food crops in the world. Most kernel oil and micro-nutrients are located in the embryo whereas starch is mainly in the endosperm. Although embryo size is important for rice grain yield and food processing, little is known about the genetic mechanisms controlling embryo size. We characterized a rice giant embryo mutant, giant embryo (ge), which was derived from wild-type Kinmaze by chemical mutagenesis. The large embryo size resulted from larger cell size. The gene controlling the giant embryo trait was cloned by a map-based approach, and shown to encode cytochrome P450 protein CYP78B5, which was previously designated as CYP78A13. Gain-of-function transgenic experiments on OsGE/CYP78B5 in the ge mutant restored the normal seed phenotype. Expression analysis showed that the OsGE/CYP78B5 gene product accumulated mainly in young developing seeds. Subcellular localization indicated that OsGE/CYP78B5 resides in the peroxisomes, and the N-terminal 51 amino acid residues function as a targeting signal. The IAA levels were one-third those of wild type in GE mutants at 6 days after fertilization, yet the embryonic cells were much larger. OsGE/CYP78B5 also regulates expression levels of auxin-responsive and cyclin-related genes. Isolation of GE provides an opportunity to manipulate the nutritive composition and distribution of the grain by marker-assisted selection and transgenic approaches.

Heading date is a key determinant of regional and seasonal adaptation in rice (Oryza sativa L.). A minor-effect quantitative trait locus (QTL), QTL for D ays t o h eading 12a (qDTH-12a), with unknown genetic action was previously coarsely detected in a recombinant inbred line population. The study reported here was designed to better define the qDTH-12a locus (designated as DTH12) in advanced segregating populations. DTH12 was initially verified in chromosome segment substitution line CSSL84. A CSSL84/Asominori//Asominori BC4F2 population was then developed, and a near-isogenic line (NIL), NIL(DTH12), was subsequently selected from this population using marker-assisted tracking that headed 8 days later than Asominori under long-day (LD) conditions but which was not significantly different in heading date in short-day environments. Using 358 Asominori/NIL(DTH12) F2:3 families grown under LD conditions, we were able to initially map DTH12 to a 26-cM interval between markers InDel12-1 and RM6296. F3 individuals heterozygous for the DTH12 regions were then chosen, and 2,388 F4:5 families were used for fine mapping. DTH12 was finally dissected as a single gene and delimited to a 153-kb genomic region with 32 open reading frames. Compared with Asominori, NIL(DTH12) showed reduced transcription of the florigen genes Heading date 3a and RICE FLOWERING LOCUS T 1, suggesting that DTH12 functions as an up-regulator of florigen genes during floral induction under LD conditions. DTH12 was also found to have an important role in rice adaptation and breeding for precise control of seed maturity. These findings provide a firm basis for cloning this minor-effect QTL involved in rice flowering.

The most important step in the cultivation of Pleurotus pulmonarius under high-temperature conditions is the cold stimulation of mature mycelium. During the summer (>28 °C), fully colonized cultivation bags may be stimulated to uniformly produce a flush mushroom after a certain degree of cold stimulation. The present study assesses the performance of mushroom initiation and yield by cold stimulation of P. pulmonarius . Various combinations of temperature and time were examined in a factorial design, in order to determine the most appropriate cold stimulation temperature treatment. In the experiments, it was shown that the substrate temperature in the bags decreased as the stimulus time increased according to the equation substrate temperature = c + a × e − b ×time , at all four stimulus temperatures covered. The increase in stimulus time enhances ( p P. pulmonarius cultivation during the summer season.

A kinesin-like protein regulates grain length and plant height by affecting expression levels of genes involved in GA synthesis and response in rice Grain shape, a complex agronomic trait, plays an important role in determining yield and quality in rice. In the present study, a mutant named short grain length (sgl) was identified among explants of tissue cultured japonica variety Kita-ake. It exhibited reduced plant height (about 72 % of WT) and short grain length (about 80 % of WT). The reduced length was due to decreased cell elongation. The Short Grain Length (SGL) gene was isolated via map-based cloning and identified to encode a kinesin-like protein. SGL was expressed in the whole plant, especially in the stem and panicles. SGL was shown to have transcriptional activity. In onion epidermal cells, SGL protein was found mainly in the nucleus. Real-time PCR analyses showed that expression levels of genes involved in gibberellin metabolic pathways were affected in the sgl mutant. These data suggested that SGL protein may be involved in regulating GA synthesis and response genes, that in turn, regulates grain length and plant height.

Heat stress is one of the major abiotic stresses that adversely affect growth and yield in Lentinula edodes (Shiitake mushroom) under natural cultivation. In this study, two parental strains (L808 and Lsm9), an F1 strain, and an F2 population derived from their hybrid progeny were used to evaluate the regeneration of mycelia after heat stress. A multi-level heat stress experiment showed that the dynamics of radial mycelium expansion of the two parents followed a linear equation after heat stress treatment at 37°C for 4–24 h, 42°C for 4–16 h, or 45°C for 4 h. Three indices were selected to describe the regeneration ability of the strains, including the number of regeneration days (NRD), the real growth rate after heat stress (Vregeneration), and the regenerative index (RI). L808 presented a faster rate of regeneration, while Lsm9 had better regeneration quality. The phenotype analysis of the F2 population showed that these indices were controlled by multiple genetic factors with high heritability. Four strains were selected from the population, pyramiding the advantages of heat resistance from the two parents. The results will help our understanding of the genetic features of this mushroom after extreme high-temperature stress.

Fat content (FC) is an important component of the nutritional quality of the rice ( Oryza sativa L.) grain and a partial determinant of grain quality. Three FC QTLs were identified from an analysis of a set of rice ‘Kasalath’/‘Koshihikari’ backcross inbred lines, which were grown in three independent environments. Two of these QTLs (qFC7.1 and qFC7.2) were located on chromosome 7, and they were detected in all three environments. The presence of qFC7.1 and qFC7.2 was further confirmed by testing a set of ‘Kasalath’ (donor) / ‘Koshihikari’ (recipient) chromosome segment substitution lines (CSSLs) across six environments. Both QTLs significantly increased grain FC and they might be involved in lipid metabolism. The two QTLs were stably expressed in a number of environments and populations, making them suitable candidates for the improvement of FC via marker assisted breeding.

Rice stripe virus (RSV) is one of the most destructive pathogens of rice (Oryza sativa L.) in East Asia. Development of resistant varieties offers a more economical and efficient way to control this disease. In the present study, tests using four inoculation methods were used on 85 backcross inbred lines of Sasanishiki (japonica)/Habataki (indica) to map quantitative trait loci (QTL) conferring resistance to RSV. One QTL on chromosome 3 and two on chromosome 11 were detected, jointly explaining 18–47 % of the trait variance. The QTL (qSTV11HAB-1 and qSTV11HAB-2) on chromosome 11 were closely linked, and mapped in the intervals G257-RM457 and RM457-RM187, respectively. The stabilities of qSTV11HAB-1 and qSTV11HAB-2 were validated using a set of 38 established chromosome segmental substitution lines. The two QTL, when combined, showed higher resistance than either of them alone in both field and mass inoculation tests, indicating additivity. Fine mapping of the two genes was carried out using 147 recombined F2:3 lines selected from 2,750 secondary F2 plants of the cross Sasanishiki/SL437. Four SSR (simple sequence repeat) and eight InDel (insertion–deletion) markers newly developed to fine-map the two loci. According to the Nipponbare genomic sequence, qSTV11HAB-1 was localized to a 333.2-kb interval which was about 230 kb from the well-known Stvb-i. The other locus, qSTV11HAB-2, which appears to be a new QTL for RSV resistance, was delimited to a 203.9-kb region. Four flanking markers (R15, RM209, R69 and R73) can be used in marker-assisted selection. These results provide an opportunity for map-based cloning of qSTV11HAB-1 and qSTV11HAB-2, thereby promoting the breeding program of RSV resistance.

Rice stripe disease, caused by rice stripe virus (RSV), is one of the most serious diseases in temperate rice-growing areas. In the present study, we performed quantitative trait locus (QTL) analysis for RSV resistance using 98 backcross inbred lines derived from the cross between the highly resistant variety, Kasalath, and the highly susceptible variety, Nipponbare. Under artificial inoculation in the greenhouse, two QTLs for RSV resistance, designated qSTV7 and qSTV11KAS, were detected on chromosomes 7 and 11 respectively, whereas only one QTL was detected in the same location of chromosome 11 under natural inoculation in the field. The stability of qSTV11KAS was validated using 39 established chromosome segment substitution lines. Fine mapping of qSTV11KAS was carried out using 372 BC3F2:3 recombinants and 399 BC3F3:4 lines selected from 7,018 BC3F2 plants of the cross SL-234/Koshihikari. The qSTV11KAS was localized to a 39.2 kb region containing seven annotated genes. The most likely candidate gene, LOC_Os11g30910, is predicted to encode a sulfotransferase domain-containing protein. The predicted protein encoded by the Kasalath allele differs from Nipponbare by a single amino acid substitution and the deletion of two amino acids within the sulfotransferase domain. Marker-resistance association analysis revealed that the markers L104-155 bp and R48-194 bp were highly correlated with RSV resistance in the 148 landrace varieties. These results provide a basis for the cloning of qSTV11KAS, and the markers may be used for molecular breeding of RSV resistant rice varieties. Electronic supplementary material The online version of this article (doi:10.1007/s00122-011-1557-0) contains supplementary material, which is available to authorized users.

Rice stripe is a serious viral disease of japonica rice (Oryza sativa L.) cultivars in Asia. Resistance to this disease can be divided into that to rice stripe virus (RSV) and to the pest (small brown planthopper, SBPH). Here we have used a doubled-haploid (DH) population bred from the cross Zhaiyeqing8 (ZYQ8) x Jingxi17 (JX17) and four separate inoculation methods to genetically dissect the rice stripe resistance present in ZYQ8. Two linked RSV resistance quantitative trait loci (QTLs) were located on chromosome 1, and one on chromosome 11, jointly explaining 30 to 44% of the trait variance. The main-effect qSTV11 was mapped close to the established RSV resistance gene Stvb-i. For resistance to SBPH, three QTLs were located, mapping to chromosomes 1, 2, and 11, and jointly explaining 44 to 51% of the trait variance. The large-effect qSBPH1 appears to be a novel QTL conferring a degree of tolerance and antibiosis against SBPH. The positive alleles at all six QTLs were present in ZYQ8. Analysis of a set of chromosome segment substitution lines (CSSLs) in which chromosomal segments of various indica varieties were present in a japonica background showed that rice stripe resistance genes/QTLs are common on the long arm of chromosome 1.

Fat content (FC) partially determines rice grain quality. The objective of this study was to identify stably expressed quantitative trait loci (QTL) for FC. A total of 85 inbred lines derived from the backcross between Sasanishiki (japonica, as the recurrent parent) and Habataki (indica) were used to detect QTLs for rice fat content. Seven QTLs (denoted as qFC-1, qFC-2, qFC-3, qFC-6, qFC-10, qFC-11, and qFC-12) were detected on chromosomes 1, 2, 3, 6 10, 11, and 12, respectively, using inclusive composite interval mapping (ICIM) method. Among them, three major QTLs (qFC-3, qFC-6, and qFC-11) with large effect were further confirmed across two different environments using some chromosome segment substitution lines (CSSLs), where Habataki was used as the donor parent and Sasanishiki as the recurrent parent. Further experiments showed that one of the major QTLs (qFC-11) could increase fat content, fat index, and grain yield together. To our knowledge, qFC-11 is a newly detected stable QTL that will ...

Fat content (FC) and fat index (FI) play an important role in determining quality of eating and nutrition for rice. The objective of this study was to determine genetic information during the grain-filling period. Seventy-one recombinant inbred lines (RILs) derived from a cross between japonica cultivar Asominori and indica cultivar IR24 were used to analyze the developmental behavior of FC and FI by conditional and unconditional quantitative trait loci (QTL) mapping methods. At four developmental stages of grain filling, 11 unconditional QTL and 10 conditional QTL for FC as well as 11 unconditional QTL and eight conditional QTL for FI were identified. In unconditional QTL analysis, qFC-11-2 and qFI-3 were consistently detected at 21 and 28 days after flowering (DAF), whereas all the conditional QTL for FC and FI could be detected at only one stage. Nine conditional and nine unconditional QTL for FC and FI were detected in the earlier three stages while three and two unconditional QTL for FC and ...

The elongation of the cooked grain determines the cooking and eating quality of Basmati rice. The identification of stable quantitative trait loci (QTLs), especially those from non-Basmati types, will extend the genetic basis of the Basmati type and facilitate the breeding of high-quality varieties. A set of recombinant inbred lines derived from an indica × japonica hybrid was used to identify QTLs controlling the elongation ratio (ER), elongation index (EI), and water absorption (WA) of the cooked grain. Three ER QTLs on chromosomes 2, 4, and 12, two EI QTLs on chromosomes 2 and 5, and two WA QTLs on chromosomes 2 and 6 were detected. Four of these QTLs were validated using a set of established chromosome segment substitution lines. The genetic effect of qER-2 was explored in an analysis of segregating generations, using 8 newly developed simple sequence repeat markers. Two tightly linked loci (qER-2a and qER-2b) were identified on chromosome 2.

Background Grain endosperm chalkiness of rice is a varietal characteristic that negatively affects not only the appearance and milling properties but also the cooking texture and palatability of cooked rice. However, grain chalkiness is a complex quantitative genetic trait and the molecular mechanisms underlying its formation are poorly understood. Results A near-isogenic line CSSL50-1 with high chalkiness was compared with its normal parental line Asominori for grain endosperm chalkiness. Physico-biochemical analyses of ripened grains showed that, compared with Asominori, CSSL50-1 contains higher levels of amylose and 8 DP (degree of polymerization) short-chain amylopectin, but lower medium length 12 DP amylopectin. Transcriptome analysis of 15 DAF (day after flowering) caryopses of the isogenic lines identified 623 differential expressed genes (P < 0.01), among which 324 genes are up-regulated and 299 down-regulated. These genes were classified into 18 major categories, with 65.3% of them belong to six major functional groups: signal transduction, cell rescue/defense, transcription, protein degradation, carbohydrate metabolism and redox homeostasis. Detailed pathway dissection demonstrated that genes involved in sucrose and starch synthesis are up-regulated, whereas those involved in non-starch polysaccharides are down regulated. Several genes involved in oxidoreductive homeostasis were found to have higher expression levels in CSSL50-1 as well, suggesting potential roles of ROS in grain chalkiness formation. Conclusion Extensive gene expression changes were detected during rice grain chalkiness formation. Over half of these differentially expressed genes are implicated in several important categories of genes, including signal transduction, transcription, carbohydrate metabolism and redox homeostasis, suggesting that chalkiness formation involves multiple metabolic and regulatory pathways.