Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development

Background: Development of the maize (Zea mays L.) female inflorescence (ear) has an important impact on corn yield. However, the molecular mechanisms underlying maize ear development are poorly understood. Results: We profiled and analyzed gene expression of the maize ear at four developmental stages: elongation phase (I), spikelet differentiation phase (II), floret primordium differentiation phase (III), and floret organ differentiation phase (IV). Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Among the ~6,800 differentially expressed genes (DEGs), 3,325 genes were differentially expressed in stage II, 3,765 genes in III, and 1,698 genes in IV, compared to its previous adjacent stages, respectively. Furthermore, some of DEGs were predicted to be potential candidates in maize ear development, such as AGAMOUS (GRMZM2G052890) and ATFP3 (GRMZM2G155281). Meanwhile, some genes were well-known annotated to the mutants during maize inflorescence development such as compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). Some DEGs were predicted targets of microRNAs such as microRNA156. K-means clustering revealed that the DEGs showed 18 major expression patterns. Thirteen transcriptional factors from 10 families were differentially expressed across three comparisons of adjacent stages (II vs. I, III vs. II, IV vs. III). Antisense transcripts were widespread during all four stages, and might play important roles in maize ear development. Finally, we randomly selected 32 DEGs to validate their expression patterns using quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The results were consistent with those from Solexa sequencing. Conclusions: DEGs technique had shown an advantage in detecting candidates, and some transcription factors during maize ear development. RT-PCR data were consistent with our sequencing data and supplied additional information on ear developmental processes. These results provide a molecular foundation for future research on maize ear development

The Impact of Genetic Relationship and Linkage Disequilibrium on Genomic Selection

Genomic selection is a promising research area due to its practical application in breeding. In this study, impact of realized genetic relationship and linkage disequilibrium (LD) on marker density and training population size required was investigated and their impact on practical application was further discussed. This study is based on experimental data of two populations derived from the same two founder lines (B73, Mo17). Two populations were genotyped with different marker sets at different density: IBM Syn4 and IBM Syn10. A high-density marker set in Syn10 was imputed into the Syn4 population with low marker density. Seven different prediction scenarios were carried out with a random regression best linear unbiased prediction (RR-BLUP) model. The result showed that the closer the real genetic relationship between training and validation population, the fewer markers were required to reach a good prediction accuracy. Taken the short-term cost for consideration, relationship information is more valuable than LD information. Meanwhile, the result indicated that accuracies based on high LD between QTL and markers were more stable over generations, thus LD information would provide more robust prediction capacity in practical applications

Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

Background In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages. Results We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed. Conclusions This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded similar to 0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of similar to 81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs

Depth-profiling of ionic distributions at cathode/liquid electrolyte interfaces in lithium-ion batteries using neutron reflectometry

identifier:oai:t2r2.star.titech.ac.jp:5068139

Depth-profiling of ionic distributions at cathode/liquid electrolyte interfaces in lithium-ion batteries using neutron reflectometry

identifier:oai:t2r2.star.titech.ac.jp:5068139

Depth-profiling of ionic distributions at cathode/liquid electrolyte interfaces in lithium-ion batteries using neutron reflectometry

identifier:oai:t2r2.star.titech.ac.jp:5068139

Systematic evaluation of TP53 codon 72 polymorphism associated with onset and progression of oral potentially malignant disorders

Abstract Background Recently, a systematic review and meta-analysis demonstrated that overexpression of p53 immunoprotein was significantly associated with progression risk of oral potentially malignant disorders (OPMD). However, the results of investigations on TP53 genetic typing in OPMD were inconsistent and inconclusive. Methods A systematic evaluation was conducted to identify all eligible case–control studies on the association of TP53 codon 72 polymorphism with both onset and progression of OPMD. Results A total of 768 OPMD patients and 1173 healthy individuals were identified from 12 eligible case–control studies on TP53 codon 72 polymorphism OPMD onset. In overall and subgroup analyses, no significantly risk of OPMD onset was observed in the cases for genetic models including allele C vs. G, homozygote CC vs. GG, heterozygote GC vs. GG, dominant GC + CC vs. GG, and recessive CC vs. GG + GC (all P-value of association test > 0.05). Further, a total of 465 OPMD patients and 775 oral squamous cell carcinoma (OSCC) ones were identified from 8 eligible case–control studies on this polymorphism in OPMD progression to OSCC. The analyses revealed that there was also no significantly risk of OPMD progression in the cases for the genetic models (all P-value of association test > 0.05). Conclusion Our data of a pooled-analysis indicates that TP53 codon 72 polymorphism may not act as genetic factor for the risk of OPMD onset and progression. Combined with the conclusion by a systematic review and meta-analysis, we put forward a new opinion that TP53 genetic typing cloud not influence p53 protein expression in OPMD

Additional file 2 of Systematic evaluation of TP53 codon 72 polymorphism associated with onset and progression of oral potentially malignant disorders

Additional file 2: Figure S1. Flow diagram of the study selection process. Figure S2. Begg’s Funnel plots of association between TP53 codon 72 polymorphism with OPMD onset in (A) allele model, (B) heterozygote model, (C) homozygote model, (D) dominant model, (E) recessive model. Figure S3. Begg’s Funnel plots of association between TP53 codon 72 polymorphism with OPMD progression in (A) allele model, (B) heterozygote model, (C) homozygote model, (D) dominant model, (E) recessive model

Additional file 1 of Systematic evaluation of TP53 codon 72 polymorphism associated with onset and progression of oral potentially malignant disorders

Additional file 1: Table S1. Search strategy in literature database