Cheng Qin

Arizona State University | ASU

This study aimed to enhance the use of male sterility in pepper to select superior hybrid generations. Transcriptomic and proteomic analyses of fertile line 1933A and nucleic male sterility line 1933B of Capsicum annuum L. were performed to identify male sterility-related proteins and genes. The phylogenetic tree, physical and chemical characterist...

Ovate family proteins (OFPs) are transcriptional inhibitors that regulate plant growth and development and play important roles in the synthesis of secondary cell walls during pollen development. This study identified the pepper OFP gene family based on the genome-wide analysis and used bioinformatics methods to provide a fundamental profile of the...

The Na⁺/H⁺ exchangers (NHXs) are a class of transporters involved in ion balance during plant growth and abiotic stress. We performed systematic bioinformatic identification and expression-characteristic analysis of CaNHX genes in pepper to provide a theoretical basis for pepper breeding and practical production. At the whole-genome level, the memb...

In this paper, an efficient approach to extract total flavonoids (TFs) from Selaginella involvens (Sw.) Spring using homogenate-ultrasound-assisted ionic liquid (IL) extraction (HUA-ILE) was first developed. The results indicated that EPyBF4 was selected as the suitable extractant. According to the single factor experiment and response surface meth...

In the study, four main biflavonoids (bilobetin (BIL), ginkgetin (GIN), isoginkgetin (IGIN) and sciadopitysin (SCI)) were extracted from Ginkgo biloba L. by ultrasonic‐assisted ionic liquid extraction (UAILE). The above four biflavonoids from Ginkgo biloba L. were simultaneously determined by the established high performance liquid chromatography (...

Plant-specific SnRK2 (sucrose nonfermenting-1-related protein kinase 2) genes play crucial roles in the coordination of plant growth and development and responses to stress. However, comprehensive studies have not been performed for this gene family in pepper (Capsicum annuum), a very important Solanaceous vegetable worldwide. To fully understand t...

A new N-containing phenolic glycoside (1) and seven known compounds were isolated from the fruits of Capsicum annuum L. Their structures were elucidated by extensive spectroscopic methods including MS, 1D and 2D NMR (HSQC, HMBC, ¹H-¹H COSY, etc.). The stereo configuration of the new compound was determined by comparison of the experimental and calc...

The microRNA (miRNA) can regulate the transcripts that are involved in eukaryotic cell proliferation, differentiation, and metabolism. Especially for plants, our understanding of miRNA targets, is still limited. Early attempts of prediction on sequence alignments have been plagued by enormous false positives. It is helpful to improve target predict...

The development and application of single nucleotide polymorphisms (SNPs) is in its infancy for pepper. Here, a set of 15,000 SNPs were chosen from the resequencing data to develop an array for pepper with 12,720 loci being ultimately synthesized. Of these, 8,199 (~64.46%) SNPs were found to be scorable and covered ~81.18% of the whole genome. With...

Nitrogen (N) deprivation or excess can lead to dramatic phenotype change, disrupt important biological processes, and ultimately limit plant productivity. To explore genes in Tibetan hulless barley responsive to varied N stress, we utilized a comparative transcriptomics method to investigate gene expression patterns under three nitrate treatments....

Pearson's correlation analysis of the RNA-Seq data.

Common differentially expressed genes (DEGs) and their expression profile between free- (FN) vs. optimal- (ON) nitrate and low-nitrate (LN) vs. ON comparisons.

Cross-comparison of pathway annotation of differentially expressed genes (DEGs) in response to N stress.

Primers for the qPCR assays of the eight RNA-Seq libraries used in this study.

Correlation between RNA-Seq and qPCR data. Each RNA-Seq expression data result was plotted against that from qPCR and fitted into a linear regression. Both x- and y-axes are shown in a log2 scale and each color represents a different gene.

Summary of mapping rate and gene expression statistics based on the RNA-Seq data.

Differentially expressed genes (DEGs) in response to N stress in Tibetan hulless barley.

Venn diagrams of differentially expressed genes (DEGs) in response to varied N stress.

Functional annotation and enrichment analysis of common differentially expressed genes (DEGs) between free- (FN) vs. optimal- (ON) nitrate and low-nitrate (LN) vs. ON comparisons. (A) Clustering and heat maps of common DEGs based on the expression profiles. (B) KEGG pathway analysis of common DEGs.

Summary of sequencing data quality for Tibetan hulless barley.

GO annotation of differentially expressed genes in response to N stress in Tibetan hulless barley.

KEGG analysis of differentially expressed genes in Tibetan hulless barley responsive to N stress.

Dof (DNA-binding One Zinc Finger) transcription factor family is unique to plants and has diverse roles associated with plant-specific phenomena, such as light, phytohormone and defense responses as well as seed development and germination. Although, genome-wide analysis of this family has been performed in many species, information regarding Dof g...

RNA-Seq RPKM expression matrix for all primary developmental stages and tissue types of Zunla-1.

Multilevel consensus sequence identified by MEME among CaDof genes in this study.

The amino acid sequences of Dof genes in Arabidopsis (At), rice (Os), and tomatoes (Sl) used in phylogenetic tree construction.

The identified nucleotide and amino acid sequences of pepper Dof genes.

Primers used for qRT-PCR.

The heat map representation of CaDof genes in response to heat and salt stress.

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45....

To safeguard the food supply for the growing human population, it is important to understand and exploit the genetic basis of quantitative traits. Next-generation sequencing technology performs advantageously and effectively in genetic mapping and genome analysis of diverse genetic resources. Hence, we combined re-sequencing technology and a bin ma...

Tobacco (Nicotiana tabacum L.) is an economically important and relatively drought-tolerant crop grown around the world. However, the molecular regulatory mechanisms involved in tobacco root development in response to drought stress are not wellknown. To gain insight into the transcriptome dynamics associated with drought resistance, genome-wide ge...

Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sou...

Bipolaris zeicola is a fungal pathogen that causes Northern corn leaf spot (NCLS), which is a serious foliar disease in maize and one of the most significant pathogens affecting global food security. Here, we report a genome-wide transcriptional profile analysis using next-generation sequencing (NGS) of maize leaf development after inoculation with...

Drought stress response is a complex trait regulated at transcriptional and post-transcriptional levels in tobacco. Since the 1990s, many studies have shown that miRNAs act in many ways to regulate target expression in plant growth, development and stress response. The recent draft genome sequence of Nicotiana benthamiana has provided a framework f...

Two independent pepper (Capsicum annuum) genomes were published recently, opening a new era of molecular genetics research on pepper. However, pepper molecular marker technologies are still mainly focusing on the simple sequence repeats derived from public database or genomic library. The development and application of the third generation marker s...

Plants adapt to adverse conditions through a series of physiological, cellular, and molecular processes, culminating in stress tolerance. However, little is known about the associated regulatory mechanisms at the epigenetic level in maize under lead (Pb) stress. Therefore, in this study, we aimed to compare DNA methylation profiles during the dynam...

MicroRNAs (miRNAs) are post-transcriptional regulators that are involved in numerous biological processes in plants. In this study, we investigate miRNAs in Honghua Dajinyuan, an agronomically important species of tobacco in China. Here, we report a comprehensive analysis of miRNA expression profiles in the leaf, stem and root using a high-throughp...

Heterosis, or hybrid vigor, contributes to superior agronomic performance of hybrids compared to their inbred parents. Despite its importance, little is known about the genetic and molecular basis of heterosis. Early maize ear inflorescences formation affects grain yield, and are thus an excellent model for molecular mechanisms involved in heterosi...

MicroRNAs (miRNAs) play a pivotal role in post-transcriptional regulation of gene expression in plants. In this study, we investigate miRNAs in an agronomically important common tobacco in China, named Honghua Dajinyuan (a drought-tolerant cultivar). Here, we report a comprehensive analysis of miRNA expression profiles in mock-treat grown (CK) and...

Significance The two pepper genomes together with 20 resequencing accessions, including 3 accessions that are classified as semiwild/wild, provide a better understanding of the evolution, domestication, and divergence of various pepper species and ultimately, will enhance future genetic improvement of this important worldwide crop.

Currently, the molecular regulation mechanisms of disease-resistant involved in maize leaf sheaths infected by banded leaf and sheath blight (BLSB) are poorly known. To gain insight into the transcriptome dynamics that are associated with their disease-resistant, genome-wide gene expression profiling was conducted by Solexa sequencing. More than fo...

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, mos...

Cytoplasmic male sterility (CMS), widely used in the production of hybrid seeds, is a maternally inherited trait resulting in a failure to produce functional pollen. In order to identify some specific proteins associated with CMS in pepper, two-dimensional gel electrophoresis (2-DE) was applied to proteomic analysis of anthers/buds between a CMS li...

microRNA (miRNAs) is a newly identified class of 20-24 nt non-protein-coding and endogenous small RNA, which plays an important role in plant growth, development and response to environmental stresses. Combined with bioinformatic method, the types, abundance, and targets of known miRNAs in root and leaf of maize (Zea mays L.) were analyzed by small...