Suyan Niu

Identification of trait-improving quantitative trait loci for grain yield components from a dent corn inbred line in an advanced backcross BC2F2 population and comparison with its F2:3 population in popcorn

Normal maize germplasm could be used to improve the grain yield of popcorn inbreds. Our first objective was to locate genetic factors associated with trait variation and make first assessment on the efficiency of advanced backcross quantitative trait locus (AB-QTL) analysis for the identification and transfer of favorable QTL alleles for grain yield components from the dent corn inbred. A second objective was to compare the detection of QTL in the BC2F2 population with results using F2:3 lines of the same parents. Two hundred and twenty selected BC2F2 families developed from a cross between Dan232 and an elite popcorn inbred N04 were evaluated for six grain yield components under two environments, and genotyped by means of 170 SSR markers. Using composite interval mapping (CIM), a total of 19 significant QTL were detected. Eighteen QTL had favorable alleles contributed by the dent corn parent Dan232. Sixteen of these favorable QTL alleles were not in the same or near marker intervals with QTL for popping characteristics. Six QTL were also detected in the F2:3 population. Improved N04 could be developed from 210 and 208 families with higher grain weight per plant and/or 100-grain weight, respectively, and 35 families with the same or higher popping expansion volume than N04. In addition, near isogenic lines containing detected QTL (QTL-NILs) for grain weight per plant and/or 100-grain weight could be obtained from 12 families. Our study demonstrated that the AB-QTL method can be applied to identify and manipulate favorable QTL alleles from normal corn inbreds and combine QTL detection and popcorn breeding efficiently.

Discovery of Genes Related to Witches Broom Disease in Paulownia tomentosa × Paulownia fortunei by a De Novo Assembled Transcriptome

In spite of its economic importance, very little molecular genetics and genomic research has been targeted at the family Paulownia spp. The little genetic information on this plant is a big obstacle to studying the mechanisms of its ability to resist Paulownia Witches’ Broom (PaWB) disease. Analysis of the Paulownia transcriptome and its expression profile data are essential to extending the genetic resources on this species, thus will greatly improves our studies on Paulownia. In the current study, we performed the de novo assembly of a transcriptome on P. tomentosa × P. fortunei using the short-read sequencing technology (Illumina). 203,664 unigenes with a mean length of 1,328 bp was obtained. Of these unigenes, 32,976 (30% of all unigenes) containing complete structures were chosen. Eukaryotic clusters of orthologous groups, gene orthology, and the Kyoto Encyclopedia of Genes and Genomes annotations were performed of these unigenes. Genes related to PaWB disease resistance were analyzed in detail. To our knowledge, this is the first study to elucidate the genetic makeup of Paulownia. This transcriptome provides a quick way to understanding Paulownia, increases the number of gene sequences available for further functional genomics studies and provides clues to the identification of potential PaWB disease resistance genes. This study has provided a comprehensive insight into gene expression profiles at different states, which facilitates the study of each gene’s roles in the developmental process and in PaWB disease resistance.

High-throughput sequencing and degradome analysis reveal microRNA differential expression profiles and their targets in Paulownia fortunei

Paulownia fortunei (family Paulowniaceae) is an economically important tree species indigenous to China. Autotetraploid cultivars of P. fortunei have better growth and wood quality than their diploid counterparts. MicroRNAs (miRNAs) play vital regulatory roles in plant growth, development, and biotic and abiotic stress responses by direct cleavage of transcripts, translational repression, or chromatin modification. Although miRNAs have been identified in various plant species, no reports of miRNAs in P. fortunei have been published so far. To study the functions of miRNAs in the autotetraploid P. fortunei, four sequencing libraries from the autotetraploid and its corresponding diploid plants were constructed. 142 conserved miRNAs grouped into 41 families, and 38 novel miRNAs were obtained. Among these miRNAs, 58 were up-regulated and 30 were down-regulated in the autotetraploid relative to the diploid. MiRNA target genes were identified using a degradome sequencing approach and the differently expressed miRNAs and their target genes were validated by real time PCR analysis. To our knowledge, this is the first study to identify conserved and novel miRNAs and their potential targets from diploid and autotetraploid Paulownia plants using high-throughput sequencing and degradome analysis. Our results provide valuable information on P. fortunei miRNAs and their targets, and will help build a foundation for future studies of the biological functions of miRNA-mediated gene regulation in P. fortunei.

Transcriptome/Degradome-Wide Discovery of MicroRNAs and Transcript Targets in Two Paulownia australis Genotypes

MicroRNAs (miRNAs) are involved in plant growth, development, and response to biotic and abiotic stresses. Most of the miRNAs that have been identified in model plants are well characterized, but till now, no reports have previously been published concerning miRNAs in Paulownia australis. In order to investigate miRNA-guided transcript target regulation in P. australis, small RNA libraries from two P. australis (diploids, PA2; and autotetraploids, PA4) genotypes were subjected to Solexa sequencing. As a result, 10,691,271 (PA2) and 10,712,733 (PA4) clean reads were obtained, and 45 conserved miRNAs belonging to 15 families, and 31 potential novel miRNAs candidates were identified. Compared with their expression levels in the PA2 plants, 26 miRNAs were up-regulated and 15 miRNAs were down-regulated in the PA4 plants. The relative expressions of 12 miRNAs were validated by quantitative real-time polymerase chain reaction. Using the degradome approach, 53 transcript targets were identified and annotated based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. These targets were associated with development, stimulus response, metabolism, signaling transduction and biological regulation. Among them, 11 targets, including TCP transcription factors, auxin response factors, squamosa promoter-binding-like proteins, scarecrow-like proteins, L-type lectin-domain containing receptor kinases and zinc finger CCCH domain-containing protein, cleaved by four known miRNA family and two potentially novel miRNAs were found to be involved in regulating plant development, biotic and abiotic stresses. The findings will be helpful to facilitate studies on the functions of miRNAs and their transcript targets in Paulownia.

Plant-Pathogen Interaction-Related MicroRNAs and Their Targets Provide Indicators of Phytoplasma Infection in Paulownia tomentosa × Paulownia fortunei.

Paulownia witches’ broom (PaWB) caused by a phytoplasma, has caused extensive losses in the yields of paulownia timber and resulted in significant economic losses. However, the molecular mechanisms in Paulownia that underlie the phytoplasma stress are poorly characterized. In this study, we use an Illumina platform to sequence four small RNA libraries and four degradome sequencing libraries derived from healthy, PaWB-infected, and PaWB-infected 15 mg·L−1 and 30 mg·L−1 methyl methane sulfonate (MMS)-treated plants. In total, 125 conserved and 118 novel microRNAs (miRNAs) were identified and 33 miRNAs responsive to PaWB disease were discovered. Furthermore, 166 target genes for 18 PaWB disease-related miRNAs were obtained, and found to be involved in plant-pathogen interaction and plant hormone signal transduction metabolic pathways. Eleven miRNAs and target genes responsive to PaWB disease were examined by a quantitative real-time PCR approach. Our findings will contribute to studies on miRNAs and their targets in Paulownia, and provide new insights to further understand plant-phytoplasma interactions.

Transcriptome analysis of the variations between autotetraploid Paulownia tomentosa and its diploid using high-throughput sequencing

Timber properties of autotetraploid Paulownia tomentosa are heritable with whole genome duplication, but the molecular mechanisms for the predominant characteristics remain unclear. To illuminate the genetic basis, high-throughput sequencing technology was used to identify the related unigenes. 2677 unigenes were found to be significantly differentially expressed in autotetraploid P. tomentosa. In total, 30 photosynthesis-related, 21 transcription factor-related, and 22 lignin-related differentially expressed unigenes were detected, and the roles of the peroxidase in lignin biosynthesis, MYB DNA-binding proteins, and WRKY proteins associated with the regulation of relevant hormones are extensively discussed. The results provide transcriptome data that may bring a new perspective to explain the polyploidy mechanism in the long growth cycle of plants and offer some help to the future Paulownia breeding.

Identification and Functional Analysis of MicroRNAs and Their Targets in Platanus acerifolia under Lead (Pb) Stress

MicroRNAs (miRNAs) play important regulatory roles in development and stress responses in plants. Lead (Pb) is a non-essential element that is highly toxic to living organisms. Platanus acerifolia is grown as a street tree in cities throughout temperate regions for its importance in improving the urban ecological environment. MiRNAs that respond to abiotic stresses have been identified in plants; however, until now, the influence of Pb stress on P. acerifolia miRNAs has not been reported. To identify miRNAs and predict their target genes under Pb stress, two small RNA and two degradome libraries were constructed from Pb-treated and Pb-free leaves of P. acerifolia seedlings. After sequencing, 55 known miRNAs and 129 novel miRNAs were obtained, and 104 target genes for the miRNAs were identified by degradome sequencing. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to predict the functions of the targets. The expressions of eight differentially expressed miRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first report about P. acerifolia miRNAs and their target genes under Pb stress. This study has provided data for further research into molecular mechanisms involved in resistance of P. acerifolia to Pb stress.

Identification and dynamic expression profiling of microRNAs and target genes of Paulownia tomentosa in response to Paulownia witches’ broom disease

Paulownia witches’ broom (PaWB) is a disastrous epidemic disease in Paulownia tomentosa trees in many parts of the world. Infected Paulownia tomentosa trees are generally characterized by witches’ brooms, proliferating branches, yellowing and withering leaves, and branch dieback. In previous studies, we found that by treating seedlings with a certain concentration of methyl methanesulphonate (MMS), PaWB could be cured. In this study, three small RNA libraries from healthy, PaWB-infected, and PaWB-infected Paulownia tomentosa treated with MMS were constructed and sequenced by Illumina sequencing and identified approximately 50 conserved and novel microRNAs (miRNAs) in each library. We investigated the expression patterns of the miRNAs in three libraries and found that 20 conserved miRNAs were significantly differently expressed in the comparison (healthy vs. PaWB-infected); nine of these conserved miRNAs were also significantly differently expressed in another comparison (PaWB-infected vs. PaWB-infected MMS-treated). The target genes of these identified miRNAs were found through degradome sequencing platform and functionally annotated. Some of the target genes encoded transcription factors, including auxin response factors, which are known regulators of plant defense responses. Further, we found that the expression levels of some of the miRNA sequences changed in response to MMS treatment and were close to their expression levels in the healthy plantlets. Our results indicate possible roles for Paulownia miRNAs associated with plants infected with PaWB and may provide available information for improving the prevention and treatment of PaWB disease in the future.

Transcriptome sequencing and comparative analysis of diploid and autotetraploid Paulownia australis

Paulownia is a fast-growing tree native to China. It can provide high-quality timber and a green environment for humans and has been planted in many countries. Compared with diploid Paulownia australis, autotetraploid P. australis exhibits predominance in terms of yields, qualities, growth, and resistance to stress. However, the molecular and biological mechanisms of its predominant characteristics are still unclear. We performed paired-end sequencing of the transcriptomes of diploid and autotetraploid P. australis plants using the Illumina/Solexa Genome Analyzer platform and compared changes in the expression of genes after chromosome doubling. We obtained a total of 48,445,468 and 46,437,758 high-quality reads from diploid P. australis (PA2) and autotetraploid P. australis (PA4), respectively. After assembly, 90,881 (PA2) and 88,566 (PA4) unigenes were obtained. The unigenes from both transcriptomes were then assembled into 93,300 all-unigenes, which included 50,892 clusters and 42,408 singletons. The all-unigene sequences were searched against public protein databases (Nr, Nt, Swiss-Prot, KOG, and KEGG) using BLASTX with a cutoff E-value of 10−5. Gene expression levels in the two libraries were compared, and a total of 8851 differentially expressed unigenes were identified. A large number of unigenes were found to be related to carbohydrate and energy metabolism, biosynthesis of cell wall, and stress tolerance. Many of the differentially expressed P. australis genes were attributable to chromosome doubling between the PA2 and PA4 plants. Functional analysis revealed variations in the mechanism of growth and stress resistance between PA2 and PA4.

Transcriptome-Wide Profiling and Expression Analysis of Diploid and Autotetraploid Paulownia tomentosa × Paulownia fortunei under Drought Stress

Paulownia is a fast-growing deciduous hardwood species native to China, which has high ecological and economic value. In an earlier study, we reported ploidy-dependent differences in Paulownia drought tolerance by the microscopic observations of the leaves. Autotetraploid Paulownia has a higher resistance to drought stress than their diploid relatives. In order to obtain genetic information on molecular mechanisms responses of Paulownia plants to drought, Illumina/Solexa Genome sequencing platform was used to de novo assemble the transcriptomes of leaves from diploid and autotetraploid Paulownia tomentosa × Paulownia fortunei seedlings (PTF2 and PTF4 respectively) grown under control conditions and under drought stress and obtained 98,671 nonredundant unigenes. A comparative transcriptome analysis revealed that hundreds of unigenes were predicted to be involved mainly in ROS-scavenging system, amino acid and carbohydrate metabolism, plant hormone biosynthesis and signal transduction, while these unigenes exhibited differential transcript alteration of the two accessions. This study provides a comprehensive map of how P. tomentosa × P. fortunei responds to drought stress at physiological and molecular levels, which may help in understanding the mechanisms involve in water-deficit response and will be useful for further study of drought tolerance in woody plants.