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Frontiers of Agricultural Science and Engineering

ISSN 2095-7505

ISSN 2095-977X(Online)

CN 10-1204/S

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Front. Agr. Sci. Eng.    2014, Vol. 1 Issue (3) : 214-222    https://doi.org/10.15302/J-FASE-2014024
RESEARCH ARTICLE
Transcriptome analysis of wheat grain using RNA-Seq
Liu WEI1,Zhihui WU1,Yufeng ZHANG1,Dandan GUO1,Yuzhou XU2,Weixia CHEN1,Haiying ZHOU1,Mingshan YOU2,Baoyun LI1,*()
1. Beijing Key Laboratory of Crop Genetic Improvement,College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
2. Key Laboratory of Crop Heterosis & Utilization, Ministry of Education,College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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Abstract

With the increase in consumer demand, wheat grain quality improvement has become a focus in China and worldwide. Transcriptome analysis is a powerful approach to research grain traits and elucidate their genetic regulation. In this study, two cDNA libraries from the developing grain and leaf-stem components of bread wheat cultivar, Nongda211, were sequenced using Roche/454 technology. There were 1061274 and 1516564 clean reads generated from grain and leaf-stem, respectively. A total of 61393 high-quality unigenes were obtained with an average length of 1456 bp after de novo assembly. The analysis of the 61393 unigenes involved in the biological processes of the grain showed that there were 7355 differentially expressed genes upregulated in the grain library. Gene ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that many transcription products and transcription factors associated with carbohydrate and protein metabolism were abundantly expressed in the grain. These results contribute to excavate genes associated with wheat quality and further study how they interact.
Keywords transcriptome analysis      wheat grain      differentially expressed genes      enrichment analysis     
Corresponding Author(s): Baoyun LI   
Online First Date: 01 December 2014    Issue Date: 27 January 2015
 Cite this article:   
Liu WEI,Zhihui WU,Yufeng ZHANG, et al. Transcriptome analysis of wheat grain using RNA-Seq[J]. Front. Agr. Sci. Eng. , 2014, 1(3): 214-222.
 URL:  
https://academic.hep.com.cn/fase/EN/10.15302/J-FASE-2014024
https://academic.hep.com.cn/fase/EN/Y2014/V1/I3/214
ItemGrainLeaf-stemTotal
Number of raw reads10673371519674-
Number of clean reads10612741516564-
Number of unigenes--61393
Average length of unigenes/bp--1456
N50 of unigenes/bp--1814
N90 of unigenes/bp--750
Min length of unigenes/bp--102
Max length of unigenes/bp--12033
Total length of unigenes/bp--89401619
Tab.1  Statistical summary of cDNA sequences generated using the Roche/454
Number of unigenesPercentage/%
Annotated in Nr5560990.57
Annotated in Nt5578090.85
Annotated in KEGG1187619.34
Annotated in SwissProt4282069.74
Annotated in Pfam4268969.53
Annotated in GO4634575.48
Annotated in KOG2818645.91
Annotated in all databases788312.84
Annotated in at least one database5872495.65
Total unigenes61393-
Tab.2  Annotation statistics of unigenes
Fig.1  Venn diagram showing the genes expressed in seed and leaf-stem tissues. The number indicated the unigenes in different tissues.
Fig.2  Volcano diagram of DEGs. The x-axis indicates the fold change in unigene expression in grain and leaf-stem, and the y-axis indicates the statistical significance of the variance in unigene expression. A larger –log10 (Q-value) indicates that the difference is more significant. The dots in the diagram represent different unigenes. Each unigene is represented by a blue dot if the difference in expression is not significant and by a red dot if the difference is significant.
Fig.3  GO enrichment analysis of upregulated DEGs. The results are summarized in three main categories: biologic process (BP), cellular component (CC) and molecular function (MF). The x-axis indicates GO terms, (the description refer to Appendix D)while the y-axis indicates the number of genes in a category.
Fig.4  KEGG pathway enrichment scatter diagram of upregulated DEGs. Only the top 20 most strongly represented pathways were displayed in the diagram. The degree of KEGG pathway enrichment was represented by an enrichment factor, the Q-value, and the number of unigenes enriched in a KEGG pathway. The enrichment factor indicates the ratio of differential expression unigenes enriched in this pathway to the total number of annotated unigenes in this pathway. The names of the KEGG pathways are listed along the y-axis. The Q-value indicates the corrected P-value, ranging from 0 and 1, and a Q-value closer to 0 indicates more enrichment.
Fig.5  Expression analysis of some upregulated genes via qPCR. (a) Genes associated with wheat storage protein, gliadin and gluten; (b)transcription factors regulating storage protein, WPBF, GAMyb, SPA.
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