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Comprehensive analysis of differentially expressed genes under salt stress in pear (Pyrus betulaefolia) using RNA-Seq

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Abstract

Pear is one of the most important fruit trees in temperate zones, and is cultivated widely throughout the world. Salt stress affects the normal growth of pear, and further affects fruit yield and quality. Pyrus betulaefolia is a common rootstock in pear orchards, which can improve salt tolerance by grafting pear onto it. However, limited availability of P. betulaefolia genomic information has hindered research on the mechanisms underlying this tolerance. Consequently, we comprehensively analyzed P. betulaefolia salt tolerance using RNA-Seq under NaCl and NaCl + LaCl3 treatments in leaf and root. Based on mapping analyses, 3796 novel transcripts were identified, which contained 18 differentially expressed genes (DEGs). There were 90,752 alternative splicing events identified, with transcription start site and transcription terminal site as the major splicing patterns. In addition, we identified 583 differential expressed exons. A total of 276 DEGs were identified among all six comparisons, and 237 of these were up-regulated and 39 were down-regulated. One DEG (Pbr038831.1) was detected in all treatments, and was up-regulated. All DEGs were divided into three clusters according to hierarchical clustering. Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that 18 DEGs were located in six significantly enriched terms, and specific enriched categories and DEGs were identified for NaCl and NaCl + LaCl3 treatments. All of these enriched genes may be related to salt stress in P. betulaefolia. This transcriptome analysis will provide a rich genetic resource for gene discovery related to salt tolerance in P. betulaefolia and closely related species. The data will serve as an important public information platform to further understanding of the molecular mechanisms involved in salt tolerance in P. betulaefolia.

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Abbreviations

DEG:

Differentially expressed gene

TSS:

Transcription start site

TTS:

Transcription terminal site

PCC:

Pearson’s correlation coefficient

DEU:

Differential exon usage

AEU:

Alternative exon usage

RPKM:

Reads per kilobase per million reads

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

DEE:

Differential expressed exon

CKR:

Control for root

CKL:

Control for leaf

NR:

NaCl treatment for root

NL:

NaCl treatment for leaf

NLR:

NaCl + LaCl3 treatment for root

NLL:

NaCl + LaCl3 treatment for leaf

qRT-PCR:

Quantitative real-time PCR

NUDT4:

Nudix hydrolase homolog 4

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Acknowledgements

This work was supported by the Jiangsu Agriculture Science and Technology Innovation Fund of China [CX(14)5018] and the National Natural Sciences Foundation of China (Grant Nos. 31372051 and 31540052). We also thank Genepioneer Biotechnologies for their help with the bioinformatics analyses.

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  1. Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People’s Republic of China

    Hui Li, Jing Lin, Qing-Song Yang, Xiao-Gang Li & You-Hong Chang

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  1. Hui Li
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  2. Jing Lin
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Li, H., Lin, J., Yang, QS. et al. Comprehensive analysis of differentially expressed genes under salt stress in pear (Pyrus betulaefolia) using RNA-Seq. Plant Growth Regul 82, 409–420 (2017). https://doi.org/10.1007/s10725-017-0266-3

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