Integrating proteomic and transcriptomic analyses of loquat (Eriobotrya japonica Lindl.) in response to cold stress

Xiaoming Lou; Huakun Wang; Xiaopeng Ni; Zhihong Gao; Shahid Iqbal

doi:10.1016/j.gene.2018.07.022

Integrating proteomic and transcriptomic analyses of loquat (Eriobotrya japonica Lindl.) in response to cold stress

Gene. 2018 Nov 30:677:57-65. doi: 10.1016/j.gene.2018.07.022. Epub 2018 Jul 11.

Authors

Xiaoming Lou¹, Huakun Wang², Xiaopeng Ni³, Zhihong Gao⁴, Shahid Iqbal³

Affiliations

¹ College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, PR China; Suzhou Polytechnic Institute of Agriculture, No.279 Xiyuan Road, Suzhou 215008, PR China.
² Extension Center for Evergreen Fruit Tree of Jiangsu Taihu, No.4 Xijing Road, Suzhou 215107, PR China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, Jiangsu, PR China.
³ College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, PR China.
⁴ College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, PR China. Electronic address: gzh71@njau.edu.cn.

PMID: 30017739
DOI: 10.1016/j.gene.2018.07.022

Abstract

The expression levels of many genes and the related proteins change and regulate physiological and metabolic processes that help the plant survive harsh environmental conditions under cold stress. Damage due to cold and freezing conditions often causes dynamic loss of loquat fruits in cultivated parts of northern China. To illustrate the mechanism of cold tolerance in the loquat, we combined the transcriptomic analysis with isobaric tags for relative and absolute quantification (iTRAQ) and RNA sequencing (RNA-Seq) data from loquat leaves under 4 °C treatment. The results showed 122,081 genes and 1210 differentially expressed genes (DEGs), while only 4582 proteins and 300 differential proteins (DEPs) were identified. Functional annotation and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that metabolic pathways and biosynthesis of secondary metabolites were the two most common pathways in transcriptional and translational processes in this study. Comparison analysis of the transcriptomic and proteomic profiles, only 27 of 3620 genes were found to be shared both in DEGs and DEPs. Further validation with Real-Time Quantitative RT-PCR analysis showed that the genes expression of NADP-dependent D-sorbitol-6-phosphate dehydrogenase, anthocyanin synthase and phenylalanine ammonia-lyase were consistent with the pattern of transcriptome profile, which suggested that these three genes might play vital roles in cold tolerance in loquat.

Keywords: Cold stress; Loquat; Proteome; Transcriptome.

MeSH terms

China
Cold Temperature
Eriobotrya / genetics*
Freezing
Fruit / genetics
Gene Expression Profiling / methods
Gene Expression Regulation, Plant / genetics*
High-Throughput Nucleotide Sequencing / methods
Metabolic Networks and Pathways / genetics
Plant Leaves / genetics
Proteome / genetics*
Proteomics / methods
Sequence Analysis, RNA / methods
Stress, Physiological / genetics*
Transcriptome / genetics*

Substances

Proteome