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

• Published in: Gene Vol. 677; pp. 57 - 65
• Main Authors: Lou, Xiaoming, Wang, Huakun, Ni, Xiaopeng, Gao, Zhihong, Iqbal, Shahid
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.11.2018
• Subjects: anthocyanins; biochemical pathways; biosynthesis; China; Cold stress; cold tolerance; environmental factors; Eriobotrya japonica; freezing; fruits; genes; leaves; Loquat; loquats; phenylalanine ammonia-lyase; proteins; Proteome; proteomics; reverse transcriptase polymerase chain reaction; secondary metabolites; sequence analysis; sorbitol-6-phosphate 2-dehydrogenase; transcription (genetics); Transcriptome; transcriptomics; China; NR; NT; ANS; COGs; Transcriptome; GO; Proteome; CTAB; BLASTx; CHS; LC-MS/MS; DEGs; CV; Cold stress; RNA-Seq; NCBI; iTRAQ; KEGG; RBH; S6PDH; PAL; DEPs; Loquat
• ISSN: 0378-1119; 1879-0038; 1879-0038
• DOI: 10.1016/j.gene.2018.07.022

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. •Low correlation between transcriptomic and proteomic data sets.•Metabolic pathways and biosynthesis of secondary metabolites were two top common pathways.•S6PDH, ANS and PAL are the key candidate genes that might play vital roles in cold tolerance in loquat.