Transcriptome analysis of postharvest blueberries (Vaccinium corymbosum ‘Duke’) in response to cold stress

Abstract

Background: Blueberry (Vaccinium spp.) is a small berry with high economic value. Although cold storage can extend the storage time of blueberry to more than 60 days, it leads to chilling injury (CI) displaying as pedicle pits; and the samples of 0°C-30 days was the critical point of CI. However, little is known about the mechanism and the molecular basis response to cold stress in blueberry have not been explained definitely. To comprehensively reveal the CI mechanisms in response to cold stress, we performed high-throughput RNA Seq analysis to investigate the gene regulation network in 0d (control) and 30d chilled blueberry. At the same time, the pitting and decay rate, electrolyte leakage (EL), malondialdehyde (MDA) proline content and GSH content were measured. Results: Two cDNA libraries from 0d (control) and 30d chilled samples were constructed and sequenced, generating a total of 35,060 unigenes with an N50 length of 1348 bp. Of these, 1852 were differentially expressed, with 1167 upregulated and 685 downregulated. Forty-five cold-induced transcription factor (TF) families containing 1023 TFs were identified. The DEGs indicated biological processes such as stress responses; cell wall metabolism; abscisic acid, gibberellin, membrane lipid, energy metabolism, cellular components, and molecular functions were significantly responsed to cold storage. The transcriptional level of 40 DEGs were verified by qRT-PCR. Conclusions: The postharvest cold storage leads serious CI in blueberry, which substantially decreases the quality, storability and consumer acceptance. The MDA content, proline content, EL increased and the GSH content decreased in this chilled process. The biological processes such as stress responses, hormone metabolic processes were significantly affected by CI. Overall, the results obtained here are valuable for preventing CI under cold storage and could help to perfect the lack of the genetic information of non-model plant species.

De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

“…The data presented here revealed that cell, cell part, intracellular, membrane-bound organelle part, cellular and metabolic processes, and catalytic activity were the most represented GO categories within the assembled unigene set ( Fig 2 ). These categories were strongly represented in other studies of ‘Bluecrop’ [ 45 , 46 ] as well as in studies of the cultivars ‘Northland’ [ 24 ], ‘O’Neal’ [ 21 ] and ‘Duke’ [ 26 ]. The vast majority of factors affecting post-harvest quality are under strong genetic control [ 47 ] and ‘Bluecrop’ and ‘Legacy’ previously displayed significant differences in their response to prolonged periods of low-temperature post-harvest storage [ 7 ], resulting in very different post-storage texture profiles of the two cultivars.…”

“…The vast majority of factors affecting post-harvest quality are under strong genetic control [ 47 ] and ‘Bluecrop’ and ‘Legacy’ previously displayed significant differences in their response to prolonged periods of low-temperature post-harvest storage [ 7 ], resulting in very different post-storage texture profiles of the two cultivars. A recent study of Zhang et al, 2020 [ 26 ] used the cultivar ‘Duke’ which previously displayed texture characteristics very similar to ‘Legacy’ [ 7 ] at harvest, but which displayed a significant decline in texture during post-harvest storage. The analysis of differentially expressed genes in ‘Duke’ identified 1,167 upregulated, and 685 down-regulated genes following 30 days storage at 0°C, which contrasted to the 2,370 down-regulated and 937 up-regulated, and 1,379 down-regulated and 542 up-regulated genes in ‘Bluecrop’ and ‘Legacy’ respectively following 21 days storage at 4°C and three days at 18°C in this study.…”

“…Validation by RT-qPCR has been used widely in transcriptomic studies of horticultural species to confirm the reliability of RNAseq data [ 26 , 48 , 49 ]. In this investigation, primer pairs were designed for four candidate genes of interest and successfully validated the RNAseq results obtained, revealing a highly significant correlation between gene expression profiles obtained by RNAseq and RT-qPCR analysis, and giving confidence in the RNASeq dataset as a whole.…”

“…Furthermore, most of the DEGs identified between harvest and post-harvest between both cultivars were putatively involved in cell wall metabolism, composition of the skin wax layer, adaptation to abiotic stress and solute transport. Zhang et al, 2020 [ 26 ] found membrane lipid metabolism, proline, glutathione and flavonoid metabolism, and hormone biosynthesis and signal transduction as the main pathways in which genes were differentially expressed in ‘Duke’, during storage at 0°C. Whilst many of the categories of DEGs observed were similar between the two studies, the differences observed in gene expression profiles between those reported here for ‘Bluecrop’ and ‘Legacy’, and those reported for ‘Duke’ most probably reflect the differences in the temperature storage protocols employed and most importantly differences in the point of sampling between the two studies.…”

“…These include a study of blueberry root tissue samples with differing tolerance to soil pH changes [ 23 ], the identification of genes regulating the anthocyanin content of blueberry fruit during ripening [ 24 ], and genes associated with changes in fruit firmness during ripening and harvest [ 25 ]. Recently, Zhang et al, 2020 [ 26 ] reported the analysis of the transcriptome of the blueberry cultivar ‘Duke’ in response to cold-stress. The authors performed RNAseq experiments on fruit of ‘Duke’ at harvest and following 30 days storage at 0 degrees C, as well as several physiological assessments.…”