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Different species of fruit trees

Different species of fruit trees


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Different species of fruit trees have very distinct growth cycles, which makes them an important resource for plant biologists. Here, we report a transcriptomic analysis of growth and development in apple rootstocks M.26-6 (M.26) and M.26-10 (M.26-10), which are both highly tolerant to apple scab (AS). For genome-wide expression profiling, we performed RNA-Seq using the Illumina sequencing platform. Transcriptome-wide analyses of expression profiles revealed that several hundred genes were highly expressed during development in either rootstock. These genes encode enzymes involved in photosynthesis, photosystem I and II components, components of the respiratory electron transport chain, cell cycle regulation, cell wall-related proteins, and defense-related proteins. In contrast, transcripts encoding enzymes related to hormone and sugar metabolism, transcription factors, and genes involved in secondary metabolism were expressed at low levels during development in both rootstocks. Notably, differentially expressed genes were also observed in the roots of M.26 and M.26-10. Our results provide new information on how M.26 and M.26-10 cope with the environment and the resources available to them during the early stages of their life cycle. It will help clarify the mechanism for how scab resistance was acquired and also may help in the development of resistant rootstocks.

Results

RNA-Seq analysis of gene expression in apple rootstocks M.26 and M.26-10 M.26 and M.26-10 (Figure 1A), two widely used rootstocks in Chinese apple orchards, exhibit very different scab resistance (Rajkumar et al., 2007). M.26 is considered to be highly resistant and is commonly used to develop scab-resistant apple rootstock clones (Rajkumar et al., 2007). M.26-10 is also resistant to scab, but is reported to be more scab-susceptible than M.26 (Rajkumar et al., 2007). Scab-resistant M.26 and scab-susceptible M.26-10 share a close genetic relationship (Wang et al., 2007).

To gain insight into the molecular mechanisms involved in this scab resistance, M.26 and M.26-10 (Table 1) were selected for transcriptome analysis by RNA-Seq using the Illumina platform. The expression of 27,966 genes in M.26 was compared to that of M.26-10 during the developmental stages of seedling (1–4 weeks), early fruiting (5–10 weeks), late fruiting (15 weeks), and in apple fruit (20 weeks). Only four genes were expressed at higher levels in M.26 than in M.26-10 (Table 2).

The apple genome, along with the expressed sequences from the two selected scab-resistant (M.26) and scab-susceptible (M.26-10) apple rootstocks, were compared for gene expression profiles, using the two-stage corrected t-test, to identify the DEGs. DEGs between M.26 and M.26-10 rootstocks were then compared to identify the genes that were DE in both rootstocks (Figure 3). This comparison of the M.26 and M.26-10 transcriptomes identified 932 genes that were DE (Table 3). Mapping of these genes to the apple genome showed that 564 DEGs were located on the A genome of the apple genome. This was compared with the other 248 genes located on the B genome of the apple genome. Interestingly, only 27 of these genes were common to both the B and A genomes, whereas there were a total of 337 genes on the B genome and 519 on the A genome. The genes from the B genome may not have played a significant role in this resistance, therefore indicating that scab resistance in this rootstock is largely controlled by the A genome. Of the 932 DEGs, 534 of the DEGs were highly expressed, with expression levels higher in M.26 than in M.26-10, and 428 genes were less expressed in M.26 than in M.26-10. It is interesting to note that of the 932 DEGs, only 4.3% (40 genes) had expression levels lower in the resistant rootstock M.26 compared to the susceptible rootstock M.26-10.

Table 3. DEGs between M.26 and M.26-10.

DEGs mapped to genome A of apple. The 564 DEGs mapped to the A genome and the remaining 372 DEGs mapped to the B genome.

Of the 564 DEGs, 41 were up-regulated and 523 were down-regulated in M.26 compared with M.26-10. Of the up-regulated DEGs, 35 were expressed higher in M.26 than in M.26-10 and 7 DEGs were expressed higher in M.26-10 than in M.26. Of the down-regulated DEGs, 472 were expressed higher in M.26-10 than in M.26 and 11 DEGs were expressed higher in M.26 than in M.26-10. Among the up-regulated DEGs, three encoded disease resistance proteins with nucleotide-binding site and leucine-rich repeat (NBS-LRR) domain and one encoded putative leucine-rich repeat (LRR) receptor-like serine/threonine-protein kinase. The up-regulated DEGs were mapped to 16 QTLs and 7 were involved in salicylic acid-mediated signalling. Of the down-regulated DEGs, 12 encoded enzymes involved in secondary metabolite biosynthesis, including 5 genes involved in the anthocyanin biosynthesis pathway.

Of the 372 DEGs mapping to the A genome, 6 DEGs were up-regulated and 366 were down-regulated in M.26 compared with M.26-10. Among the up-regulated DEGs, seven encoded proteins with RNA binding activity and two encoded ribosome-associated proteins. Most down-regulated DEGs (354) encoded proteins involved in the biosynthesis of phenylpropanoids, secondary metabolites, including flavonoid and phenylpropanoid biosynthesis.

Of the 976 DEGs, 39 were up-regulated and 937 were down-regulated in M.26-10 compared with M.26. Among the up-regulated DEGs, six encoded proteins involved in cell wall synthesis. Of the down-regulated DEGs, 974 encoded proteins with catalytic activity and three DEGs encoded ribosomal proteins.

3. Discussion {#sec3-ijms-19-02440}

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3.1. DEGs Involved in Tolerance to Alkali Stress {#sec3dot1-ijms-19-02440}

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The primary difference in the responses to alkali stress between M.26-10 and M.26 is that the former showed less tolerance and higher mortality compared with the latter. It seems to be logical that the up-regulation of protein-coding genes of ABA signal transduction pathways and stress-related genes in M.26-10 would cause more severe reactions to NaHCO~3~-induced alkali stress, thus inducing alkali stress-related responses and causing greater mortality in M.26. Alkali stress induced significant up-regulation of *ERF*s (*ERF102*, *ERF113* and *ERF1*), which encodes a key transcription factor involved in the ABA signal transduction pathway, suggesting that the ABA signalling pathway is activated in M.26-



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