Transcriptomic Analyses Reveal Molecular Mechanisms Involved In Growth Vigor Of Rubber Tree Seedlings

High and stable yield of crops is based on the seedlings with growth vigor. The seedlings with growth vigor can not only shorten cultivation time of seedlings, but also increase survival rate of seedlings, therefore cultivating seedlings with growth vigor is key work of seedling breeding. Among various factors affecting seedling growth, seedling genotype is the most important one. Revealing molecular mechanisms underlying seedlings with growth vigor is very important work, which can provide theory basis for cultivating seedlings with growth vigor. In contrast to researches on high-yield,and stress resistance,etc,molecular mechanisms underlying seedlings with growth vigor is very limited, especially in rubber tree. In this study,two rubber tree clones with the same parents, Wenchang 11 (WC 11) and Baoting 3410 (BT 3410) indicating significantly differences on growth vigor, are utilized as materials. The height and girth of one-year old seedling are measured and analyzed;the differently expressed genes between WC 11 and BT 3410 (seedling growth-related genes) are identified based on leaves transcriptome sequencing, assembly and annotation. In addition,annotation,GO, and KEGG of seedling growth-related genes are further analyzed to reveal molecular mechanisms underlying seedlings with growth vigor. The main results are as following:(1) The seedling heights of BT 3410 and WC 11 are separately 353.8 ± 20.2 and 258.6 ± 13.9 centimeter (cm); the seedling girth of BT 3410 and WC 11 are 8.82 ±0.32 and 57 ± 0.21 cm, respectively, indicating that BT 3410 possesses obvious growth vigor in contrast to WC 11.(2) A total of 152,231 unigenes were obtained by assembling high-quality reads from all four rubber tree varieties (RRIM 600, PR 107, BT 3410, and WC 11). The average and N50 lengths of the assembled unigenes are 731 bp and 1193 bp,respectively. Of 152,231 unigenes, 96,971 (?63.69%) indicate homology to the genes or their protein products from all or at least one of seven databases including NCBI Nr and Nt,Pfam,KOG/COG,Swiss-prot,KEGG,and GO. Among 152,231 unigenes,52096 ones are annotated within GO database. Binding, cell, and cellular process are predominant in molecular function, cellular component, and biological process,respectively; a total of 28265 unigenes are annotated within KEGG database. Of annotated KEGG pathways, translation is the biggest one, followed by signal transduction and carbohydrate metabolism; 28773 ones are annotated within KOG database. Of KOG classifications, general function prediction only is most predominant, followed by posttranslational modification, protein turnover, chaperones,signal transduction mechanisms, and translation, ribosomal structure and biogenesis,etc. The aforementioned results indicate that active carbohydrate metabolism and signal transduction occur in rubber tree leaves, which is closely associated with photosynthesis and material transport in leaves.(3) With the assembled 152,231 unigenes as reference transcriptome, the high-quality reads of BT 3410 and WC 11 are separately realigned to the assembled 152,231 unigenes. With a padj < 0.05 as a threshold, 1,066 unigenes (seedling growth-related genes) are identified as the differently expressed genes (DEGs)between BT 3410 and WC 11 using DESeq R software. Compared with WC 11, 588 and 478 were up- or down-regulated in BT 3410, respectively. We randomly selected 30 seedling growth-related genes to validate their expression profiles between BT 3410 and WC 11 using qRT-PCR method, and all seedling growth-related genes were confirmed by qRT-PCR, suggesting that the DEGs identified from RNA-seq data were highly reliable in our study.(4) The seedling growth-related genes are divided into 44 GO terms, and they are significantly enriched in catalytic activity, single-organism process, and metabolic process. In addition, the seedling growth-related genes are divided into 95 KEGG pathways, and -58% seedling growth-related genes are predominant in metabolism.Interestingly, the seedling growth-related genes are significantly enriched in found to be significantly enriched in flavone and flavonol biosynthesis, flavonoid biosynthesis,anthocyanin biosynthesis, linoleic acid metabolism, DDT degradation, and plant-pathogen interaction. Our results might provide new insights into molecular mechanisms underlying growth vigor and weakness of rubber tree seedlings,suggesting that the DEGs involved in enriched GO and KEGG are closely related to growth vigor of rubber tree seedling and play important roles on regulating seedling growth.(5) Consistent with previous results in other species, the genes involved in carbohydrate metabolic process, androgen metabolic process, and oxidation-reduction process were upregulated, whereas some genes underlying defense response were downregulated in BT 3410, which might contribute its seedling growth vigor.