Comparative transcriptomic analysis identifies genes responsible for fruit count and oil yield in the oil tea plant Camellia chekiangoleosa

Abstract

Fruit yield is an important trait for horticultural crops. However, the limited fruit yield of Camellia chekiangoleosa, a novel promising oil tree, restricts the production of oil. The breeding improvement is little due to its long generation time and lack of available genomic sequence. We identified distinct fruit count phenotypes, high-yield (HY) and low-yield (LY). To understand the underlying genetic basis, we focused on global gene discovery and expression levels in floral buds, which affect fruit count. A total of 140,299 de novo assembled unigenes were obtained using RNA-seq technology, and more genes were expressed in HY than in LY. 2395 differentially expressed genes (DEGs) were identified and enriched in membrane, energy metabolism, secondary metabolism, fatty acid biosynthesis and metabolism, and 18 other metabolic pathways. Of the DEGs, twelve identified transcription factors, including AP2, mostly involve in inflorescence and flower development and in hormone networks. Key DEGs in fatty acid biosynthesis (Fab) FabB, FabF, FabZ, and AccD were highly expressed in floral buds and associated with high oil yield in fruits. We hypothesized that a potential link exists between fruit count and its oil yield. These findings help to elucidate the molecular cues affecting fruit count and oil yield.

Figure 1

Camellia chekiangoleosa trees with two distinct fruit yields. Image shows the comparison of the flower count, fruit count and ratio of fruit/flower count. **Represents significance at p < 0.01 by two-way statistical ANOVA analysis.

Figure 2

Distribution of expressed unigenes in two types of Camellia chekiangoleosa. Image a shows the commonly or specifically expressed unigenes. Image b shows the differentially expressed genes (red) with expression changes of more than 2-fold, p < 0.05 and q < 0.001 (hypergeometric test). The fold change was relative to the expression level in the LY type after the log₂(FPKM) calculation. HY and LY represent high and low yields based on fruit count.

Figure 3

Top enriched GO terms of differentially expressed genes. Image shows the top enriched GO terms of the DEGs ranked by the number of genes. Only the top ten up- or down-regulated DEGs in each category (biological process, cellular component and molecular function) are shown.

Figure 4

Key genes differentially regulated in the fatty acid synthesis pathway in C. chekiangoleosa. Image shows the key enzymes encoded by DEGs highlighted in the pink box in the fatty acid synthesis pathway. The heatmap at the bottom right shows the expression levels of the corresponding DEGs in the pathway. LY and HY represent the low-yield and high-yield phenotypes of C. chekiangoleosa. ACC, FabF, FabG and FabB represent the key enzymes acetyl-CoA carboxylase 1 [EC:6.4.1.2], 3-oxoacyl-[acyl-carrier-protein] synthase II [EC:2.3.1.179] (FabF), 3-oxoacyl-[acyl-carrier protein] reductase [EC:1.1.1.100] (FabG), and fatty acyl-ACP thioesterase B [EC:3.1.2.14] (FabB), respectively. ACC-1, -2, and -3 represent three different encoding genes.

Figure 5

Oil yield and expression levels of transcription factors and regulators among the DEGs. Image a shows the oil yield per fruit. Bars represent the mean value plus error, which was calculated from 10–20 fruits per tree per year with weight normalization relative to HY. Image b shows the expression levels of transcription factors and regulators. LY and HY represent low yield and high yield of fruits in C. chekiangoleosa. The name to the right of each line represents the ID of the differentially expressed unigene.