Transcriptome sequencing and differential expression analysis of seed starch accumulation in Chinese chestnut Metaxenia

Abstract

Background: Chestnut seeds are important kinds of edible nuts rich in starch and protein. The characteristics and nutrient contents of chestnut have been found to show obvious metaxenia effects in previous studies. To improve the understanding of the effect of metaxenia on chestnut starch and sucrose metabolism, this study used three varieties of chestnut, 'Yongfeng 1', 'YongRen Zao' and 'Yimen 1', as male parents to pollinate the female parent, 'Yongfeng 1', and investigated the mechanisms of starch and sucrose metabolism in three starch accumulation stages (70 (S1), 82 (S2), and 94 (S3) days after pollination, DAP) in chestnut seed kernels.

Result: Most carbohydrate metabolism genes were highly expressed in YFF (self-pollinated 'Yongfeng 1') in stage S2 and in YFR ('Yongfeng 1' × 'Yongren Zao') and YFM ('Yongfeng 1' × 'Yimen 1') in stage S3. In stage S3, hub genes encoding HSF_DNA-binding, ACT, Pkinase, and LIM proteins and four transcription factors were highly expressed, with YFF showing the highest expression, followed by YFR and YFM. In addition, transcriptome analysis of the kernels at 70, 82 and 94 DAP showed that the starch granule-bound starch synthase (EC 2.4.1.242) and ADP-glucose pyrophosphorylase (EC 2.7 .7.27) genes were actively expressed at 94 DAF. Chestnut seeds regulate the accumulation of soluble sugars, reducing sugars and starch by controlling glycosyl transferase and hydrolysis activity during development.

Conclusion: These results and resources have important guiding significance for further research on starch and sucrose metabolism and other types of metabolism related to chestnut metaxenia.

Keywords: Chestnut; Differential gene expression; Metaxenia; Seed development; Starch synthesis.

Fig. 1

Chestnut samples and physiological characteristics at three stages. A Comparison of sugar contents in three stages. B Comparison of starch contents in three stages. C Comparison of enzyme activity in three stages. D Illustration of seeds at three stages that were included in the study. Note: Lowercase letters indicate significant differences (P < 0.05)

Fig. 2

Principal component analysis (PCA) of the global transcriptome obtained from three pollination combinations

Fig. 3

DEG counts and the top eight GO terms in seeds from three pollination combinations. A Comparison of DEGs in seeds from different pollination combinations. B Development-related GO terms in seeds from three pollination combinations

Fig. 4

Expression patterns of genes in the seeds of three pollination combinations at three stages. A Expression patterns of all genes, B expression patterns of key genes

Fig. 5

Analysis of key modules based on WGCNA. A Purple module key genes; B pink module key genes; C blue module key genes; D expression patterns of TFs

Fig. 6

Network of starch and sugar synthesis in chestnut seeds

Fig. 7

Expression of seven selected genes measured by RNA sequencing and qRT-PCR