Enrichment Analysis of Differentially Expressed Genes during Endosperm Grouting Periods in Non-waxy and Waxy Foxtail Millets

Abstract

The content of amylose and amylopectin is an important trait affecting cooking and eating quality in millet. During process of kernel grouting, the synthesis of starch involves different pathways and components in non-waxy and waxy millets. Immature grouting grains of waxy millet ‘Gonggu68’ and non-waxy millet ‘Chigu4’ (grouting period 1 and 5 days) were used to analyze their transcriptome sequences by using Illumina Hiseq4000. The results showed that: (1) GBSSⅠ enzymes activity of waxy and non-waxy millet was low-high-low. There were some differences between the two activities. 665 upregulated differentially expressed genes were screened on day 5 and day 1 during grouting period in waxy cultivar ‘Gonggu68’, there were 431 more upregulated genes than downregulated genes. There were 97 more up-regulated genes than down-regulated genes in non-waxy cultivar ‘Chigu4’ on day 5 and day 1 in grouting period. (2) In the A 2 -VS-A 1 waxy comparison group, the differential genes were mainly GO enriched in 7 functions such as the seed oil body biogenic function, 17-β-ketosteroid reductase activity function and so on. it was mainly enriched in biological processes and molecular functions. In the B 2 -VS-B 1 non-waxy comparison group, the differential genes were mainly GO enriched in 8 functions such as the light capturing function and the pigment binding function in the light system I for non-waxy millet. (3) Differentially expressed genes were mainly KEGG enriched in caffeine metabolism pathway, linoleic acid metabolism pathway, anthocyanin biosynthesis pathway, aflatoxin biosynthesis pathway in waxy A 2 -VS-A 1 , but which were mainly KEGG enriched in the synergy-antenna protein pathway, the linoleic acid metabolic pathway, the caffeine metabolic pathway, the brassinosteroid biopathway in non-waxy B 2 -VS-B 1 . These two comparative groups were enriched Caffeine metabolism pathway and linoleic acid metabolism pathway appeared in the process. (4) Three ( SSII-3 , PHO1 , AS ) and four ( PHO1-1 , AS , AGP16 , WAXY ) genes with significant differences and related to waxy and non-waxy millet were screened. With Actin (Si001873) as the internal reference gene, the above seven differentially expressed genes were verified by qRT-PCR, which was consistent with the transcriptome results, indicating that the differentially expressed genes were related to waxy or non-waxy endosperm.