Research Article

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

Qiang Li1* , Tao Li2* , Shihua Guo1 , Yuting Bai1 , Xingcong Li1
1 College of Agriculture, Inner Mongolia Agricultural University, Hohhot, 010019, China
2 Crop institute, Inner Mongolia Academy of Agriculture and Animal Husbandry, Hohhot, 010031, China
* These authors contributed equally to this work
Author    Correspondence author
Molecular Plant Breeding, 2020, Vol. 11, No. 12   doi: 10.5376/mpb.2020.11.0012
Received: 18 Jun., 2020    Accepted: 28 Aug., 2020    Published: 30 Sep., 2020
© 2020 BioPublisher Publishing Platform
This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Li Q., Li T., Guo S.H., Bai Y.T., and Li X.C., 2020, Enrichment analysis of differentially expressed genes during endosperm grouting periods in non-waxy and waxy foxtail millets, Molecular Plant Breeding, 11(12): 1-8 (doi: 10.5376/mpb.2020.11.0012)


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 ‘Gonggu 68’ and non-waxy millet ‘Chigu 4’ (grouting period 1 and 5 days) were used to analyze their transcriptome sequences by using Illumina Hiseq4000. The results showed that: (1) GBSSⅠenzymes activity of waxy and non-waxy millet was low-high-low. There were some differences between the two activities. 665 up-regulated differentially expressed genes were screened on day 5 and day 1 during grouting period in waxy cultivar ‘Gonggu 68’, there were 431 more up-regulated genes than down-regulated genes. There were 97 more up-regulated genes than down-regulated genes in non-waxy cultivar ‘Chigu 4’ on day 5 and day 1 in grouting period. (2) In the A2-VS-A1 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 B2-VS-B1 non-waxy comparison group, the differential genes were mainly GO enriched in 8 functions such as the light harvesting in photosystem I function and the pigment binding function 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 A2-VS-A1, 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 B2-VS-B1. These two comparative groups were enriched Caffeine metabolism pathway and linoleic acid metabolism pathway appeared in the process. (4) Three (SSII-3PHO1AS) and four (PHO1-1ASAGP16WAXY) 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.

Non-waxy millet; Waxy millet; Enzyme activity; Grouting period; Transcriptome; qRT-PCR
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