The dynamic transcriptome of waxy maize ( Zea mays L. sinensis Kulesh ) during seed development
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Genes & Genomics https://doi.org/10.1007/s13258-020-00967-z
RESEARCH ARTICLE
The dynamic transcriptome of waxy maize (Zea mays L. sinensis Kulesh) during seed development Wei Gu1,2 · Diansi Yu1,2 · Yuan Guan1,2 · Hui Wang1,2 · Tao Qin1,2 · Pingdong Sun1,2 · Yingxiong Hu1,2 · Jihui Wei1,2 · Hongjian Zheng1,2 Received: 27 April 2020 / Accepted: 3 July 2020 © The Genetics Society of Korea 2020
Abstract Background Waxy maize (Zea mays L. sinensis Kulesh) is a mutant of maize (Zea mays L.) with a mutation at Waxy1 (Wx1) gene locus. The seed of waxy maize has higher viscosity compared to regular maize. By now, we know little about the expression patterns of genes that involved in the seed development of waxy maize. Objective By analyzing the transcriptome data during waxy maize seed development, we attempt to dig out the genes that may influence the seed development of waxy maize. Methods The seeds of waxy maize inbred line SWL01 from six phases after pollination were used to do RNA-seq. Bioinformatics methods were used to analyze the expression patterns of the expressed genes, to identify the genes involved in waxy maize seed development. Results A total of 24,546 genes including 1611 transcription factors (TFs) were detected during waxy maize seed development. Coexpression analysis of expressed genes revealed the dynamic processes of waxy maize seed development. Particularly, 2457 genes including 177 TFs were specially expressed in waxy maize seed, some of which mainly involved in the process of seed dormancy and maturation. In addition, 2681, 5686, 4491, 4386, 3669 and 4624 genes were identified to be differential expressed genes (DEGs) at six phases compared to regular maize B73, and 113 DEGs among them may be key genes that lead the difference of seed development between waxy and regular maizes in milk stage. Conclusion In summary, we elucidated the expression patterns of expressed genes during waxy maize seed development globally. A series of genes that associated with seed development were identified in our research, which may provide an important resource for functional study of waxy maize seed development to help molecular assisted breeding. Keywords Waxy maize · Seed development · Transcriptome · Seed-specific expressed genes · DEGs
Introduction
Wei Gu and Diansi Yu contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13258-020-00967-z) contains supplementary material, which is available to authorized users. * Hongjian Zheng [email protected] 1
Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
CIMMYT‑China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
2
Maize (zea mays) is one of the most productive crops in the world, and it is an important resource of food, feed and biofuel (Godfray et al. 2010). Due to its numerous morphological types and relatively large seed, maize has been used as an excel
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