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.
Genes Genomics. 2020 Sep;42(9):997-1010. doi: 10.1007/s13258-020-00967-z. Epub 2020 Jul 16.
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.
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.
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.
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.
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.
蜡质玉米（Zea mays L. sinensis Kulesh）是玉米（Zea mays L.）中 Wx1 基因座突变的突变体。与普通玉米相比，蜡质玉米的种子具有更高的粘性。到目前为止，我们对参与蜡质玉米种子发育的基因的表达模式知之甚少。
通过分析蜡质玉米种子发育过程中的转录组数据，尝试挖掘可能影响蜡质玉米种子发育的基因。
使用授粉后六个阶段的蜡质玉米自交系 SWL01 的种子进行 RNA-seq。使用生物信息学方法分析表达基因的表达模式，以鉴定参与蜡质玉米种子发育的基因。
在蜡质玉米种子发育过程中共检测到 24546 个基因，包括 1611 个转录因子（TFs）。表达基因的共表达分析揭示了蜡质玉米种子发育的动态过程。特别是，在蜡质玉米种子中专门表达的 2457 个基因，包括 177 个 TFs，其中一些主要涉及种子休眠和成熟过程。此外，与普通玉米 B73 相比，在六个阶段中分别鉴定出 2681、5686、4491、4386、3669 和 4624 个差异表达基因（DEGs），其中 113 个 DEGs 可能是导致乳期蜡质玉米和普通玉米种子发育差异的关键基因。
综上所述，我们全面阐明了蜡质玉米种子发育过程中表达基因的表达模式。在本研究中鉴定出一系列与种子发育相关的基因，这可能为蜡质玉米种子发育的功能研究提供重要资源，有助于分子辅助育种。
