Nutri-cereal tissue-specific transcriptome atlas during development: Functional integration of gene expression to identify mineral uptake pathways in little millet (Panicum sumatrense)

We present a developmental transcriptome atlas of little millet. It has superior nutritional properties including high micronutrients (Fe, Zn, Ca, Mn), dietary fiber content, and low glycemic index with potential health prospective. This crop is cultivated by tribal people in the marginal areas, and it is adapted to a wide range of growing environments. Overall design: Seeds of Little millet, Panicum sumatrense, genotype JK-8, were obtained from the University of Agricultural Sciences, Bengaluru, India. Ten different plant tissues were sampled at Agriculture and Agri-Food Canada, Saskatoon, Canada; Germinating seeds (2 days after sowing (DAS)), plumule and radicle (3 DAS), young leaf and young root (13 DAS), crown meristem (26 DAS), vegetative stem (48 DAS), panicle early (61 DAS), panicle mid (73 DAS), panicle late (85 DAS). Total RNA was extracted from 100 mg of harvested tissues using RNeasy Plant Mini Kit (Qiagen) or Triazol (Sigma-Aldrich) and purified using the RNeasy MinElute cleanup kit (Qiagen) according to manufacturer's protocol. Purified RNA was quantified using a NanoDrop ND-100 spectrophotometer (Thermo Scientific), and its integrity evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA libraries were prepared using a TruSeq1 RNA sample preparation Kit (Illumina). De novo transcriptome assembly was performed with Trinity. TPM (transcripts per million) were estimated using Kallisto.

本研究构建了小粟（Panicum sumatrense）的发育转录组图谱。该作物具备优异的营养特性：富含微量营养素（铁Fe、锌Zn、钙Ca、锰Mn）与膳食纤维，且低血糖生成指数，拥有良好的健康应用前景。该作物多由边际区域的原住民种植，且可适应多样的生长环境。

整体实验设计：实验所用小粟JK-8基因型种子采自印度班加罗尔农业科学大学。加拿大学萨斯卡通的加拿大农业与农业食品研究院对10种不同植物组织进行采样，具体包括：播种后2天（2 DAS）的萌发种子、播种后3天（3 DAS）的胚芽与胚根、播种后13天（13 DAS）的幼叶与幼根、播种后26天（26 DAS）的茎尖分生组织、播种后48天（48 DAS）的营养生长期茎秆、播种后61天（61 DAS）的早期穗状花序、播种后73天（73 DAS）的中期穗状花序，以及播种后85天（85 DAS）的晚期穗状花序。

称取100 mg收获的组织样本，按照制造商说明书，使用RNeasy植物微量提取试剂盒（Qiagen，凯杰）或Triazol试剂（Sigma-Aldrich，西格玛奥德里奇）提取总RNA，并通过RNeasy MinElute纯化试剂盒（Qiagen，凯杰）完成RNA纯化。使用NanoDrop ND-100分光光度计（Thermo Scientific，赛默飞世尔科技）对纯化后的RNA进行定量，并采用Agilent 2100生物分析仪（Agilent Technologies，安捷伦科技）评估RNA完整性。使用TruSeq1 RNA样本制备试剂盒（Illumina，因美纳）构建cDNA文库。采用Trinity软件进行从头转录组组装。使用Kallisto软件估算TPM（每百万转录本数，transcripts per million）值。