The peanut cultivation and physiological and ecological innovation team of Shandong Academy of Agricultural Sciences has made important progress in peanut spatial transcriptome research
By: Date: 2022-07-13 Categories: foodtechnology Tags: ,
Recently, the peanut cultivation and physiological ecology innovation team of Shandong Academy of Agricultural Sciences, in cooperation with Qingdao Huada Gene Research Institute, published an online publication entitled”spatial trans” in the plant biotechnology Journal (if=13.263, Q1), the top journal of the first district of the Chinese Academy of Sciencescriptome analysis on peanut tissues shed light on cell heterogeneity of the peg”( https://doi.org/10.1111/pbi.13884 )Research papers. Shandong Academy of Agricultural Sciences and Qingdao Huada jointly developed a high-resolution spatial transcriptome preparation technology suitable for non model plants such as peanut. Using the 500 nm microsphere array chip independently developed by Huada, the spatial information of gene expression in different tissues/cells of peanut was detected, and the spatial gene expression map of non model plants was drawn for the first time, setting up a new bridge for the study of Plant Microstructure and gene function, It provides a new method for the research of plant development and crop breeding.
 
In recent years, single cell sequencing technology has achieved rapid development, but its application in the field of plants still faces many challenges:some plant tissues have a high degree of differentiation, resulting in difficulties in the preparation of protoplasts; In the process of protoplast preparation, the immediate transcription state of cells or tissues cannot be preserved, and it is not suitable for tissue samples treated by external conditions (such as pathogen infection, temperature change, etc.); Ignoring the heterogeneity of cells in spatial location, we cannot obtain the spatial location information of cells. We can only speculate the location of cells with the help of known key maker genes. The newly developed spatial transcriptome (spatio-temporal group) technology can effectively make up for the shortcomings of single-cell sequencing technology, which can not only analyze the development and differentiation trajectory of cells in the time dimension, but also interpret the gene expression characteristics of each cell in the space dimension. Because of its powerful ability of in situ characterization of high-throughput gene expression, space transcriptome technology has shown a wide range of potential applications in life science research.
 
In this study, we first improved the preparation method of plant samples and created a”two-step” permeabilization technology, which greatly improved the capture efficiency of plant mRNA. For the highly differentiated hypocotyl cortex, the average number of gene capture in a single cell region still reached 1449. In addition, the plant materials used in this study were frozen and fixed within a few seconds after taking the materials, so as to maintain the immediate transcription state in the samples to the greatest extent. On this basis, this study further used this technology to compare and analyze four kinds of peanut tissues, revealing the cell heterogeneity of peanut needle, a special tissue. Peanut has the biological characteristics of flowering on the ground and fruiting underground. After fertilization, the pistils of peanut develop into needles and grow towards the ground, and then develop into fruits underground. Fruit needle is a unique tissue of peanut, which has similar anatomical characteristics with the stem, but is similar to the root in physiological function. In this study, we compared the spatial transcriptome of peanut needles with tissues with similar structures such as stems, roots and hypocotyls, analyzed the different cell groups contained in peanut needles and the spatial location information of each cell group, and identified the cell types contained in different tissues. The study found that the cell types in the vascular bundle area (phloem and xylem) in the fruit needle are similar to those in the root and stem, and the cell types in the epidermis, cortex and pith of the fruit needle are different from those in the stem and root, indicating that the fruit needle is a kind of tissue that is quite different from the stem and root. Further analysis of the gene expression characteristics of each cell group in the fruit needle showed that the epidermal (exoderm) cells at the tip and middle and rear of the fruit needle were clustered into two different clusters. Functional analysis showed that the genes involved in glycoside and saponin synthesis were enriched in the epidermis of the tip of the fruit needle to protect the ovules at the tip of the fruit needle from underground pests; The genes that sense environmental signals are enriched in the middle and rear epidermis of the fruit needle, giving it the biological characteristics of sensing soil stimulation and initiating embryo and fruit development underground.
 
Liu Yiyang of Shandong Academy of Agricultural Sciences and Li Chunhua of Qingdao Huada gene research institute are the co first authors of the paper, and WAN Shubo, researcher Li Guowei and Dr. Xu Guoxin are the co corresponding authors of the paper. The research was supported by the National Natural Science Foundation of China, Taishan Scholars project, Shandong science and technology plan project and other funds.