A global gene expression atlas of cultivated groundnut provides insights into seed development, oil biosynthesis and allergens

Authors: SINHA, PALLAVI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; BAJAJ, PRASAD - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; PAZHAMALA, LEKHA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; NAYAK, SPURTHI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; PANDEY, NAMISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; CHITIKINENI, ANNAPURNA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; HUAI, DONGXIN - Chinese Academy Of Agricultural Sciences; KHAN, AAMIR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; DESAI, AARTHI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; JIANG, HUIFANG - Chinese Academy Of Agricultural Sciences; ZHUANG, WEIJIAN - Fujian Agricultural & Forestry University; Guo, Baozhu; LIAO, BOSHOU - Chinese Academy Of Agricultural Sciences; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/26/2020
Publication Date: 3/13/2020
Citation: Sinha, P., Bajaj, P., Pazhamala, L.T., Nayak, S.N., Pandey, N.K., Chitikineni, A., Huai, D., Khan, A.W., Desai, A., Jiang, H., Zhuang, W., Guo, B., Liao, B., Varshney, R.K. 2020. A global gene expression atlas of cultivated groundnut provides insights into seed development, oil biosynthesis and allergens. Plant Biotechnology Journal. pp. 1-14. https://doi.org/10.1111/pbi.13374.
DOI: https://doi.org/10.1111/pbi.13374

Interpretive Summary: Cultivated peanut carrying two different subgenomes (A and B) pose several challenges in conducting structural and functional genomics studies. Nevertheless, availability of reference genomes for diploid progenitor species i.e., A. duranensis and A. ipaensis have accelerated the pace of genomics research in peanut. Gene expression atlases have been developed for several plant species, including rice, soybean and corn. These studies aimed to investigate the complex and distinct biological processes involved in pod development, seed formation, seed maturation, and oil biosnthesis. Availability of global transcriptome technologies offered the opportunity to understand the transcriptional pattern of plant growth and development. The transcriptional map or gene expression atlas provides a comprehensive overview of the expression patterns during the developmental processes. This study sampled 19 tissues/organs throughout the life cycle of the cultivated peanut genotype ICGV 91114, a widely adapted high-yielding variety in India. The primary goal in this study was to develop global gene expression atlas showing genome-wide expression of transcripts/genes in different tissues during the course of entire plant lifecycle of peanut. In addition, we provided the useful insights on the oil biosynthesis and expression of different allergens during various stages of seed development. These data could be used in various peanut functional genomics studies, such as understanding the underlying dynamics of the global gene expression pattern during the development of different tissues or organs in peanut.

Technical Abstract: Gene expression information across different growth stages and different plant parts plays crucial role in functional genomics of any species. In this context, we developed Arachis hypogaea gene expression atlas (AhGEA) based on RNA-Seq data using 19 important tissues from five different stages of an early maturing, high yielding, drought tolerant groundnut variety, ICGV 91114. A total of 458.26 million paired-end reads were generated to identify 81,906 transcripts with =1 FPKM (Fragments Per Kilobase of exon per Million) in at least one of the samples with their expression patterns across different tissues and stages. Global transcriptome analysis provided regulatory networks in germinal, vegetative and reproductive tissues reflecting tissue specificity and important developmental processes in groundnut. AhGEA has also enhanced understanding of important biological processes during seed development and nodulation in groundnut. Furthermore, AhGEA identified several transcriptional signatures that provide insights into the oil biosynthesis during seed development. A large number of transcripts were investigated for their involvement in oil biosynthesis and those encoding allergens. Taken together, AhGEA includes various important and key features of cultivated groundnut and provides a reference for accelerating functional genomics research in groundnut.