Abstract
SummarySpatio‐temporal and developmental stage‐specific transcriptome analysis plays a crucial role in systems biology‐based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world's widest cultivated subsp. fastigiata based on RNA‐seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired‐end filtered reads were generated followed by identification of 81 901 transcripts from an early‐maturing, high‐yielding, drought‐tolerant groundnut variety, ICGV 91114. Further, 57 344 genome‐wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in‐depth analysis of the global transcriptome sheds light into complex regulatory networks namely gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer‐friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits.
Highlights
Cultivated groundnut or peanut (Arachis hypogaea L), one of the leading legume and oilseed crop with high oil content, nutritional and protein values, plays a significant role in ensuring nutritional food security in many developing countries in Asia and Africa (Varshney et al, 2013)
95.84% of the high-quality reads were mapped onto the reference genome for subsp. fastigiata of cultivated groundnut (Zhuang et al, 2019) ranging from 81.60% in nodules to 98.10% in immature bud (Table S1)
While analysing the transcription factor (TF) families in the peg, we found that to response to darkness and mechanical stimulus, transcripts encoding for GRAS, MYB-related, bHLH and B3 TF families were expressed which in turn influence expression of hormone signalling genes for peg gravitropic response
Summary
Cultivated groundnut or peanut (Arachis hypogaea L), one of the leading legume and oilseed crop with high oil content, nutritional and protein values, plays a significant role in ensuring nutritional food security in many developing countries in Asia and Africa (Varshney et al, 2013). Due to its multiple use in the form of seed, fodder, processed oil and cake, groundnut contributes to improving the livelihood of the smallholder farmers This crop faces an array of biotic and abiotic stress challenges in addition to certain food safety issues caused by aflatoxin and allergens to consumers’ health (Pandey et al, 2019a). Mere availability of genome sequences is not enough for developing better understanding on key traits, and a holistic ‘Omics approach’ or systems biology research is required wherein the information from genomics, transcriptomics, proteomics, metabolomics, epigenomics and interactomics studies is integrated. Development of a global genome-wide gene expression atlas is essential to understand the flow of genetic information in addition to trait- and tissue-specific transcriptomes
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