Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications

Sinha, P and Bajaj, P and Pazhamala, L T and Nayak, S N and Pandey, M K and Chitikineni, A and Huai, D and Khan, A W and Desai, A and Jiang, H and Zhuang, W and Guo, B and Liao, B and Varshney, R K (2020) Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications. Plant Biotechnology Journal (TSI). pp. 1-14. ISSN 1467-7644

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Abstract

Spatio-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.

Item Type:	Article
Divisions:	Research Program : Genetic Gains
CRP:	CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords:	Arachis hypogaea, Allergens, Gene expression atlas, Gravitropism, Oil biosynthesis, Photomorphogenesis
Subjects:	Others > Smallholder Farmers Others > Livelihoods Mandate crops > Groundnut Others > Oilseeds Others > Genetics and Genomics Others > Food and Nutrition Others > Legume Crops
Depositing User:	Mr Arun S
Date Deposited:	15 May 2020 09:20
Last Modified:	15 May 2020 09:20
URI:	http://oar.icrisat.org/id/eprint/11506
Official URL:	https://doi.org/10.1111/pbi.13374
Projects:	UNSPECIFIED
Funders:	Bill and Melinda Gates Foundation
Acknowledgement:	We would like to thank Genotypic Technology Pvt Ltd, Bengaluru, India, for generating RNAseq data for some samples as sequencing service provider. This work was supported by the Bill & Melinda Gates Foundation and the CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC). ICRISAT is a member of CGIAR Consortium.
Links:	Google Scholar

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