Abstract
Cereals are the most important food crops and are considered key contributors to global food security. Loss due to abiotic stresses in cereal crops is limiting potential productivity in a significant manner. The primary reasons for abiotic stresses are abrupt temperature, variable rainfall, and declining nutrient status of the soil. Varietal development is the key to sustaining productivity under influence of multiple abiotic stresses and must be studied in context with genomics and molecular breeding. Recently, advances in a plethora of Next Generation Sequencing (NGS) based methods have accelerated the enormous genomic data generation associated with stress-induced transcripts such as microarray, RNAseq, Expressed Sequenced Tag (ESTs), etc. Many databases related to microarray and RNA-seq based transcripts have been developed and profusely utilized. However, an abundant amount of transcripts related to abiotic stresses in various cereal crops arising from EST technology are available but still remain underutilized in absence of a consolidated database. In this study, an attempt has been made with a primary goal to integrate, analyse, and characterise the available resources of ESTs responsive to abiotic stresses in major cereals. The developed CerealESTdb presents a customisable search in two different ways in the form of searchable content for easy access and potential use. This database comprises ESTs from four major cereal crops, namely rice (Oryza sativa L.), wheat (Triticum aestivum L.), sorghum (Sorghum bicolour L.), and maize (Zea mays L.), under a set of abiotic stresses. The current statistics of this cohesive database consists of 55,826 assembled EST sequences, 51,791 predicted genes models, and their 254,609 gene ontology terms including extensive information on 1,746 associated metabolic pathways. We anticipate that developed CerealESTdb will be helpful in deciphering the knowledge of complex biological phenomena under abiotic stresses to accelerate the molecular breeding programs towards the development of crop cultivars resilient to abiotic stresses. The CerealESTdb is publically available with the URL http://cabgrid.res.in/CerealESTDb.
Highlights
To provide more than nine billion people by 2050 with essential nutrients and energy in their everyday diet, food production must be increased by 70% with reduced fertilizer inputs (Wani et al, 2021; Kumar et al, 2018; Balyan et al, 2016)
Out of 610,893 Expressed Sequence Tags (EST) downloaded for abiotic stresses viz., abscisic acid (ABA), cold, drought, heat, and salt across all four crops viz., maize, rice, sorghum, and wheat, only 9% were assembled into contigs (55,826 in number)
The CerealESTdb, a user-friendly, searchable, and interactive database has been developed with a primary goal to provide information on assembled and annotated ESTs from four major crop plants, namely wheat, rice, maize, and sorghum under multiple environmental stresses including cold, heat, drought, and salt stress as well as on the application of ABA
Summary
To provide more than nine billion people by 2050 with essential nutrients and energy in their everyday diet, food production must be increased by 70% with reduced fertilizer inputs (Wani et al, 2021; Kumar et al, 2018; Balyan et al, 2016). At the genome and transcriptome level, the pathway reconstruction will play a principal role in quantifying and characterising the genotype to phenotype relationship (Gupta et al, 2020; Zhang et al, 2020; Feist and Palsson, 2008) In this ongoing genomic era, a huge amount of genomic data have been generated and analysed to provide key information leading to the development of crop cultivars resilient to abiotic stresses (Alter et al, 2015). EST libraries are a cost-effective tool and can serve as a starting point for the development of effective molecular genetic markers, such as gene-linked microsatellites, single nucleotide polymorphisms, etc These EST resources are too scattered to provide insight into the biological process including the involvement of genes/regulatory elements and their functional role in responding to different abiotic stresses. Efforts were made in the past by several research groups related to the development of EST resources in cereals such as Gramene (Jaiswal, 2011), cerealsDB (Wilkinson et al, 2012), Wheat
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