Chickpea Gbrowse

Edwards, David and Chan, Kenneth (2014): Chickpea Gbrowse. The University of Queensland. Collection.


 
Related Publications and Datasets
 
Project name Chickpea: The Project For an Abiotic Stress-Tolerant Chickpea
Project description
In collaboration with partners in India (ICRISAT), this AISRF-funded project is focussed towards the development of efficient selection methods for tolerance to abiotic stress and the application of molecular tools to assist chickpea breeding.

The key objective is to develop and build a collaborative chickpea genomics program comprising advanced pre-breeding tools for the discovery and validation of novel genes and traits leading to development of abiotic stress tolerant chickpea.

The project will utilise diverse chickpea germplasm including world core collections and elite breeding lines from Australia and India to produce outputs that may assist chickpea breeding efforts in both countries.

Chickpea forms a critical component of the Australian and Indian farming system, offering offer a high value alternative to cereals, an important disease break, opportunities for grass weed control and respite from high nitrogen application.

Chickpea is the major pulse produced in Australia and India, but abiotic stresses such as salinity, drought and heat regularly limit production. Drought alone reduces yield significantly, compounded by high sensitivity to heat and salinity. This situation will become more severe under predicted climate change scenarios and hence specific breeding and selection for tolerance to drought, heat and salinity are urgently required in chickpea.

Chickpea is one of the world’s most important pulse crops, ranking third in world food legume production. Globally, chickpea production covers an area of 11.9 Mha producing 10.9 Mt (FAOSTAT, 2010). India is the world’s biggest producer with an annual production of around 7.48 Mt representing 68% of total world production. Existing production in India is insufficient to meet demand and every year India imports large quantities of chickpea.

In Australia, chickpea is also grown as a high value pulse, but serious production only began around 20 years ago. Chickpea has rapidly grown to be Australia’s most valuable pulse crop (602,000 tonnes in 2010, FAOSTAT). A significant quantity of this high value crop is exported to India and other countries for human consumption.

Chickpea offers significant benefits for human health. The seed is high in protein (20-30%) and dietary fibre, contains approximately 40% carbohydrates and only 3-6% oil. Furthermore, chickpea is a good source of essential minerals such as calcium, magnesium, potassium, phosphorus, iron, zinc and manganese, and has been recognised as one of the nutritionally best composed legumes for human consumption.
Contact name David Edwards
Contact email dave.edwards@uq.edu.au
Creator name Edwards, David
Chan, Kenneth
Creator(s) role Chief Investigator
Postdoctoral Bioinformatics Researcher
Dataset name Chickpea Gbrowse
Dataset description
The Chickpea genome contains 8 Chromosomes with ~740 million bases pairs (Mbp) and 28,269 genes. It is a challenge to visualise and explore such a huge quantity of data, especially for non-bioinformatics researchers. We are part of the Chickpea Consortium and we published the Chickpea genome in Nature Biotechnology in early 2014.

Currently, only the raw data of the Chickpea genome can be downloaded in NCBI, thus limiting the analysis to researchers with strong computing skills. Setting up a well-featured genome browser for the Chickpea genome is important for the plant research community, and especially beneficial to the Chickpea research community.  The Chickpea browsing system will be the first Chickpea genome browser, and will attract the Chickpea research community to use it. Additionally, it will also benefit the plant research community, especially for genome comparative study.

Both the Kabuli and Desi genomes can be downloaded in full as well as being searchable through Gbrowse.
Access conditions Open Access
ANZSRC Field of Research (FoR) Code 060407 Genome Structure and Regulation
0607 Plant Biology
060102 Bioinformatics
Type of data Various text and binary format
FASTA
FASTQ
sam
bam
gff3
Data Volume 0.5TB
Software required Tools are available through the Gbrowse portal.
Language eng
Keyword Chickpea
Genomic analyses
Plant biology
Collection type Collection
Publisher The University of Queensland
Publication Year 2014
Copyright notice 2014, The University of Queensland

Document type: Data Collection
Collections: School of Agriculture and Food Sciences
Research Data Collections
 
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Created: Wed, 12 Nov 2014, 14:50:04 EST by Belinda Weaver