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Genome-wide DNA polymorphisms in low phosphate tolerant and sensitive rice genotypes

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Title Genome-wide DNA polymorphisms in low phosphate tolerant and sensitive rice genotypes
 
Creator Mehra, Poonam
Pandey, Bipin K.
Giri, Jitender
 
Subject Abiotic
Agricultural genetics
 
Description Accepted date: 17 July 2015
Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern rice genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant traditional cultivars and landraces have genetic potential to sustain well under low P. Identification of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These identified variants can serve as a useful source of genetic variability for improving low P tolerance and root architecture of high yielding modern genotypes.
 
Date 2016-01-20T06:37:44Z
2016-01-20T06:37:44Z
2015
 
Type Article
 
Identifier Scientific Reports, 5: 13090
2045-2322
http://172.16.0.77:8080/jspui/handle/123456789/547
http://www.nature.com/articles/srep13090
10.1038/srep13090
 
Language en_US
 
Publisher Nature Publishing Group