An imputation platform to enhance integration of rice genetic resources

Diane R. Wang, Francisco J. Agosto-Pérez, Dmytro Chebotarov, Yuxin Shi, Jonathan Marchini, Melissa Fitzgerald, Kenneth L. McNally, Nickolai Alexandrov and Susan R. McCouch ()
Additional contact information
Diane R. Wang: School of Integrated Plant Sciences, Cornell University
Francisco J. Agosto-Pérez: School of Integrated Plant Sciences, Cornell University
Dmytro Chebotarov: International Rice Research Institute
Yuxin Shi: School of Integrated Plant Sciences, Cornell University
Jonathan Marchini: University of Oxford
Melissa Fitzgerald: University of Queensland
Kenneth L. McNally: International Rice Research Institute
Nickolai Alexandrov: International Rice Research Institute
Susan R. McCouch: School of Integrated Plant Sciences, Cornell University

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract As sequencing and genotyping technologies evolve, crop genetics researchers accumulate increasing numbers of genomic data sets from various genotyping platforms on different germplasm panels. Imputation is an effective approach to increase marker density of existing data sets toward the goal of integrating resources for downstream applications. While a number of imputation software packages are available, the limitations to utilization for the rice community include high computational demand and lack of a reference panel. To address these challenges, we develop the Rice Imputation Server, a publicly available web application leveraging genetic information from a globally diverse rice reference panel assembled here. This resource allows researchers to benefit from increased marker density without needing to perform imputation on their own machines. We demonstrate improvements that imputed data provide to rice genome-wide association (GWA) results of grain amylose content and show that the major functional nucleotide polymorphism is tagged only in the imputed data set.

Date: 2018
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-018-05538-1 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05538-1

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-018-05538-1

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().