An imputation platform to enhance integration of rice genetic resources

Nature Communications
Diane R WangSusan R McCouch

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.

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Citations

Nov 14, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Qin WangXuehui Huang
Dec 19, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Joshua N CobbJ Damien Platten
Dec 18, 2019·Journal of Experimental Botany·Giovanni MelandriCarolien Ruyter-Spira
Mar 28, 2020·Genome Biology·Jie QiuLongjiang Fan
Jan 6, 2021·Nature Communications·Myung-Shin KimSoon-Chun Jeong

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Methods Mentioned

BETA
genotyping

Software Mentioned

Rice Imputation Server
SHAPEIT
RP
RICE
IMPUTE2
R package rehh
plink1
rrBLUP
qqman R package
fastStructure

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