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Type: Journal article
Title: Unmasking novel loci for internal phosphorus utilization efficiency in rice germplasm through genome-wide association analysis
Author: Wissuwa, M.
Kondo, K.
Fukuda, T.
Mori, A.
Rose, M.
Pariasca-Tanaka, J.
Kretzschmar, T.
Haefele, S.
Rose, T.
Citation: PLoS One, 2015; 10(4):e0124215-1-e0124215-21
Publisher: PLoS
Issue Date: 2015
ISSN: 1932-6203
Statement of
Matthias Wissuwa, Katsuhiko Kondo, Takuya Fukuda, Asako Mori, Michael T. Rose, Juan Pariasca-Tanaka, Tobias Kretzschmar, Stephan M. Haefele, Terry J. Rose
Abstract: Depletion of non-renewable rock phosphate reserves and phosphorus (P) fertilizer price increases has renewed interest in breeding P-efficient varieties. Internal P utilization efficiency (PUE) is of prime interest because there has been no progress to date in breeding for high PUE. We characterized the genotypic variation for PUE present within the rice gene pool by using a hydroponic system that assured equal plant P uptake, followed by mapping of loci controlling PUE via Genome-Wide Association Studies (GWAS). Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12. The highest PUE was associated with a minor indica-specific haplotype on chromosome 1 and a rare aus-specific haplotype on chromosome 11. Comparative variant and expression analysis for genes contained within the chromosome 1 haplotype identified high priority candidate genes. Differences in coding regions and expression patterns between genotypes of contrasting haplotypes, suggested functional alterations for two predicted nucleic acid-interacting proteins that are likely causative for the observed differences in PUE. The loci reported here are the first identified for PUE in any crop that is not confounded by differential P uptake among genotypes. Importantly, modern rice varieties lacked haplotypes associated with superior PUE, and would thus benefit from targeted introgressions of these loci from traditional donors to improve plant growth in phosphorus-limited cropping systems.
Keywords: Plant Shoots
Plant Roots
Plant Proteins
Chromosome Mapping
Sequence Alignment
Sequence Analysis, DNA
Amino Acid Sequence
Polymorphism, Single Nucleotide
Genome, Plant
Quantitative Trait Loci
Molecular Sequence Data
Genome-Wide Association Study
Rights: © 2015 Wissuwa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
DOI: 10.1371/journal.pone.0124215
Appears in Collections:Agriculture, Food and Wine publications
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