Unmasking Novel Loci for Internal Phosphorus Utilization Efficiency in Rice Germplasm through Genome-Wide Association Analysis.
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.
Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan.
Matthias
M
Wissuwa
Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan.
Katsuhiko
K
Kondo
Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan.
Takuya
T
Fukuda
Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan.
Asako
A
Mori
Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan; School of Chemistry, Monash University, Clayton, Victoria, Australia.
Michael T
MT
Rose
Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan.
Juan
J
Pariasca-Tanaka
International Rice Research Institute (IRRI), Los Banos, Philippines.
Tobias
T
Kretzschmar
Australian Centre for Plant Functional Genomics (ACPFG), Glen Osmond, South Australia, Australia.
Stephan M
SM
Haefele
Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan; Centre for Plant Sciences, Southern Cross University, Lismore, New South Wales, Australia.
Terry J
TJ
Rose
D000595:Amino Acid Sequence; D018533:Biomass; D002874:Chromosome Mapping; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010758:Phosphorus / Q000378:metabolism*; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D018520:Plant Shoots / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D010940:Plant Proteins; D010758:Phosphorus