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Unmasking Novel Loci for Internal Phosphorus Utilization Efficiency in Rice Germplasm through Genome-Wide Association Analysis.

Wissuwa M, Kondo K, Fukuda T, Mori A, Rose MT, Pariasca-Tanaka J, Kretzschmar T, Haefele SM, Rose TJ - PLoS ONE (2015)

Bottom Line: Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12.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.

View Article: PubMed Central - PubMed

Affiliation: Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan.

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.

No MeSH data available.


Related in: MedlinePlus

Manhattan plots for PUE (total biomass/total P) based on fixed (GLM) and mixed model (MLM) calculations in experiments 1 and 2.Colors indicate different chromosomes while the horizontal lines indicate a common significance level of P = 0.0001 [-log(P) = 4.0].
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pone.0124215.g002: Manhattan plots for PUE (total biomass/total P) based on fixed (GLM) and mixed model (MLM) calculations in experiments 1 and 2.Colors indicate different chromosomes while the horizontal lines indicate a common significance level of P = 0.0001 [-log(P) = 4.0].

Mentions: In Exp1 main loci for PUE were detected on chromosomes 1, 5 and 11 with good agreement between MLM and GLM (Table 3; Fig 2). In Exp2 only one locus exceeding P < 1.0E-04 was detected using MLM (chromosome 12) while GLM identified peaks on all chromosomes. Table 3 summarizes main loci identified across experiments based on an analysis across all subpopulations as this typically produced most significant peaks. The exception is the locus on chromosome 4 where an indica-only analysis enhanced significance by two orders of magnitude. Two peaks on chromosome 1 (7.3 Mb) and chromosome 11 (16.7 Mb) were discerned across experiments. To determine whether variation for root or shoot biomass contributed over-proportionally to PUE peak significance, further analyses using shoot, root or total biomass as traits were conducted. Results indicate that peaks for PUE on chromosomes 4 (17.7 Mb) and 12 (26.6 Mb) were associated with variation for shoot biomass while peaks on chromosomes 1 (30.5 Mb) and 5 (4.3 Mb) were associated with variation for root biomass (Table 3). The remaining loci were most significant for total plant biomass. Given that overall PUE was less tightly correlated with root biomass we consider PUE peaks attributed to variation in total biomass and shoot biomass as being the main loci of interest. Of PUE loci detected in the low-P treatments in Exp1, only the peak on chromosome 11 was also significant for non-stress biomass. This peak also appeared in the high-P treatment in Exp2 as did three other loci (Table 3).


Unmasking Novel Loci for Internal Phosphorus Utilization Efficiency in Rice Germplasm through Genome-Wide Association Analysis.

Wissuwa M, Kondo K, Fukuda T, Mori A, Rose MT, Pariasca-Tanaka J, Kretzschmar T, Haefele SM, Rose TJ - PLoS ONE (2015)

Manhattan plots for PUE (total biomass/total P) based on fixed (GLM) and mixed model (MLM) calculations in experiments 1 and 2.Colors indicate different chromosomes while the horizontal lines indicate a common significance level of P = 0.0001 [-log(P) = 4.0].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414551&req=5

pone.0124215.g002: Manhattan plots for PUE (total biomass/total P) based on fixed (GLM) and mixed model (MLM) calculations in experiments 1 and 2.Colors indicate different chromosomes while the horizontal lines indicate a common significance level of P = 0.0001 [-log(P) = 4.0].
Mentions: In Exp1 main loci for PUE were detected on chromosomes 1, 5 and 11 with good agreement between MLM and GLM (Table 3; Fig 2). In Exp2 only one locus exceeding P < 1.0E-04 was detected using MLM (chromosome 12) while GLM identified peaks on all chromosomes. Table 3 summarizes main loci identified across experiments based on an analysis across all subpopulations as this typically produced most significant peaks. The exception is the locus on chromosome 4 where an indica-only analysis enhanced significance by two orders of magnitude. Two peaks on chromosome 1 (7.3 Mb) and chromosome 11 (16.7 Mb) were discerned across experiments. To determine whether variation for root or shoot biomass contributed over-proportionally to PUE peak significance, further analyses using shoot, root or total biomass as traits were conducted. Results indicate that peaks for PUE on chromosomes 4 (17.7 Mb) and 12 (26.6 Mb) were associated with variation for shoot biomass while peaks on chromosomes 1 (30.5 Mb) and 5 (4.3 Mb) were associated with variation for root biomass (Table 3). The remaining loci were most significant for total plant biomass. Given that overall PUE was less tightly correlated with root biomass we consider PUE peaks attributed to variation in total biomass and shoot biomass as being the main loci of interest. Of PUE loci detected in the low-P treatments in Exp1, only the peak on chromosome 11 was also significant for non-stress biomass. This peak also appeared in the high-P treatment in Exp2 as did three other loci (Table 3).

Bottom Line: Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12.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.

View Article: PubMed Central - PubMed

Affiliation: Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan.

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.

No MeSH data available.


Related in: MedlinePlus