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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

In silico investigation of SNP variation and predicted gene models (MSU6.1) across the indica specific PUE locus on chromosome1, delimited by haplotype and linkage block to 7.247–7.343 Mb.The location of SNP locations with most significant association to PUE is indicated. SNP patterns shown are based on 1479 accessions represented in the RiceVarMap database and indicate specific SNPs detected in accessions belonging to the rare high-PUE haplotype (HT1-7) group (haplotype frequence of 7.3%). A total of 550 SNPs are displayed, of which 332 SNPs cluster towards the downstream limit (red bar on top).
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pone.0124215.g005: In silico investigation of SNP variation and predicted gene models (MSU6.1) across the indica specific PUE locus on chromosome1, delimited by haplotype and linkage block to 7.247–7.343 Mb.The location of SNP locations with most significant association to PUE is indicated. SNP patterns shown are based on 1479 accessions represented in the RiceVarMap database and indicate specific SNPs detected in accessions belonging to the rare high-PUE haplotype (HT1-7) group (haplotype frequence of 7.3%). A total of 550 SNPs are displayed, of which 332 SNPs cluster towards the downstream limit (red bar on top).

Mentions: LD and haplotype analyses defined chromosomal regions likely containing causal variation on chromosomes 1, 4, 11 and 12 (Fig 3 and S5 Fig). The 100 kb region on chromosome 1 contained 14 predicted gene loci, some of which had been previously identified in microarray studies [12,19] as being regulated by P deficiency (Fig 5; S5 Table). QTL regions on chromosomes 4 and 11 contained 21 and 24 predicted gene loci, respectively (S6 and S7 Tables). The QTL on chromosome 12 was not defined by a clear linkage block; thus, all gene models in a 500 kb flanking region are listed (S8 Table). Taking predicted function and reported P-responsiveness into account, a priority list of candidate genes that merit further investigation was drafted (Table 4).


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)

In silico investigation of SNP variation and predicted gene models (MSU6.1) across the indica specific PUE locus on chromosome1, delimited by haplotype and linkage block to 7.247–7.343 Mb.The location of SNP locations with most significant association to PUE is indicated. SNP patterns shown are based on 1479 accessions represented in the RiceVarMap database and indicate specific SNPs detected in accessions belonging to the rare high-PUE haplotype (HT1-7) group (haplotype frequence of 7.3%). A total of 550 SNPs are displayed, of which 332 SNPs cluster towards the downstream limit (red bar on top).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0124215.g005: In silico investigation of SNP variation and predicted gene models (MSU6.1) across the indica specific PUE locus on chromosome1, delimited by haplotype and linkage block to 7.247–7.343 Mb.The location of SNP locations with most significant association to PUE is indicated. SNP patterns shown are based on 1479 accessions represented in the RiceVarMap database and indicate specific SNPs detected in accessions belonging to the rare high-PUE haplotype (HT1-7) group (haplotype frequence of 7.3%). A total of 550 SNPs are displayed, of which 332 SNPs cluster towards the downstream limit (red bar on top).
Mentions: LD and haplotype analyses defined chromosomal regions likely containing causal variation on chromosomes 1, 4, 11 and 12 (Fig 3 and S5 Fig). The 100 kb region on chromosome 1 contained 14 predicted gene loci, some of which had been previously identified in microarray studies [12,19] as being regulated by P deficiency (Fig 5; S5 Table). QTL regions on chromosomes 4 and 11 contained 21 and 24 predicted gene loci, respectively (S6 and S7 Tables). The QTL on chromosome 12 was not defined by a clear linkage block; thus, all gene models in a 500 kb flanking region are listed (S8 Table). Taking predicted function and reported P-responsiveness into account, a priority list of candidate genes that merit further investigation was drafted (Table 4).

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