Limits...
Two in one sweep: aluminum tolerance and grain yield in P-limited soils are associated to the same genomic region in West African sorghum.

Leiser WL, Rattunde HF, Weltzien E, Cisse N, Abdou M, Diallo A, Tourè AO, Magalhaes JV, Haussmann BI - BMC Plant Biol. (2014)

Bottom Line: Significant genotype-by-phosphorus interaction was detected but with small magnitude compared to the genotype variance component.Using genome wide association mapping based on 220 934 SNPs we identified one genomic region on chromosome 3 that was highly associated to grain yield production.The identified SNPs can help accelerate breeding for increased sorghum productivity under unfavorable soil conditions and contribute to assuring food security in WA.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Sorghum (Sorghum bicolor L. Moench) productivity is severely impeded by low phosphorus (P) and aluminum (Al) toxic soils in sub-Saharan Africa and especially West Africa (WA). Improving productivity of this staple crop under these harsh conditions is crucial to improve food security and farmer's incomes in WA.

Results: This is the first study to examine the genetics underlying sorghum adaptation to phosphorus limitation in a wide range of WA growing conditions. A set of 187 diverse sorghum genotypes were grown in 29 -P and + P field experiments from 2006-2012 in three WA countries. Sorghum grain yield performance under -P and + P conditions was highly correlated (r = 0.85***). Significant genotype-by-phosphorus interaction was detected but with small magnitude compared to the genotype variance component. We observed high genetic diversity within our panel, with rapid linkage disequilibrium decay, confirming recent sequence based studies in sorghum. Using genome wide association mapping based on 220 934 SNPs we identified one genomic region on chromosome 3 that was highly associated to grain yield production. A major Al-tolerance gene in sorghum, SbMATE, was collocated in this region and SbMATE specific SNPs showed very high associations to grain yield production, especially under -P conditions, explaining up to 16% of the genotypic variance.

Conclusion: The results suggest that SbMATE has a possible pleiotropic role in providing tolerance to two of the most serious abiotic stresses for sorghum in WA, Al toxicity and P deficiency. The identified SNPs can help accelerate breeding for increased sorghum productivity under unfavorable soil conditions and contribute to assuring food security in WA.

Show MeSH

Related in: MedlinePlus

Associations of SNPs within a 78 kb region on chromosome 3 grain yield BLUPs across 29 environments combined over –P and + P conditions, with annotated genes, LD among SNPs, imputation rate (dot size) of SNPs and minor allele frequency (color range) of SNPs across 187 sorghum genotypes.P values are shown on a log10 scale and Bonferroni threshold at p < 0.05 is indicated with dashed line.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4256928&req=5

Fig4: Associations of SNPs within a 78 kb region on chromosome 3 grain yield BLUPs across 29 environments combined over –P and + P conditions, with annotated genes, LD among SNPs, imputation rate (dot size) of SNPs and minor allele frequency (color range) of SNPs across 187 sorghum genotypes.P values are shown on a log10 scale and Bonferroni threshold at p < 0.05 is indicated with dashed line.

Mentions: We identified one SNP (S3_71178053) for grain yield across –P and + P environments that was significant based on a p < 0.05 Bonferroni threshold (Figure 3) and explained 15% of the genotypic variance. The mean yield of accessions harboring the A allele was 44 g m−2 (=440 kg ha−1) higher than that of accessions with the G allele, a difference equivalent to a 37% yield increase of the A- over the G-allele genotypes (Additional file 8). Three other SNPs with significant association probabilities with grain yield (–log10(p) > 5) were detected at a physical distance less than 78 kb and were in tight LD (R2 > 0.65) with S3_71178053 (Figure 4). All other GBS derived SNPs within this region had low –log10(p)-values, which was not caused by lower MAF or higher imputation rates (Figure 4) and were not in strong LD with S3_71178053.Figure 3


Two in one sweep: aluminum tolerance and grain yield in P-limited soils are associated to the same genomic region in West African sorghum.

Leiser WL, Rattunde HF, Weltzien E, Cisse N, Abdou M, Diallo A, Tourè AO, Magalhaes JV, Haussmann BI - BMC Plant Biol. (2014)

Associations of SNPs within a 78 kb region on chromosome 3 grain yield BLUPs across 29 environments combined over –P and + P conditions, with annotated genes, LD among SNPs, imputation rate (dot size) of SNPs and minor allele frequency (color range) of SNPs across 187 sorghum genotypes.P values are shown on a log10 scale and Bonferroni threshold at p < 0.05 is indicated with dashed line.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4256928&req=5

Fig4: Associations of SNPs within a 78 kb region on chromosome 3 grain yield BLUPs across 29 environments combined over –P and + P conditions, with annotated genes, LD among SNPs, imputation rate (dot size) of SNPs and minor allele frequency (color range) of SNPs across 187 sorghum genotypes.P values are shown on a log10 scale and Bonferroni threshold at p < 0.05 is indicated with dashed line.
Mentions: We identified one SNP (S3_71178053) for grain yield across –P and + P environments that was significant based on a p < 0.05 Bonferroni threshold (Figure 3) and explained 15% of the genotypic variance. The mean yield of accessions harboring the A allele was 44 g m−2 (=440 kg ha−1) higher than that of accessions with the G allele, a difference equivalent to a 37% yield increase of the A- over the G-allele genotypes (Additional file 8). Three other SNPs with significant association probabilities with grain yield (–log10(p) > 5) were detected at a physical distance less than 78 kb and were in tight LD (R2 > 0.65) with S3_71178053 (Figure 4). All other GBS derived SNPs within this region had low –log10(p)-values, which was not caused by lower MAF or higher imputation rates (Figure 4) and were not in strong LD with S3_71178053.Figure 3

Bottom Line: Significant genotype-by-phosphorus interaction was detected but with small magnitude compared to the genotype variance component.Using genome wide association mapping based on 220 934 SNPs we identified one genomic region on chromosome 3 that was highly associated to grain yield production.The identified SNPs can help accelerate breeding for increased sorghum productivity under unfavorable soil conditions and contribute to assuring food security in WA.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Sorghum (Sorghum bicolor L. Moench) productivity is severely impeded by low phosphorus (P) and aluminum (Al) toxic soils in sub-Saharan Africa and especially West Africa (WA). Improving productivity of this staple crop under these harsh conditions is crucial to improve food security and farmer's incomes in WA.

Results: This is the first study to examine the genetics underlying sorghum adaptation to phosphorus limitation in a wide range of WA growing conditions. A set of 187 diverse sorghum genotypes were grown in 29 -P and + P field experiments from 2006-2012 in three WA countries. Sorghum grain yield performance under -P and + P conditions was highly correlated (r = 0.85***). Significant genotype-by-phosphorus interaction was detected but with small magnitude compared to the genotype variance component. We observed high genetic diversity within our panel, with rapid linkage disequilibrium decay, confirming recent sequence based studies in sorghum. Using genome wide association mapping based on 220 934 SNPs we identified one genomic region on chromosome 3 that was highly associated to grain yield production. A major Al-tolerance gene in sorghum, SbMATE, was collocated in this region and SbMATE specific SNPs showed very high associations to grain yield production, especially under -P conditions, explaining up to 16% of the genotypic variance.

Conclusion: The results suggest that SbMATE has a possible pleiotropic role in providing tolerance to two of the most serious abiotic stresses for sorghum in WA, Al toxicity and P deficiency. The identified SNPs can help accelerate breeding for increased sorghum productivity under unfavorable soil conditions and contribute to assuring food security in WA.

Show MeSH
Related in: MedlinePlus