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

Abstract

BackgroundSorghum (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.ResultsThis 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.ConclusionThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0206-6) contains supplementary material, which is available to authorized users.

Duplicate and Conquer: Multiple Homologs ofPHOSPHORUS-STARVATION TOLERANCE1Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus Soils

“…As SNPs associated with grain yield were also found within Alt SB and SbMATE, this suggests a possible pleiotropic effect of SbMATE in providing tolerance to aluminum toxicity and to low-P conditions (Leiser et al, 2014b). The 71178053 SNP and one Alt SB -specific SNP showed grain yield effects of 240 kg ha 21 (W. Leiser, personal communication) and 250 kg ha 21 , respectively, under low P (Leiser et al, 2014b).…”

“…The 71178053 SNP and one Alt SB -specific SNP showed grain yield effects of 240 kg ha 21 (W. Leiser, personal communication) and 250 kg ha 21 , respectively, under low P (Leiser et al, 2014b). In turn, the grain yield effect for SNPs within Sb03g006765 and Sb03g031680 were 154 to 200 kg ha 21 , which was comparable to the effects reported by Leiser et al (2014b). The grain yield effect for SNPs within SbPSTOL1 genes described in this study are now being validated in different sorghum breeding contexts, including random mating populations, which should provide for a more realistic view of the breeding value of SbPSTOL1 genes when targeting adaptation to acid soil conditions.…”

“…In a genome-wide association study targeting adaptation to low P in sorghum (Leiser et al, 2014b), the most significant association with grain yield was found for an SNP at position 71.1 Mb on chromosome 3 (71178053), only 35.7 kb from the aluminum tolerance gene Sorghum bicolor multidrug and toxic compound extrusion (SbMATE), which underlies the aluminum tolerance locus Aluminum tolerance Sorghum bicolor (Alt SB ; Magalhaes et al, 2007). As SNPs associated with grain yield were also found within Alt SB and SbMATE, this suggests a possible pleiotropic effect of SbMATE in providing tolerance to aluminum toxicity and to low-P conditions (Leiser et al, 2014b).…”

“…The West African sorghum diversity panel consists of 187 sorghum genotypes from six West and Central African countries, consisting of seven racial groups (three pure races and four intermediate groups) including breeding accessions and landraces with various degrees of photoperiod sensitivity and internode lengths (Leiser et al, 2014b).…”

Association analysis of low-phosphorus tolerance in West African pearl millet using DArT markers

“…Association mapping utilizes ancestral recombination in natural populations to overcome the limitations associated with classical linkage mapping of reduced resolution of biparental mapping populations due to small population sizes and modest degrees of recombination (Flint-Garcia et al 2003, 2005: Kraakman et al 2004Stich et al 2008). Using association mapping, Leiser et al (2014) and Hufnagel et al (2014) have detected several genomic regions in sorghum associated with various low-P tolerance traits at different stages of crop maturity.…”