Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers

Bouchet, Sophie; Pot, David; Deu, Monique; Rami, Jean-François; Billot, Claire; Perrier, Xavier; Rivallan, Ronan; Gardès, Laëtitia; Lan, Xiujin; Wenzl, Peter; Kilian, Andrzej; Glaszmann, Jean-Christophe

doi:10.1371/journal.pone.0033470

Cited by 88 publications

(88 citation statements)

References 67 publications

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“…Of 27,412 annotated genes in the reference sorghum genome, 72% were tagged by a SNP within the gene and 99% were tagged by a SNP within 10 kb. Importantly, this genome-wide map of SNP variation is of sufficient resolution for GWAS in sorghum, given >100,000 SNPs are estimated to be required (14). Additionally, because of simultaneous SNP discovery and genotyping, this sequencing-based SNP map will have little ascertainment bias and greater power for mapping studies (20).…”

Section: Resultsmentioning

confidence: 99%

“…In addition, genome-wide association studies (GWAS) have been used to elucidate the genetic basis of agronomic traits in rice (12) and maize (10). Nucleotide diversity scans (13,14) and association studies (5,15) have been carried out in sorghum, but the resolution and sensitivity of these studies has been limited by the small number of markers (14). Thus, compared with maize and rice, less is known about the genetic basis of agronomic traits in sorghum.…”

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confidence: 99%

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Population genomic and genome-wide association studies of agroclimatic traits in sorghum

Morris

Ramu

Deshpande

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

752

820

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Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNP map, we have characterized population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to diverse agroclimatic regions across Africa and Asia. To better understand the genomic patterns of diversification in sorghum, we quantified variation in nucleotide diversity, linkage disequilibrium, and recombination rates across the genome. Analyzing nucleotide diversity in landraces, we find evidence of selective sweeps around starch metabolism genes, whereas in landrace-derived introgression lines, we find introgressions around known height and maturity loci. To identify additional loci underlying variation in major agroclimatic traits, we performed genome-wide association studies (GWAS) on plant height components and inflorescence architecture. GWAS maps several classical loci for plant height, candidate genes for inflorescence architecture. Finally, we trace the independent spread of multiple haplotypes carrying alleles for short stature or long inflorescence branches. This genome-wide map of SNP variation in sorghum provides a basis for crop improvement through marker-assisted breeding and genomic selection.Sorghum bicolor | quantitative trait locus | adaptation

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

Morris

Ramu

Deshpande

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

752

820

View full text Add to dashboard Cite

show abstract

“…The 310 randomly distributed SNP markers used here do not provide genome saturation within the low LD context in the association panel (Bouchet et al, 2012); consequently, the chances of association with the phenotypic traits can be considered negligible. Thus, it provides a null distribution to test the efficiency of different models to control for false-positive associations.…”

Section: Sapstmentioning

confidence: 99%

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

et al. 2014

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Low soil phosphorus (P) availability is a major constraint for crop production in tropical regions. The rice (Oryza sativa) protein kinase, PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was previously shown to enhance P acquisition and grain yield in rice under P deficiency. We investigated the role of homologs of OsPSTOL1 in sorghum (Sorghum bicolor) performance under low P. Association mapping was undertaken in two sorghum association panels phenotyped for P uptake, root system morphology and architecture in hydroponics and grain yield and biomass accumulation under low-P conditions, in Brazil and/or in Mali. Root length and root surface area were positively correlated with grain yield under low P in the soil, emphasizing the importance of P acquisition efficiency in sorghum adaptation to low-P availability. SbPSTOL1 alleles reducing root diameter were associated with enhanced P uptake under low P in hydroponics, whereas Sb03g006765 and Sb03g0031680 alleles increasing root surface area also increased grain yield in a low-P soil. SbPSTOL1 genes colocalized with quantitative trait loci for traits underlying root morphology and dry weight accumulation under low P via linkage mapping. Consistent allelic effects for enhanced sorghum performance under low P between association panels, including enhanced grain yield under low P in the soil in Brazil, point toward a relatively stable role for Sb03g006765 across genetic backgrounds and environmental conditions. This study indicates that multiple SbPSTOL1 genes have a more general role in the root system, not only enhancing root morphology traits but also changing root system architecture, which leads to grain yield gain under low-P availability in the soil.

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“…The DArT system produces hyper variable dominant markers [75], with over 5,000 polymorphic loci currently available in eucalypts [75,76]. Despite the lower information content per marker due to dominance, using such large marker datasets and similar methods to those used here would presumably lead to highly [77]. Alternatively, with so many markers it may be possible to identify subsets of species-specific loci or alleles that could differentiate hybrid generations with greater power than microsatellite based systems, without the need to assay all 5,000 loci.…”

Section: Performance Of the Approachmentioning

confidence: 99%

Assessing a Bayesian Approach for Detecting Exotic Hybrids between Plantation and Native Eucalypts

Larcombe

Vaillancourt

Jones

et al. 2014

International Journal of Forestry Research

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Eucalyptus globulus is grown extensively in plantations outside its native range in Australia. Concerns have been raised that the species may pose a genetic risk to native eucalypt species through hybridisation and introgression. Methods for identifying hybrids are needed to enable assessment and management of this genetic risk. This paper assesses the efficiency of a Bayesian approach for identifying hybrids between the plantation species E. globulus and E. nitens and four at-risk native eucalypts. Range-wide DNA samples of E. camaldulensis, E. cypellocarpa, E. globulus, E. nitens, E. ovata and E. viminalis, and pedigreed and putative hybrids (n = 606), were genotyped with 10 microsatellite loci. Using a two-way simulation analysis (two species in the model at a time), the accuracy of identification was 98% for first and 93% for second generation hybrids. However, the accuracy of identifying simulated backcross hybrids was lower (74%). A six-way analysis (all species in the model together) showed that as the number of species increases the accuracy of hybrid identification decreases. Despite some difficulties identifying backcrosses, the two-way Bayesian modelling approach was highly effective at identifying 1 , which, in the context of E. globulus plantations, are the primary management concern.

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Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers

Cited by 88 publications

References 67 publications

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

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

Assessing a Bayesian Approach for Detecting Exotic Hybrids between Plantation and Native Eucalypts

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