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

Abstract

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

Evolutionarily Distinct BAHD N-acyltransferases are Responsible for Natural Variation of Aromatic Amine Conjugates in Rice

“…Unlike complex quantitative traits (such as flowering time) for which little epistasis has been detected (Buckler et al, 2009;Morris et al, 2013;Zuo and Li, 2014), variation in levels of metabolites, especially specialized metabolites, is predominately controlled by epistasis in both RILs (Kliebenstein et al, 2002;Loudet et al, 2003;Calenge et al, 2006;Lisec et al, 2008;Rowe et al, 2008;Gong et al, 2013) and natural populations (Chan et al, 2011;Chen et al, 2014;Sauvage et al, 2014;Dong et al, 2015;Matsuda et al, 2015). Similar results were observed between some of the loci identified in our study (Supplemental Figure 5 and Supplemental Table 3).…”

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

“…Supplemental Figure S2A reveals an evident change in DK with four subpopulations, indicating that this is a reasonable level of differentiation for the SAPst. As described previously, the pattern of genetic diversity in sorghum largely reflects racial and geographical origins (Casa et al, 2008;Caniato et al, 2011;Morris et al, 2013). The largest subpopulation, with 112 accessions, comprised mostly caudatum sorghums, followed by subpopulations with prevalence of durra, guinea/kafir, and breeding lines, with 93, 50, and 32 accessions, respectively.…”

Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition

“…The genotyped by sequencing SNP markers for the SAP lines used in this study have been described previously (Morris et al, 2013). After removing SNPs with more than 20% missing data and minor allele frequencies below 0.05, genotype data for 78,012 SNPs remained.…”

“…These lines were previously genotyped by sequencing (Morris et al, 2013). The SAP lines were grown in three experiments: Lubbock, Texas, in 2008(SAP 2008Puerto Vallarta, Mexico, in 2012(SAP 2012; and two field replicates produced in Florence, South Carolina, in 2013(SAP 2013-1 and SAP 2013.…”

“…Furthermore, a GWA mapping population is composed of lines that have undergone numerous recombination events, allowing for a narrower mapping interval. Previous GWA studies in maize (Tian et al, 2011), rice , and sorghum (Morris et al, 2013) have been successful in identifying the genetic basis for various agronomic traits. Here, we analyzed the seed ionome from a communitygenerated association panel to identify potential loci underlying seed element accumulation in sorghum.…”