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Abstract
Integration of confidence intervals identified by traditional QTL mapping and phenotype-genotype associations determined by SNP based association mapping reveals genomic regions for genes influencing traits of interest, and provides for comparisons to investigate relative merits of these two mapping strategies. Using 354 accessions from a sorghum association panel (SAP) characterized at 265,487 SNPs, we performed genome-wide association studies (GWAS) on 9 traits related to inflorescence morphology, 6 traits related to plant height and 2 components of leaf architecture, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. Hybridization and selection have played important roles in shaping morphological characteristics and the genetic basis of the inflorescence and plant height in cultivated sorghum. Genetic comparison across subpopulations in sorghum, such as wild types, tropical landraces, conversion lines and elite varieties allowed us to evaluate genome-wide effects resulting from hybridization and selection. Comparative studies across taxa show functionally conserved hotspots in sorghum, rice and maize for the key domestication traits that do not appear to reflect conserved single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum.