A High Resolution Genome-Wide Map of Recombination Rates and Hotspots in Sorghum

Genome-wide characterization of recombination rates and hotspots is essential to accelerate marker-assisted breeding and to understand genome organization and evolution. Here we quantify recombination rates and hotspots across all ten chromosomes of Sorghum bicolor in four panels (landraces, breeding lines, wild genotypes and a recombination inbred line [RIL] population) using 373,446 SNPs generated through genotyping-by-sequencing (GBS). Average genome-wide recombination rate (ρ, expressed in 4N_er/kb) in sorghum varies greatly from 9.66 (landraces) to 3.85 (breeding lines). The number of recombination hotspots per chromosome ranged from 2148 in landraces to 907 in RILs. The average number high-intensity hotspots (>20 times the background rate) range from 67/chr (landraces) to 16/chr (RILs).  Breeding lines have an average of 45 hotspots/chr (67% of landraces). This suggests that 33% of hotspot regions were lost in breeding lines during the process of evolution from landrace to elite cultivar. In eleven diverse wild sorghum genotypes, we observed lower recombination rates and hotspot density (2.35 4N_er/kb and 12 hotspots/chr) suggesting limited recombination among distinct wild population. Density of hotspots is greater in distal chromosome regions as compared to centromeric regions. We are also defining haplotypes created by historical recombination events to help in identification of haplotype-trait associations.