Sorghum MAGIC Population: Structure and Potential for Genetics Research and Breeding

Multi-parent advanced generation intercross (MAGIC) populations have emerged as the most powerful next generation mapping resources that combine high genetic recombination and variability. We describe here the construction, genome-wide SNP map and genomic structure of a nineteen-parent MAGIC population.

This is the first and the most advanced sorghum MAGIC population developed thus far with the aid of a genetic male sterility system. It consists of one thousand S₇ inbreds, derived by single seed descent (SSD) from a random mated base population. Genotyping-by-sequencing (GBS) of a subset of 200 sorghum MAGIC lines identified 79,728 genome-wide SNPs. High SNP density corresponded with genomic regions of high gene content. The proportion of SNPs on each chromosome relative to the total detected SNPs ranged from 6% on chromosome seven to 15% on chromosome one. The 79K SNPs clustered the nineteen MAGIC founders into three groups. However, PCA, structure analysis and neighbor-joining tree provided no strong evidence for population structure in the MAGIC population. The lack of evidence of population structure makes this population amenable for GWAS. Patterns of linkage disequilibrium (LD) showed the MAGIC population to be highly recombined. LD blocks decayed to r² 0.2 within 50-100 kb.

The sorghum MAGIC population therefore, serves a dual purpose: highly recombined mapping resource for precise QTL mapping and genetically diverse for use in variety development. Distinct from naturally diverse germplasm, this population is custom-made for breeders from multiple elite lines with wide array of useful traits.