Development and characterization of a sorghum multi-parent advanced generation intercross (MAGIC) population for capturing diversity among seed parent gene pool.

Kumar N, Boatwright JL, Brenton ZW, Sapkota S, Ballén-Taborda C, Myers MT, Cox WA, Jordan KE, Kresovich S, Boyles RE

Published: 10 February 2023 in G3 (Bethesda, Md.)
Keywords: DArT markers, QTL mapping, genome-wide association study (GWAS), multiparent advanced generation inter-cross (MAGIC), sorghum
Pubmed ID: 36755443
DOI: 10.1093/g3journal/jkad037

Multiparent advanced eneration inter-cross (MAGIC) populations improve the precision of quantitative trait loci (QTL) mapping over biparental populations by incorporating increased diversity and opportunities to reduce linkage disequilibrium among variants. Here, we describe the development of a MAGIC B-Line (MBL) population from an inter-cross among 4 diverse founders of grain sorghum [Sorghum bicolor (L.) Moench] across different races (kafir, guinea, durra, and caudatum). These founders were selected based on genetic uniqueness and several distinct qualitative features including panicle architecture, plant color, seed color, endosperm texture, and awns. A whole set of MBL (708 F6) recombinant inbred lines along with their founders were genotyped using Diversity Arrays Technology (DArTseq) and 5,683 single-nucleotide polymorphisms (SNPs) were generated. A genetic linkage map was constructed using a set of polymorphic, quality-filtered markers (2,728 SNPs) for QTL interval-mapping. For population validation, 3 traits (seed color, plant color, and awns) were used for QTL mapping and genome-wide association study (GWAS). QTL mapping and GWAS identified 4 major genomic regions located across 3 chromosomes (Chr1, Chr3, and Chr6) that correspond to known genetic loci for the targeted traits. Founders of this population consist of the fertility maintainer (A/B line) gene pool and derived MBL lines could serve as female/seed parents in the cytoplasmic male sterility breeding system. The MBL population will serve as a unique genetic and genomic resource to better characterize the genetics of complex traits and potentially identify superior alleles for crop improvement efforts to enrich the seed parent gene pool.

Department of Energy - Advanced Research Project Agency DE-AR0001134
Foundation for Food and Agriculture Research CA21-SS-0000000061
NIFA - Multistate Hatch project - “Plant Genetic Resources 30 Conservation and Utilization” 1016646
United States Department of Agriculture 2011-67009-30594