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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #319892

Research Project: Genetic Enhancement of Sorghum as a Versatile Crop

Location: Plant Stress and Germplasm Development Research

Title: A sorghum mutant resource as an efficient platform for gene discovery in grasses

Author
item Jiao, Yinping
item Burke, John
item Chopra, Ratan
item Burow, Gloria
item Chen, Junping
item Wang, Bo - Cold Spring Harbor Laboratory
item Hayes, Chad
item Emendack, Yves
item Ware, Doreen
item Xin, Zhanguo

Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2016
Publication Date: 6/27/2016
Citation: Jiao, Y., Burke, J.J., Chopra, R., Burow, G.B., Chen, J., Wang, B., Hayes, C.M., Emendack, Y., Ware, D., Xin, Z. 2016. A sorghum mutant resource as an efficient platform for gene discovery in grasses. The Plant Cell. 28:1551-1562.

Interpretive Summary: Sorghum (Sorghum bicolor L. Moench) is a versatile crop that can be used for food, animal feed, and bioenergy. We developed a pedigreed mutant library using ethyl methanesulfonate (EMS) treated seeds of BTx623, the elite inbred line used to generate the reference genome sequence. Conventionally, the EMS-induced mutations are identified by techniques that can detect single-nucleotide mismatches in heteroduplexes of individual PCR amplicons. We applied whole-genome sequencing to 256 phenotyped mutant lines of sorghum to 16x coverage. Comparisons with the reference sequence revealed >1.8 million canonical EMS-induced G/C to A/T mutations, 22% of which were in genic regions, affecting >95% of genes in the sorghum genome. The vast majority (97.5%) of the induced mutations were distinct from natural variations. By applying the mutation database to phenotype analysis, we identified four causal gene mutations affecting drought tolerance, two mutations affecting heat tolerance, and two mutations affecting seed size that corresponded to previously reported seed size QTLs. Our results demonstrate that this collection of sequenced mutant lines can be used to efficiently discover new traits and their underlying causal mutations, thereby accelerating sorghum breeding. The sequenced mutant lines provide an efficient platform for rapid discovery of causal gene mutations underlying traits that have potential to be directly used in sorghum improvement.

Technical Abstract: Ethyl methanesulfonate (EMS) efficiently generates high-density mutations in genomes. Conventionally, these mutations are identified by techniques that can detect single-nucleotide mismatches in heteroduplexes of individual PCR amplicons. We applied whole-genome sequencing to 256 phenotyped mutant lines of sorghum (Sorghum bicolor L. Moench) to 16x coverage. Comparisons with the reference sequence revealed >1.8 million canonical EMS-induced G/C to A/T mutations, 22% of which were in genic regions, affecting >95% of genes in the sorghum genome. The vast majority (97.5%) of the induced mutations were distinct from natural variations. By applying the mutation database to phenotype analysis, we identified four causal gene mutations affecting drought tolerance, two mutations affecting heat tolerance, and two mutations affecting seed size that corresponded to previously reported seed size QTLs. Our results demonstrate that this collection of sequenced mutant lines can be used to efficiently discover new traits and their underlying causal mutations, thereby accelerating sorghum breeding.