Genetic architecture of chilling tolerance in sorghum dissected with a nested association mapping population

Authors: MARLA, SANDEEP - Kansas State University; Burow, Gloria; CHOPRA, RATAN - University Of Minnesota; Hayes, Chad; OLATOYE, MARCUS - Kansas State University; FELDERHOFF, TERRY - Kansas State University; HU, ZHENBIN - Kansas State University; RAYMUNDO, RUBI - Kansas State University; PERUMAL, RAMASAMY - Kansas State University; MORRIS, GEOFFREY - Kansas State University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/26/2019
Publication Date: 12/1/2019
Citation: Marla, S., Burow, G.B., Chopra, R., Hayes, C.M., Olatoye, M., Felderhoff, T., Hu, Z., Raymundo, R., Perumal, R., Morris, G. 2019. Genetic architecture of chilling tolerance in sorghum dissected with a nested association mapping population. G3, Genes/Genomes/Genetics. 9:4045-4057. https://doi.org/10.1101/622894.
DOI: https://doi.org/10.1101/622894

Interpretive Summary: Grain sorghum in the United States lacks early season chilling tolerance (also known as early season cold tolerance) which prevents full season growth and hampers yield. To help solve this challenge, USDA-ARS scientists at Lubbock, Texas, developed a sorghum multiparent population with 771 lines for use in an in-depth genetic characterization of response to early season cool temperatures in cooperation with scientists at Kansas State University. Genetic analysis revealed 5–10 DNA sites or loci controlled early-season chilling tolerance in these sorghums. These findings suggest that co-inheritance of chilling tolerance loci with non-favorable traits for sorghum grains could have hindered conventional breeding efforts aimed at developing US grain sorghum with chilling tolerance. Therefore, molecular techniques may need to be developed to guide development of sorghums with chilling tolerance without undesirable traits.

Technical Abstract: Information on the genetic architecture underlying abiotic stress tolerance in agronomic crops is critical for crop improvement, specifically in the light of fluctuating climatic conditions. We investigated the genetic basis of early-season chilling tolerance in sorghum (Sorghum bicolor [L.] Moench), a tropical-origin C4 cereal that recently adapted to chilling stress in northern China. A US × Chinese Kaoliangs multi-parental population (MPP) resource, comprising of 771 recombinant inbred lines (RILs) was genotyped by sequencing at 43,320 single nucleotide polymorphisms (SNPs). The MPP was evaluated for chilling tolerance (emergence and seedling vigor) and agronomic traits (>75,000 phenotypes from ~16,000 plots), in multi-environment field trials in Kansas, at early (30–45 days) and conventional planting dates. A joint-multiple family linkage analysis with stepwise regression using the best linear unbiased predictors from early-planted (cooler temperature) trials detected 5–10 significant positive loci explaining 20–41% variance of early-season chilling tolerance traits. Moreover, the chilling tolerance loci detected on chromosomes 2, 4, 7, and 9 co-localized with tannin genes, B1 (Tan2) and B2 (Tan1), and classical dwarfing genes, Dw3 and Dw1, respectively. These results suggest the complex nature of early-season chilling tolerance and that the genes conferring the traits are tightly linked genes to major temperate zone adaptation genes including short stature and low tannins, or could have pleiotropic to these genes. Given that grain tannin and tall stature are traits considered unfavorable for US grain sorghums, our findings suggest that chilling susceptibility was inadvertently selected due to coinheritance with favored alleles for low-tannin and short stature. The greater power and resolution afforded by newly developed MPP revealed how genetic architecture of chilling tolerance could have hindered previous breeding efforts and these current results offer novel approaches forward for molecular breeding for improved chilling tolerance in sorghum.