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

Sandeep R. Marla, Gloria Burow, Ratan Chopra, Chad Hayes, Marcus O. Olatoye, Terry Felderhoff, Zhenbin Hu, Rubi Raymundo, Ramasamy Perumal, Geoffrey P. Morris

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


Dissecting the genetic architecture of stress tolerance in crops is critical to understand and improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could provide longer growing seasons and drought escape, but chilling tolerance (,15̊) is generally lacking in tropical-origin crops. Here we developed a nested association mapping (NAM) population to dissect the genetic architecture of early-season chilling tolerance in the tropical-origin cereal sorghum (Sorghum bicolor [L.] Moench). The NAM resource, developed from reference line BTx623 and three chilling-tolerant Chinese lines, is comprised of 771 recombinant inbred lines genotyped by sequencing at 43,320 single nucleotide polymorphisms. We phenotyped the NAM population for emergence, seedling vigor, and agronomic traits (.75,000 data points from ~16,000 plots) in multi-environment field trials in Kansas under natural chilling stress (sown 30-45 days early) and normal growing conditions. Joint linkage mapping with early-planted field phenotypes revealed an oligogenic architecture, with 5-10 chilling tolerance loci explaining 20-41% of variation. Surprisingly, several of the major chilling tolerance loci co-localize precisely with the classical grain tannin (Tan1 and Tan2) and dwarfing genes (Dw1 and Dw3) that were under strong directional selection in the US during the 20th century. These findings suggest that chilling sensitivity was inadvertently selected due to coinheritance with desired nontannin and dwarfing alleles. The characterization of genetic architecture with NAM reveals why past chilling tolerance breeding was stymied and provides a path for genomics-enabled breeding of chilling tolerance.

Original languageEnglish (US)
Pages (from-to)4045-4057
Number of pages13
JournalG3: Genes, Genomes, Genetics
Issue number12
StatePublished - 2019

Bibliographical note

Funding Information:
The authors would like to thank Halee Hughes and Matt Davis for excellent technical support. Development of the NAM was supported by USDA ARS CRIS#3096-21000-021-00D and United Sorghum Checkoff Program (USCP) Grant on “Sorghum Genetic Enhancement” to USDA-ARS, Lubbock, TX. Dr. Ratan Chopra was supported by a grant from United Sorghum Checkoff Program. The study was supported by the Kansas Grain Sorghum Commission and Kansas Department of Agriculture. The study was carried out using the Beocat high-performance computing facility and Integrated Genomics Facility at Kansas State University. This study is contribution 20-054-J from the Kansas Agricultural Experiment Station. We thank the three anonymous reviewers and editor for suggestions that improved the manuscript.

Publisher Copyright:
Copyright © 2019 Marla et al.


  • Adaptation
  • Antagonistic
  • Climate
  • Cold tolerance
  • Crop evolution
  • Linkage drag
  • Multiparental
  • Pleiotropy
  • Population

PubMed: MeSH publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Journal Article


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