Genomics and Phenomics Enabled Prebreeding Improved Early-Season Chilling Tolerance in Sorghum

Sandeep Marla, Terry Felderhoff, Chad Hayes, Ramasamy Perumal, Xu Wang, Jesse Poland, Geoffrey P Morris

Research output: Contribution to journalArticlepeer-review


In temperate climates, earlier planting of tropical-origin crops can provide longer growing seasons, reduce water loss, suppress weeds, and escape post-flowering drought stress. However, chilling sensitivity of sorghum, a tropical-origin cereal crop, limits early planting and over 50 years of conventional breeding has been stymied by coinheritance of chilling tolerance (CT) loci with undesirable tannin and dwarfing alleles. In this study, phenomics and genomics-enabled approaches were used for prebreeding of sorghum early-season CT. Uncrewed aircraft systems (UAS) high-throughput phenotyping platform tested for improving scalability showed moderate correlation between manual and UAS phenotyping. UAS normalized difference vegetation index (NDVI) values from the chilling nested association mapping population detected CT QTL that colocalized with manual phenotyping CT QTL. Two of the four first-generation KASP molecular markers, generated using the peak QTL SNPs, failed to function in an independent breeding program as the CT allele was common in diverse breeding lines. Population genomic FST analysis identified SNP CT alleles that were globally rare but common to the CT donors. Second-generation markers, generated using population genomics, were successful in tracking the donor CT allele in diverse breeding lines from two independent sorghum breeding programs. Marker-assisted breeding, effective in introgressing CT allele from Chinese sorghums into chilling-sensitive US elite sorghums, improved early-planted seedling performance ratings in lines with CT alleles by up to 13–24% compared to the negative control under natural chilling stress. These findings directly demonstrate the effectiveness of high-throughput phenotyping and population genomics in molecular breeding of complex adaptive traits.
Original languageEnglish (US)
JournalG3 (Bethesda, Md.)
StatePublished - May 26 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-06-07
Acknowledgements: This research was partially funded by the Foundation for Food and Agriculture Research, Seeding Solution CA18-SS-0000000094, Bridging the Genome-to-Phenome Breeding Gap for Water-Efficient Crop Yields, and the Kansas Grain Sorghum Commission. This research was supported by funding from the Kansas Grain Sorghum Commission (KGSC), Foundation for Food and Agriculture Research (FFAR), and TERRA-REF: US Department of Energy’s Advanced Research Projects Agency- Energy (ARPA-E). The study was carried out using the Beocat high-performance computing facility. This study is a contribution --- from the Kansas Agricultural Experiment Station. We would like to thank Matt Davis and Troy Ostmeyer for excellent technical support. The authors state that they have no conflict of interest to declare for this research.

ASJC Scopus subject areas

  • General Medicine


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