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

Abstract

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 colocialized 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.

Precise colocalization of sorghum’s major chilling tolerance locus with Tannin1 due to tight linkage drag rather than antagonistic pleiotropy

“…From the segregating progeny, homozygotes for both alleles of the QTL of interest were selected, making eight total BC4F2 lines. Those eight lines were then advanced to the BC4F5 generation through single seed descent generating four pairs of NIL siblings (Marla et al 2023 ).…”

Temperature‐smart plants: A new horizon with omics‐driven plant breeding

“…They also demonstrated that exposure to HS (45 C) for 6 h provided more precise differentiation between heat-treated and control plants compared to other long-term exposures (Gao et al, 2020). Marla et al (2022) used an unmanned aircraft system (UAS) high-throughput phenotyping platform to analyze sorghum phenotypes for chilling tolerance. The UAS-derived normalized difference vegetation index values obtained from phenomic mapping were correlated with QTL related to CS tolerance identified in the same study (Marla et al, 2022).…”

“…Marla et al (2022) used an unmanned aircraft system (UAS) high-throughput phenotyping platform to analyze sorghum phenotypes for chilling tolerance. The UAS-derived normalized difference vegetation index values obtained from phenomic mapping were correlated with QTL related to CS tolerance identified in the same study (Marla et al, 2022). Despite significant progress in high-throughput genotyping in recent decades, the development of rapid and efficient phenotyping methods has lagged.…”

The role of phenomics and genomics in delineating the genetic basis of complex traits in millets

“…QTL mapping has been used in sorghum to study genomics and phenomics. For example, a study utilized a chilling nested association mapping population with 43 K GBS SNPs and uncrewed aircraft system (UAS) high‐throughput phenotyping to provide high‐resolution chilling tolerance (CT) mapping, addressing weak trait‐to‐QTL association from previous sorghum CT studies (Marla et al 2023). UAS‐based high‐throughput phenotyping offers promising avenues for enhancing millet research and crop improvement.…”