Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population

Abstract

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 (<15°) 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.

Crop modeling defines opportunities and challenges for drought escape, water capture, and yield increase using chilling-tolerant sorghum

“…In breeding and genetics studies, chilling tolerance is most often characterized through seedling emergence rate and seedling vigor scores, usually based on visual evaluation (Burow et al, 2011; Franks et al, 2006; Marla et al, 2019; Parra-Londono et al, 2018). By contrast, crop models simulate days to emergence, seedling biomass weight, and leaf area.…”

“…For planting dates in early and mid June, CERES-Sorghum has shown satisfactory predictions for anthesis, grain yield, and evapotranspiration across Kansas (Araya et al, 2017; Staggenborg and Vanderlip, 2005; White et al, 2015). To evaluate the model accuracy in predicting days to emergence for a chilling-tolerant genotype (Kaoliang), simulations were conducted to match field experiments that were planted in April, May, and June in 2016–2018 at three sites in Kansas (Marla et al, 2019). For these simulations, cultivar specific-parameters (G) were obtained for full-season hybrids (80 days to anthesis and 140 days to physiological maturity) and short-season hybrids (60 days to anthesis and 110 to physiological maturity) (Araya et al, 2018).…”

“…The model accuracy was quantified using the root mean square error (RMSE) that determines the distance of model prediction from a perfect prediction (Wallach et al, 2014). Unlike commercial grain sorghum hybrids with semi-dwarf stature and high sink capacity, kaoliang sorghum has undesirable traits for this cropping system such as tall plants and low harvest index (Marla et al, 2019). Due to these differences, the direct comparison of observed and simulated grain weight for these known chilling tolerant genotypes is not possible.…”

Sorghum breeding in the genomic era: opportunities and challenges

“…Another study of cold tolerance identified eight regions associated with final emergence percentage (FEP) and seedling survival (SR) on chromosomes SBI-01, -02, -03, -06, -09 and -10 (Parra-londono et al 2018b ). Colocalisation of chilling tolerance loci with grain tannin and dwarfing genes further indicated that selection for nontannin and dwarfing alleles in early grain sorghum breeding inadvertently resulted in chilling sensitivity (Marla et al 2019 ). Similarly, heat stress affects sorghum growth and photosynthesis.…”

Evidence for microbiome-dependent chilling tolerance in sorghum

“…While sorghum germplasm resources are diverse and under development for early season chilling tolerance (Chopra et al 2015, Marla et al 2019, Moghimi et al 2019, Ostmeyer et al 2020), the potential for early season microbial-enhanced chilling tolerance in sorghum has not yet been explored. Simultaneously evaluating diverse sorghum genotypes for genetic chilling tolerance and microbe-enhanced chilling tolerance would leverage a novel synergistic approach to early season chilling tolerance.…”