31Dissecting the genetic architecture of stress tolerance in crops is critical to understand and 32 improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could 33 provide longer growing seasons and drought escape, but chilling tolerance (<15°) is generally 34 lacking in tropical-origin crops. Here we developed a nested association mapping (NAM) 35 population to dissect the genetic architecture of early-season chilling tolerance in the tropical-36 origin cereal sorghum (Sorghum bicolor [L.] Moench). The NAM resource, developed from 37 reference line BTx623 and three chilling-tolerant Chinese lines, is comprised of 771 recombinant 38 inbred lines genotyped by sequencing at 43,320 single nucleotide polymorphisms. We 39 phenotyped the NAM population for emergence, seedling vigor, and agronomic traits (>75,000 40data points from ~16,000 plots) in multi-environment field trials in Kansas under natural chilling 41 stress (sown 30-45 days early) and normal growing conditions. Joint linkage mapping with 42 early-planted field phenotypes revealed an oligogenic architecture, with 5-10 chilling tolerance 43 loci explaining 20-41% of variation. Surprisingly, several of the major chilling tolerance loci co-44 localize precisely with the classical grain tannin (Tan1 and Tan2) and dwarfing genes (Dw1 and 45Dw3) that were under strong directional selection in the US during the 20th century. These 46 findings suggest that chilling sensitivity was inadvertently selected due to coinheritance with 47 desired nontannin and dwarfing alleles. The characterization of genetic architecture with NAM 48 reveals why past chilling tolerance breeding was stymied and provides a path for genomics-49 enabled breeding of chilling tolerance. 50 51
Article Summary 52Chilling sensitivity limits productivity of tropical-origin crops in temperate climates, and remains 53 poorly understood at a genetic level. We developed a nested association mapping resource in 54 sorghum, a tropical-origin cereal, to understand the genetic architecture of chilling tolerance. 55Linkage mapping of growth traits from early-planted field trials revealed several major chilling 56 tolerance loci, including some colocalized with genes that were selected in the origin of US grain 57 sorghum. These findings suggest chilling sensitivity was inadvertently selected during 20th 58 century breeding, but can be bypassed using a better understanding of the underlying genetic 59 architecture. 60 61