Association genetics of early season cold and late season frost tolerance in Sorghum bicolor

Sorghum [Sorghum bicolor (L.) Moench] is a multipurpose crop that is highly susceptible to low temperature stress. Early season cold (ESC) greatly affects seed germination, seedling vigor, and root architecture, whereas late-season frost (LSF) reduces fertility, yield, and nutrition quality and content in sorghum. Here, an association mapping study was conducted to delineate the genetics of ESC and LSF tolerance in sorghum. A total of 10 single nucleotide polymorphisms (SNPs) and 17 quantitative trait loci (QTL) were identified for ESC, and 40 SNPs were identified for LSF. The diversity panel exhibited extensive variation for plant traits measured for their association with ESC and LSF tolerance. Two QTL colocalized with the classical tannin genes Tan1 (S4_61580203) and Tan2 (S2_7777693) were identified for ESC tolerance. We also identified additional putative candidate genes such as Sobic.001G157100 (Nonphototropic hypocotyl 3, NPH3), Sobic.001G156600 (Lectin receptor-like serine/threonine kinase), and Sobic.006G061100 (Sucrose nonfermenting 1 related protein kinase 1, SnRK1) for ESC tolerance and Sobic.006G139900 (UDP-glucoronosyl and UDP-glucosyl transferase), Sobic.002G187400 (Serine/threonine protein kinase), and Sobic.004G333700 (Ca²⁺/calmodulin-dependent protein phosphatase) for LSF tolerance. Tan1 and Tan2 play a major role in seed dormancy and induce resistance against soil-borne pathogens under cold and wet soil conditions. Seed tannin content may be used as an indirect selection marker for identifying cold tolerant germplasm for breeding. NPH3 and SnRK1 regulate seed germinability under cold stress in various crops. Candidates identified in this study could be further exploited to develop low temperature tolerant cultivars as proxies in marker-assisted breeding, genomic selection, and genetic engineering.