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.

Genomic selection in maize (Zea mays L.) has been one factor that has increased the rate of genetic gain when compared with other cereals. However, the technological foundations in maize also exist in other cereal crops that would allow prediction of hybrid performance based on general (GCA) and specific (SCA) combining abilities applied through genomic-enabled prediction models. Further, the incorporation of genotype × environment (G × E) interaction effects present an opportunity to deploy hybrids to targeted environments. To test these concepts, a factorial mating design of elite yet divergent grain sorghum lines generated hybrids for evaluation. Inbred parents were genotyped, and markers were used to assess population structure and develop the genomic relationship matrix (GRM). Grain yield, height, and days to anthesis were collected for hybrids in replicated trials, and best linear unbiased estimates were used to train classical GCA-SCA-based and genomic (GB) models under a hierarchical Bayesian framework. To incorporate population structure, GB was fitted using the GRM of both parents and hybrids. For GB models, G × E interaction effects were included by the Hadamard product between GRM and environments. A leave-one-out cross-validation scheme was used to study the prediction capacity of models. Classical and genomic models effectively predicted hybrid performance and prediction accuracy increased by including genomic data. Genomic models effectively partitioned the variation due to GCA, SCA, and their interaction with the environment. A strategy to implement genomic selection for hybrid sorghum [Sorghum bicolor (L.) Moench] breeding is presented herein.

Stomatal density (SD) and stomatal complex area (SCA) are important traits that regulate gas exchange and abiotic stress response in plants. Despite sorghum (Sorghum bicolor) adaptation to arid conditions, the genetic potential of stomata-related traits remains unexplored due to challenges in available phenotyping methods. Hence, identifying loci that control stomatal traits is fundamental to designing strategies to breed sorghum with optimized stomatal regulation. We implemented both classical and deep-learning methods to characterize genetic diversity in 311 grain sorghum accessions for stomatal traits at two different field environments. Nearly 12,000 images collected from abaxial and adaxial leaf surfaces revealed substantial variation in stomatal traits. Our study demonstrated significant accuracy between manual and deep-learning methods in predicting SD and SCA. In sorghum, SD was 32-39% greater on the abaxial vs. the adaxial surface, while SCA on the abaxial surface was 2-5% lower than on the adaxial surface. GWAS identified 71 genetic loci (38 were environment-specific) with significant genotype to phenotype associations for stomatal traits. Putative causal genes underlying the phenotypic variation were identified. Accessions with similar SCA but carrying contrasting haplotypes for SD were tested for stomatal conductance and carbon assimilation under field conditions. Our findings provide a foundation for further studies on the genetic and molecular mechanisms controlling stomata patterning and regulation in sorghum. An integrated physiological, deep learning, and genomic approach allowed us to clarify the genetic control of natural variation in stomata traits in sorghum, and can be applied to other plants.

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

Host-plant resistance has been a fundamental component of aphid management in cereal crops. Over decades, various sources of resistance to greenbug, Schizaphis graminum (Rondani), were bred into cultivars of sorghum, Sorghum bicolor (L.) Moench, to counter recurring virulent greenbug biotypes. The recent invasion of sugarcane aphid, Melanaphis sacchari (Zehntner), raised questions about plant-mediated interactions between the two aphids and the possibility of using greenbug antibiosis against sugarcane aphid. The present work was undertaken to characterize the impact of PI 550610 resistance to 'biotype I' greenbug, expressed in seed parental line KS 116B, on aphid life histories and to observe plant-mediated interactions between aphid species in its presence and absence. At 23°C, sugarcane aphid nymphs matured 1.5 d faster than greenbug nymphs on susceptible hybrid P8500, but at similar rates on the resistant line, which delayed maturity by 1-1.5 d in both species and increased juvenile mortality by three- to fourfold. Sugarcane aphid reproductive rate was double that of greenbug on susceptible sorghum (4.45 vs. 2.30 nymphs per female per day), but not significantly different on the resistant one (3.09 vs. 2.27). Thus, PI 550610 expresses antibiosis, not tolerance, to these aphids. Coinfestation of P8500 had a positive effect on greenbug intrinsic rate of increase (rm), which changed to negative on KS 116B, whereas the rm of sugarcane aphid was unaffected by coinfestation with greenbug on either cultivar. The results indicate that KS 116B will be useful for producing sugarcane aphid-resistant hybrids, and that PI 550610 antibiosis changes the sugarcane aphid-greenbug interspecific relationship from commensalism to amensalism.

In the cereal crop sorghum (Sorghum bicolor) inflorescence morphology variation underlies yield variation and confers adaptation across precipitation gradients, but its genetic basis is poorly understood. We characterized the genetic architecture of sorghum inflorescence morphology using a global nested association mapping (NAM) population (2200 recombinant inbred lines) and 198,000 phenotypic observations from multi-environment trials for four inflorescence morphology traits (upper branch length, lower branch length, rachis length, and rachis diameter). Trait correlations suggest that lower and upper branch length are under somewhat independent control, while lower branch length and rachis diameter are highly pleiotropic. Joint linkage and genome-wide association mapping revealed an oligogenic architecture with 1–22 QTL per trait, each explaining 0.1–5.0% of variation across the entire NAM population. There is a significant enrichment (2.twofold) of QTL colocalizing with grass inflorescence gene homologs, notably with orthologs of maize Ramosa2 and rice Aberrant Panicle Organization1 and TAWAWA1. Still, many QTL do not colocalize with inflorescence gene homologs. In global georeferenced germplasm, allelic variation at the major inflorescence QTL is geographically patterned but only weakly associated with the gradient of annual precipitation. Comparison of NAM with diversity panel association suggests that naive association models may capture some true associations not identified by mixed linear models. Overall, the findings suggest that global inflorescence diversity in sorghum is largely controlled by oligogenic, epistatic, and pleiotropic variation in ancestral regulatory networks. The findings also provide a basis for genomics-enabled breeding of locally-adapted inflorescence morphology.

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Obesity is one of the leading public health problems that can result in life-threatening metabolic and chronic diseases such as cardiovascular diseases, diabetes, and cancer. Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important cereal crop in the world and certain genotypes of sorghum have high polyphenol content. PI570481, SC84, and commercially available sumac sorghum are high-polyphenol genotypes that have demonstrated strong anti-cancer activities in previous studies. The objective of this study was to explore a potential anti-obesity use of extracts from sorghum bran in the differentiation of 3T3-L1 preadipocytes and to investigate cellular and molecular responses in differentiated adipocytes to elucidate related mechanisms. None of the four different sorghum bran extracts (PI570481, SC84, Sumac, and white sorghum as a low-polyphenol control) caused cytotoxicity in undifferentiated and differentiated 3T3-L1 cells at doses used in this study. Sorghum bran extracts (PI570481, SC84, and Sumac) reduced intracellular lipid accumulation and expression of adipogenic and lipogenic proteins in a dose-dependent manner in differentiated 3T3-L1 cells. The same polyphenol containing sorghum bran extracts also repressed production of reactive oxygen species (ROS) and MAPK signaling pathways and repressed insulin signaling and glucose uptake in differentiated 3T3-L1 cells. These data propose a potential use of high-phenolic sorghum bran for the prevention of obesity.