GWAS analysis for plant height and stem diameter in sorghum using multiple phenotyping approaches

Authors: BOATWRIGHT, LUCAS - Corteva Agriscience; THUDI, MAHENDAR - Fort Valley State University; SANGIREDDAY, MANOJ K - Fort Valley State University; Coffin, Alisa; TADESSE, HAILE - University Of Maryland; VUTLA, SAIRAM - Fort Valley State University; Harris-Shultz, Karen; Knoll, Joseph; Cuevas, Hugo; KUMAR, NEERAJ - Clemson University; SOMAN, CHINMAY - Earthsense, Inc; SCHNABLE, JAMES - University Of Nebraska; PUNNURI, SOMASHEKHAR - Fort Valley State University

Submitted to: The Plant Phenome Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2024
Publication Date: 12/17/2024
Citation: Boatwright, L., Thudi, M., Sangiredday, M.R., Coffin, A.W., Tadesse, H.K., Vutla, S., Harris-Shultz, K.R., Knoll, J.E., Cuevas, H.E., Kumar, N., Soman, C., Schnable, J., Punnuri, S. 2024. GWAS analysis for plant height and stem diameter in sorghum using multiple phenotyping approaches. The Plant Phenome Journal. 7, e70008. https://doi.org/10.1002/ppj2.70008.
DOI: https://doi.org/10.1002/ppj2.70008

Interpretive Summary: Sorghum is the fifth most important cereal crop in the world, and is mainly cultivated in the arid and semi-arid regions across the globe. Reducing plant height and increasing stem diameter helps improve lodging resistance, resulting in enhanced grain yield and quality, whereas increasing height increases the total plant biomass, which can be used for forage or bioenergy. To identify the genomic regions responsible for plant height and stem diameter, a subset of the Sorghum Association Panel comprising of 287 accessions was assessed using manual, ground-based robot, and drone-based approaches during 2019 and 2020 at Tifton, GA. Manual and drone-based measurements of plant heights had a lower correlation (r = 0.55) than the manual and ground-robot based measurements (r = 0.61), suggesting the ground-based robot was slightly better at measuring plant height than the drone. Further analysis showed that both the robot and drone tended to underestimate plant height, particularly for taller sorghum accessions. Stem diameters were also measured using the ground-based robot. We performed genome-wide association studies to detect genetic markers associated with plant height and stem diameter using two different mathematical models. We were able to detect all four known major dwarfing genes that control plant height (Dw1 through Dw4) using manual measurement data, which indicates that our models performed well. In contrast, only Dw2 was identified using ground robot-based measurement. Numerous other genetic markers for plant height and stem diameter were identified. These markers could be used for manipulating plant height and stem diameter in sorghum for enhancing biomass, yield, and lodging resistance.

Technical Abstract: Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important cereal crop cultivated in the arid and semi-arid region across the globe. Reducing plant height and increasing stem diameter help improve lodging resistance, resulting in enhanced grain yield, grain quality, and biomass on a global scale. T o identify the genomic regions responsible for plant height and stem diameter, a subset of the Sorghum Association Panel comprising of 287 germplasm accessions was phenotyped using manual, robot and drone-based phenotyping approaches during 2019 and 2020 at Tifton, GA. Manual and drone-based measurements of plant heights had a lower correlation (r = 0.55) than the manual and ground-robot based measurements (r = 0.61). Using phenotypic data and single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and copy number variants (CNVs), we performed genome-wide association studies. A total of 136 and 18 SNP loci associated with plant height were identified using MLM and FarmCPU models. In addition, we report novel associations using structural variants (16 indels and 20 CNVs) with plant height. For the first time, we report eight significant SNPs associated with stem diameter using a ground-based robot. We were able to detect all four major dwarfing genes (Dw1 through Dw4) using manual phenotyping; in contrast, Dw2 was identified using both manual and ground robot-based phenotyping. Sorbi.3004G093400, gene on SBI-04, a member of the glycoside hydrolase superfamily 35 plays a role in stem diameter, plant height, and is interconnected with their involvement in cell wall modifications, starch metabolism, and secondary cell wall formation. Novel associations (eight for stem diameter), SNPs and SVs identified in this study can be used for manipulating plant height and stem diameter in sorghum for enhancing the biomass, yield and lodging resistance.