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

• Published in: Plant phenome journal 2024-12, Vol.7 (1), p.n/a
• Main Authors: Boatwright, Lucas, Thudi, Mahendar, Sangireddy, Manoj Kumar Reddy, Coffin, Alisa W., Tadesse, Haile K., Vutla, Sairam, Harris‐Shultz, Karen, Knoll, Joseph E., Cuevas, Hugo, Kumar, Neeraj, Soman, Chinmay, Schnable, James, Punnuri, Somashekhar M.
• Format: Article
• Language: English
• Subjects: Agricultural production; Aircraft; Biomass energy; Biomechanics; Copy number; Drones; Gene loci; Genomes; Genomic analysis; Germplasm; Glycoside hydrolase; Glycosides; Phenotyping; Photogrammetry; Robots; Single-nucleotide polymorphism; Sorghum; Unmanned aerial vehicles; Variance analysis
• ISSN: 2578-2703; 2578-2703
• DOI: 10.1002/ppj2.70008

Sorghum (Sorghum bicolor (L.) Moench) is an important cereal crop cultivated around the globe. To identify the genomic regions responsible for plant height and stem diameter, a subset of the sorghum association panel was phenotyped using manual, ground‐robot, and drone‐based phenotyping approaches during 2019 and 2020 at Tifton, GA. Manual and ground‐robot‐based plant heights had a lower correlation (r =  0.55) than the manual and drone‐based measurements (r =  0.61). Tukey's mean difference plot analysis indicated that both high‐throughput methods were less accurate with taller accessions. In genome‐wide association studies using single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and copy number variants, a total of 136 and 18 SNP loci associated with plant height were identified using mixed linear model and fixed and random model circulating probability unification models. 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, a gene located 19 kb upstream of the SNP locus SBI‐04_7987371 and a member of the glycoside hydrolase superfamily 35, plays a role in stem diameter, plant height, and is involved in cellular processes. Novel associations (eight for stem diameter), SNPs, and structural variants identified in this study can be used for manipulating plant height and stem diameter in sorghum. Core Ideas Manual and robot‐based plant heights had a lower correlation (r = 0.55) than the manual and drone (r = 0.61). A total of 154 single‐nucleotide polymorphisms (SNPs), 20 copy number variants, and 15 insertions and deletions were associated with plant height, and eight SNPs were associated with stem diameter. All four known genomic loci associated with plant height, Dw1–Dw4 (where dw is dwarfing genes), were detected. Dw2 gene was identified using both manual and ground‐robot‐based phenotyping approaches.