Development and evaluation of a cost-effective, mid-density SNP array as a sorghum community genotyping resource

Authors: KUMAR, VIVEK - Cold Spring Harbor Laboratory; Klein, Robert; KAUFMAN, BENJAMIN - Consultant; WINANS, NOAH - Texas A&M University; CROSIER, DANIEL - Texas A&M University; ROONEY, WILLIAM - Texas A&M University; Harrison, Melanie; Hayes, Chad; TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory; Gladman, Nicholas; OLSON, CHRISTOPHER - Cold Spring Harbor Laboratory; Burow, Gloria; PUNNURI, SOMASHEKHAR - Fort Valley State University; Knoll, Joseph; DAHLBERG, JEFF - Consultant; Ware, Doreen

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 2/23/2026
Publication Date: 2/23/2026
Citation: Kumar, V., Klein, R.R., Kaufman, B., Winans, N., Crosier, D., Rooney, W., Harrison, M.L., Hayes, C.M., Tello-Ruiz, M., Gladman, N.P., Olson, C., Burow, G.B., Punnuri, S., Knoll, J.E., Dahlberg, J., Ware, D. 2026. Development and evaluation of a cost-effective, mid-density SNP array as a sorghum community genotyping resource. bioRxiv. 2026.02.20.706663. https://doi.org/10.64898/2026.02.20.706663.
DOI: https://doi.org/10.64898/2026.02.20.706663

Interpretive Summary: Sorghum is a drought-resilient cereal crop grown worldwide for food, feed, and fuel. However, the adoption of molecular breeding strategies in sorghum has been limited by the high cost and complexity of genotyping technologies. To address this challenge, a collaborative effort involving researchers from academia, government, and industry developed a mid-density SNP genotyping panel tailored to the needs of the sorghum breeding community. This genotyping resource, based on the PlexSeq sequencing platform, includes genetic markers distributed across all 10 sorghum chromosomes, including markers associated with important agronomic traits. Designed to be both cost-effective and high-throughput, the panel was tested on diverse public and private sorghum germplasm to evaluate its ability to capture genome-wide variation and support applications such as diversity analysis and genomic selection. Results showed strong agreement with existing high-resolution genotyping platforms but at a significantly lower cost and with greater scalability. This new marker panel enables sorghum breeders to efficiently track genetic variation, accelerate trait mapping, and make more informed decisions in variety development. By lowering the technical and financial barriers to molecular breeding, this tool represents an important step toward increasing the rate of genetic gain in sorghum improvement programs.

Technical Abstract: The development of accessible and cost-effective genotyping platforms is essential to accelerate genetic gain in crop improvement. To address the U.S. sorghum community’s need for a standardized, mid-density genotyping resource, we developed and validated a targeted single-nucleotide polymorphism (SNP) array using the PlexSeq™ next-generation sequencing (NGS) platform. The resulting genotyping array includes 2,421 SNPs spanning all ten Sorghum bicolor chromosomes and integrates trait-linked and quality control markers selected by public and private stakeholders. Genotyping 2,726 diverse accessions, including the Sorghum Association Panel (SAP), demonstrated high call rates (>90% for most samples and markers), low missing data, and accurate resolution of population structure consistent with prior whole-genome studies. In comparative genomic prediction analyses, the mid-density array performed equivalently to high-density genotype-by-sequencing (GBS) platforms for key traits such as grain yield and plant height across multi-environment trials. Designed for broad utility in breeding pipelines, the array enables marker-assisted selection, genomic prediction, identity verification, and germplasm quality control. Moreover, its adoption by the USDA National Plant Germplasm System facilitates the curation of genebanks and the management of core collections. This community-driven genotyping platform offers a scalable, reproducible, and customizable tool to support molecular breeding in sorghum and underscores the value of targeted marker systems in resource-optimized crop improvement programs.