Location: Crop Germplasm Research
2025 Annual Report
Objectives
Objective 1: Integrate genomic selection technology into traditional methods of sorghum genetic improvement to accelerate the rate of genetic gain for grain sorghum hybrids.
Objective 2: Utilize modern biological tools to conduct fundamental molecular research into end-use quality traits including the black pericarp phenotype in sorghum.
Approach
This project aims to integrate recent advances in genomic selection technology augmented with phenomic and enviromic resources. The ultimate goal is to accelerate the rate of genetic gain in sorghum hybrids and to utilize modern biological tools to conduct fundamental molecular research into end-use quality traits including the black pericarp phenotype in sorghum. The challenge facing crop geneticists and breeders is how to develop strategies that combine the traditional tools available to crop genetics with new genomic- and phenomic-assisted approaches that leverage the extensive 'omics' resources available to crop improvement programs. Utilizing elite sorghum inbreds from U.S. public breeding programs along with novel genetically diverse germplasm developed by the previous project plan, this project aims to emulate the modern genomics-based approach of commercial maize hybrid improvement programs to transform existing sorghum breeding strategies in both public and private sector in the U.S. In addition to the need for an "omics-assisted" approach to hybrid sorghum breeding, there is a need to enhance value-added traits that improve end-use quality of sorghum grain. Black pericarp sorghum, and the associated accumulation of the high-value phytochemicals 3-deoxyanthocyanidins, represents one such value-added trait with enhanced nutritional quality desired by processors and consumers. This project aims to elucidate the genes, gene networks, and novel genomic features (e.g., structural variation, epigenetic control) controlling the black pericarp trait to eliminate knowledge gaps that limit our capacity to improve this valued trait. The products of this research will include an assessment of appropriate genomic- and phenomic-assisted methods to integrate into breeding programs, more effective hybrid breeding programs through the introduction of genomic and phenomic selection models into sorghum breeding pipelines (Obj. 1), and critical knowledge of cellular control of black pericarp phenotype required to devise effective biotechnology- or breeding-based approaches to improve the expression of this trait. (Obj. 2)
Progress Report
Work under this project during FY 2025, in collaboration with Texas A&M University partners, resulted in significant progress in sorghum germplasm evaluation and development, which included optimization of genomic prediction models for sorghum hybrid performance. The discoveries made by this collaborative team will facilitate ongoing efforts focused on exploiting novel technologies to develop improved hybrids for effective utilization by farmers in all sorghum production areas of the United States. FY 2025 progress under Objective 1 included the implementation of genomic prediction models in elite hybrid yield trials. This work resulted in the creation and implementation of highly predictive performance equations for use in sorghum breeding programs. Significant progress under Objective 2 was made towards utilizing sophisticated molecular biology approaches, including techniques known as NexGen sequencing, genome annotation pipelines, genetic linkage map resources, and DAP-Seq technology, to understand the genes that control the black pericarp trait in sorghum; black sorghum occupies a significant niche in U.S. sorghum production. This work identified genes and novel features of the genome that are critical to developing improving black sorghums for productive use by farmers. The work also is important to breeders who are working to introduce the high value "black" trait into other cereal species.
Accomplishments
1. Breakthrough in sorghum breeding. The yield potential in grain sorghum hybrids has increased at a slower rate than for other cereal crops including its close relative maize (corn). While there are several reasons for this lag, one major reason is the lack in sorghum of what is known to crop geneticists and breeders as a haploid induction system. If sorghum could be induced to express an active haploid induction system, it would be a major advancement in helping breeders to develop new and more productive sorghum types. ARS researchers at College Station, Texas, working with university collaborators, developed a panel of haploid-inducing sorghum lines that generate a high percentage of haploids; this will markedly reduce the time required to develop elite sorghum inbreds and hybrids. This accomplishment is highly significant in that it reaches a goal long sought by sorghum breeders, and it will with near certainty be quickly applied to develop improved sorghum types for widespread, productive, and profitable use by U.S. farmers.
Review Publications
Schumaker, B., Fedenia, L., Klein, R.R., Mandal, S., Dykes, L., Gladman, N.P., Rooney, W., Burson, B.L., Klein, P. 2024. UV-induced reactive oxygen species and transcriptional control of 3-deoxyanthocyanidin biosynthesis in black sorghum pericarp. Frontiers in Plant Science. 15. Article 1451215. https://doi.org/10.3389/fpls.2024.1451215.
Kent, M.A., Fonseca, J.M., Klein, P.E., Klein, R.R., Hayes, C.M., Rooney, W.L. 2023. Assessing the agronomic potential of sorghum B-lines using genomic prediction. Crop Science. 63(6):3367-3381. https://doi.org/10.1002/csc2.21107.
Kent, M.A., Fonseca, J.M., Klein, P.E., Klein, R.R., Hayes, C.M., Rooney, W.L. 2025. Inclusion of genotype by environment interactions into genomic prediction models for sorghum seed parents in hybrid testcrosses. Journal of Crop Improvement. 39(2):146-166. https://doi.org/10.1080/15427528.2025.2460571.
Jordan, D., Klein, R.R., Melonek, J., Small, I., Cruishank, A., Bradburn, L., Malory, S., Tao, Y., Hunt, C., Amenu, L., Mace, E. 2025. The genetic architecture of temperature-induced partial fertility restoration in A1 cytoplasm in sorghum (Sorghum bicolor (L.) Moench). Theoretical and Applied Genetics. 138. Article 170. https://doi.org/10.1007/s00122-025-04946-4.