A chromosome 16 deletion conferring a high sucrose phenotype in soybean

Authors: OSTEZAN1, ALEXANDRA - University Of Georgia; PRENGER, ELIZABETH - University Of Georgia; ROSSO, LUCIANA - Virginia Tech; ZHANG, BO - Virginia Tech; STUPAR, ROBERT - University Of Minnesota; GLENN, TRAVIS - University Of Georgia; Mian, Rouf; LI, ZENGLU - University Of Georgia

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2023
Publication Date: 4/11/2023
Citation: Ostezan, A., Prenger, E., Rosso, L., Zhang, B., Stupar, R., Glenn, T., Mian, R.M., Li, Z. 2023. A chromosome 16 deletion conferring a high sucrose phenotype in soybean. Journal of Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-023-04354-6.
DOI: https://doi.org/10.1007/s00122-023-04354-6

Interpretive Summary: The primary end-use of soybean in U.S. and worldwide is for livestock feed. However, recently there is new focus on using plant proteins, including soybean protein, as sustainable alternatives to animal meat products. In addition to protein, the feed and food products, higher sucrose is desired due to its role as an easily digestible energy source. An elite soybean line was irradiated with fast neutrons and the plants were screened for altered seed composition with near-infrared spectroscopy (NIR). One mutant line, G15FN-54, was identified to have higher sucrose content (8-9%) than the parental line (5-6%). Comparative genomic hybridization (CGH) revealed three large deletions on chromosomes (Chrs) 10, 13, and 16 in the mutant, which were confirmed through whole genome sequencing (WGS). A bi-parental population derived from the mutant G15FN-54 and a cultivar Benning was developed to conduct a bulked segregant analysis (BSA) with SoySNP50K BeadChips, revealing that the deletion on Chr 16 might be responsible for the altered phenotype. The mapping result using the bi-parental population confirmed that the deletion on Chr 16 conferred elevated sucrose content and a total of 21 genes are located within this Chr 16 deletion. NIR and high-pressure liquid chromatography (HPLC) were used to confirm the stability of the phenotype across generations in the bi-parental population. The mutation will be useful to understand the genetic control of soybean seed sucrose content as well as improving the easily digestible energy in the feed and food products derived from soybean.

Technical Abstract: Soybean is one of the most economically important crops in the United States. A primary end-use of soybean is for livestock feed. Therefore, genetic improvement of seed composition is one of the most important goals in soybean breeding programs. Sucrose is desired in animal feed due to its role as an easily digestible energy source. An elite soybean line was irradiated with fast neutrons and the plants were screened for altered seed composition with near-infrared spectroscopy (NIR). One mutant line, G15FN-54, was found to have higher sucrose content than the parent. Comparative genomic hybridization (CGH) revealed three large deletions on chromosomes (Chrs) 10, 13, and 16 in the mutant, which were confirmed through whole genome sequencing (WGS). A bi-parental population derived from the mutant G15FN-54 and a cultivar Benning was developed to conduct a bulked segregant analysis (BSA) with SoySNP50K BeadChips, revealing that the deletion on Chr 16 might be responsible for the altered phenotype. The mapping result using the bi-parental population confirmed that the deletion on Chr 16 conferred elevated sucrose content and a total of 21 genes are located within this Chr 16 deletion. NIR and high-pressure liquid chromatography (HPLC) were used to confirm the stability of the phenotype across generations in the bi-parental population. The mutation will be useful to understand the genetic control of soybean seed sucrose content.