Identification and characterization of a temperature sensitive chlorotic soybean mutant

Authors: HANCOCK, NATHAN - University Of South Carolina; GERMANY, TETANDIANOCEE - University Of South Carolina; REDD, PRISCILLA - University Of South Carolina; TIMMONS, JACK - University Of South Carolina; LIPFORD, JEFFERY - University Of South Carolina; BURNS, SAMANTHA - University Of South Carolina; HANCOCK, LIA - University Of South Carolina; CERVANTES-PEREZ, SERGIO - University Of Nebraska; LIBAULT, MARK - University Of Missouri; SHEN, WENHAO - Donald Danforth Plant Science Center; An, Yong-Qiang - Charles; KANIZAY, LISA - University Of Georgia; YERKA, MELINDA - University Of Nevada School Of Medicine; PARROTT, WAYNE - University Of Georgia

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 2/3/2024
Publication Date: 2/3/2024
Citation: Hancock, N.C., Germany, T., Redd, P., Timmons, J., Lipford, J., Burns, S., Hancock, L.R., Cervantes-Perez, S.A., Libault, M., Shen, W., An, Y., Kanizay, L., Yerka, M., Parrott, W. 2024. Identification and characterization of a temperature sensitive chlorotic soybean mutant. bioRxiv. https://doi.org/10.1101/2024.02.02.578604.
DOI: https://doi.org/10.1101/2024.02.02.578604

Interpretive Summary: Soybean is an important crop in the US and the world. It provides a rich source of plant-based protein and oil for food, feed, and various industrial applications. Soybean is one of the few major crops with the ability to fix nitrogen. Therefore, soybean is emerging as an ideal crop to address global food security, nutritional needs, and sustainable agriculture in the next generation. The study discovered a temperature sensitive chlorotic soybean mutant with a smaller stature, weaker stems, and a smaller root system. Having applied a combination of molecular biology, genetics, genomics and data science approaches, we discovered the gene and gene mutation responsible for the phenotypic changes. Knowledge from the study is valuable for researchers to engineer soybean photosynthesis, stature and root systems to increase soybean productivity and resilience to climate change.

Technical Abstract: Screening a collection of mutagenized soybean lines discovered a chlorotic mutant with a smaller stature, weaker stems, and a smaller root system. Genome sequencing and molecular characterization identified 15 genes as candidates for the causal gene. Amplicon sequencing of a segregating population identified a single-nucleotide mutant that disrupts splicing of the second intron of a Glyma.07G102300 (annotated as Cytochrome P450). Single-cell transcriptomic analysis showed that this gene is expressed preferentially in mesophyll cells. We also showed that the gene is upregulated by cold stress in germinating seedlings, consistent with a previous report that cool treatment increases the severity of the chlorotic phenotype caused by mutation of its homologous gene in rice mutant. Lower temperature also caused a more severe phenotype in the soybean mutant. Transgenic expression of its wild-type allele can functionally rescue the chlorotic phenotype in its Arabidopsis mutant, further supporting that the gene and the single nucleotide mutation are responsible for the phenotypic changes in the soybean mutant.