Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean

Prakash Basnet; Taeyoung Um; Neha Samir Roy; Woo Suk Cho; Soo Chul Park; Kyong-Cheul Park; Ik-Young Choi

doi:10.3389/fgene.2022.805347

Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean

Front Genet. 2022 Feb 24:13:805347. doi: 10.3389/fgene.2022.805347. eCollection 2022.

Authors

Prakash Basnet¹, Taeyoung Um¹, Neha Samir Roy¹, Woo Suk Cho², Soo Chul Park², Kyong-Cheul Park¹, Ik-Young Choi¹

Affiliations

¹ Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, South Korea.
² Department of Agricultural Biotechnology/National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea.

Abstract

In cultivated plants, shoot morphology is an important factor that influences crop economic value. However, the effects of gene expression patterns on shoot morphology are not clearly understood. In this study, the molecular mechanism behind shoot morphology (including leaf, stem, and node) was analyzed using RNA sequencing to compare weedy (creeper) and cultivar (stand) growth types obtained in F₇ derived from a cross of wild and cultivated soybeans. A total of 12,513 (in leaves), 14,255 (in stems), and 11,850 (in nodes) differentially expressed genes were identified among weedy and cultivar soybeans. Comparative transcriptome and expression analyses revealed 22 phytohormone-responsive genes. We found that GIBBERELLIN 2-OXIDASE 8 (GA2ox), SPINDLY (SPY), FERONIA (FER), AUXIN RESPONSE FACTOR 8 (ARF8), CYTOKININ DEHYDROGENASE-1 (CKX1), and ARABIDOPSIS HISTIDINE KINASE-3 (AHK3), which are crucial phytohormone response genes, were mainly regulated in the shoot of weedy and cultivar types. These results indicate that interactions between phytohormone signaling genes regulate shoot morphology in weedy and cultivar growth type plants. Our study provides insights that are useful for breeding and improving crops to generate high-yield soybean varieties.

Keywords: cultivar type; differentially expressed genes; phytohormone; transcriptome; weedy type.