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

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.

Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks

“…However, cotton QTL localization faces problems such as large localization intervals, small recombination exchange probability, and high density of genetic linkage maps, which are still challenging for mining fiber development-related genes. Fortunately, as traditional sequencing technologies are refined and updated, RNA-seq provides a suitable mining process that has been widely applied to transcriptome studies in several species, including Arabidopsis [ 65 ], poplar [ 66 ], soybean [ 67 ], rice [ 68 ], wheat [ 69 ], cotton [ 70 , 71 , 72 , 73 ], and maize [ 74 ]. By comparing the transcriptomes of different cotton fiber development samples, the majority of genes responsive to cell development can be identified quickly and efficiently [ 75 , 76 ].…”