Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of Glycine max and Glycine soja

Abstract

Short crop height is the preferred breeding trait since there is a positive correlation between lodging resistance and a crop yield increase. Alternative splicing can alter transcriptome diversity and contribute to plant adaptation to environmental stress. We characterized the transcriptomes obtained from dwarf and normal soybean lines derived from a cross of Glycine max var. Peking (G. max) and G. soja var. IT182936 in an F7 RIL population to study the differences between the isoforms. Full-length mRNA derived from leaf tissues was sequenced using the PacBio RSII platform, generating 904,474 circular consensus sequence (CCS) reads. Using the Structural and Quality Annotation of Novel Transcript Isoforms (SQANTI) process, 42,582 and 44,762 high-quality isoforms, and 91 and 179 polished low-quality isoforms were obtained in dwarf and normal cells, respectively. As a result, 832 and 36,772 nonredundant transcripts were generated. Approximately 30% of the identified genes were estimated to produce two or more isoforms. We detected an average of 166,171 splice junctions (SJs), of which 93.8% were canonical SJs. We identified that novel isoforms accounted for 19% of all isoforms, among which 12% fell within coding regions. The dwarf soybean demonstrated a greater number of isoforms in most of the annotated genes, particularly in genes related to growth hormones and defense responses. Our study provides comprehensive isoform and gene information that may accelerate transcriptome research in G. max and provide a basis to further study the impact of these isoforms on plant growth.

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

“…Splice variants affect agronomic characteristics in crops, e.g., floral development in cereals [247], seed shattering and weight in rice [248], grain size and weight in wheat [191,249], plant architecture in soybean [250], and nutritional quality in rice [210,251], soybean [252,253], tomato [254], and wheat [255]. Genome-wide association genetic analysis (GWAS) can further reveal how AS variants diversify gene function and regulate variation in crops, as shown by Chen et al [22] in maize.…”