The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome

Long intergenic noncoding RNAs (lincRNAs) are emerging as important regulators of diverse biological processes. However, our understanding of lincRNA abundance and function remains very limited especially for agriculturally important plants. Soybean (Glycine max) is a major legume crop plant providing over a half of global oilseed production. Moreover, soybean can form symbiotic relationships with Rhizobium bacteria to fix atmospheric nitrogen. Soybean has a complex paleopolyploid genome and exhibits many vegetative and floral development complexities. Soybean cultivars have photoperiod requirements restricting its use and productivity. Molecular regulators of these legume-specific developmental processes remain enigmatic. Long noncoding RNAs may play important regulatory roles in soybean growth and development. In this study, over one billion RNA-seq read pairs from 37 samples representing nine tissues were used to discover 6,018 lincRNA loci. The lincRNAs were shorter than protein-coding transcripts and had lower expression levels and more sample specific expression. Few of the loci were found to be conserved in two other legume species (chickpea [Cicer arietinum] and Medicago truncatula), but almost 200 homeologous lincRNAs in the soybean genome were detected. Protein-coding gene-lincRNA coexpression analysis suggested an involvement of lincRNAs in stress response, signal transduction, and developmental processes. Positional analysis of lincRNA loci implicated involvement in transcriptional regulation. lincRNA expression from centromeric regions was observed especially in actively dividing tissues, suggesting possible roles in cell division. Integration of publicly available genome-wide association data with the lincRNA map of the soybean genome uncovered 23 lincRNAs potentially associated with agronomic traits.