Identification of lncRNAs Associated with β-conglycinin α-null Allele Based on a Genome-wide Transcriptome Analysis of α-null-type Hypoallergenic Soybean（Glycine max） Near-isogenic Lines

Soybean mutants with α-null β-conglycinin are associated with high nutritional value and low allergenic risk. Although long noncoding RNAs（lncRNAs） are increasingly recognized as functional regulatory components affecting eukaryotic gene expression, little is known about lnc RNA profiles in α-null-type hypoallergenic soybeans. In this study, a genome-wide integrative analysis of lncRNAs, m RNAs and epigenomic data in the soybean cgy-2（confirmed α-null） near-isogenic line（NIL） and its recurrent parent Dongnong47（DN47） was conducted. Nineteen novel lncRNAs that were differentially expressed（DE） only in the NIL at 18 days after flowering（i.e., α-null-associated DE lncRNAs） were delected. Sixteen putative soybean stress-responsive lncRNAs were identified, and observed to regulate 257 stress-related genes DE in the NIL. This result indicated that the α-null allele might represent an intrinsic defect stress that altered the expression of various stress-related genes in α-null-type hypoallergenic soybean. Additionally, 25 epigenetic-related lncRNAs regulated 831 DE epigenetic-related genes and simultaneously initiated multiple epigenetic activities, including ubiquitination, methylation and acetylation. Kyoto encyclopedia of genes and genomes（KEGG） analysis indicated that the biosynthesis of amino acids pathway was enriched with 83 DE genes regulated by nine DE lncRNAs. Changes in the expression of these lncRNAs and genes might be the reason for the altered amino acid composition in the NIL. Among all detected DE lncRNAs, MSTRG.12518 was the most conspicuous α-null-specific cis/trans-lnc RNA that played an efficient, versatile and vital role in the NIL. The data indicated that the lnc RNA profile differed between the NIL and DN47. Variations in lncRNAs, gene expression levels and DNA methylation states likely contributed to the intrinsic defect stress response mechanism in α-null-type hypoallergenic soybeans.