Transcriptome profile of near-isogenic soybean lines for ß-conglycinin α-subunit deficiency during seed maturation

Crossing, backcrossing and molecular marker assisted background selection produced a soybean (Glycine max) near isogenic line (cgy-2NIL) containing cgy-2 allele, which is responsible for the absence of allergen α-subunit of ß-conglycinin. To identify α-null-related transcriptional changes, the gene expressions of ‘cgy-2NIL’and its recurrent parent ‘DN47’ were compared using Illumina high-throughput RNA-sequencing on samples at 25 days after flowering (DAF), 35 DAF, 50 DAF and 55 DAF. Seeds at 18 DAF served as the control. Comparison of the transcript profiles revealed 3543 differentially expressed genes (DEGs) between the two genotypes, with 2193genes down-regulated and 1350 genes up-regulated. The largest numbers of DEGs were identified at 55DAF. The DEGs identified at 25DAF represented a unique pattern of GO category distributions. KEGG pathway analyses identified 541 altered metabolic pathways in cgy-2NIL. At 18DAF, 12 DEGs were involved in arginine and proline metabolism. The cgy-2 allele in the homozygous form modified the expression of Cupin allergen genes. The cgy-2 allele is an alteration of function allele that is closely related to soybean protein nutritional quality, and is useful for hypoallergenic soybean breeding programs that aim to improve seed protein quality.