Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/7/2016
Publication Date: 8/17/2016
Publication URL: http://handle.nal.usda.gov/10113/63147
Citation: Song, B., An, L., Han, Y., Gao, H., Ren, H., Zhao, X., Wei, X., Krishnan, H.B., Liu, S. 2016. Transcriptome profile of near-isogenic soybean lines for ß-conglycinin a-subunit deficiency during seed maturation. PLoS One. 11(8):e0159723. doi:10.1371/journal.pone.0159723.

Interpretive Summary: Soybean ranks among the eight most significant food allergens for humans. Soybean meal (SBM), the major by-product of soybean oil extraction, is the main protein source for poultry and swine diets globally. Previously we have identified soybean ß-conglycinin a-subunit as being a major allergen in animal feed. At a time when US soybean meal is facing increasing competition from alternative feed ingredients and other soybean producing countries, it would benefit US soybean farmers if soybeans devoid of major allergens can be developed for both food and animal feed. In this study we have developed soybean lines that lack this important allergen by traditional breeding and have examined in detail what has changed in this line by the removal of the allergen. We have identified several altered metabolic pathways, some of which are related to improved protein quality. Information from this study will assist in the development of non-allergenic high yielding US soybean cultivars. Development of allergen-free soybeans will greatly enhance the nutritive value of soybean and increase the profitability of soybean growers.

Technical Abstract: Crossing, backcrossing and molecular marker assisted background selection produced a near isogenic line (‘cgy-2NIL’) containing cgy-2 allele, which is responsible for the absence of allergen a-subunit of ß-conglycinin. To identify a-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.