title: Transcriptome Profile of Near-Isogenic Soybean Lines for β-Conglycinin α-Subunit Deficiency during Seed Maturation.
abstract: Crossing, backcrossing, and molecular marker-assisted background selection produced a soybean (Glycine max) near-isogenic line (cgy-2-NIL) containing the cgy-2 allele, which is responsible for the absence of the allergenic α-subunit of β-conglycinin. To identify α-null-related transcriptional changes, the gene expressions of cgy-2-NIL and its recurrent parent DN47 were compared using Illumina high-throughput RNA-sequencing of samples at 25, 35, 50, and 55 days after flowering (DAF). Seeds at 18 DAF served as the control. Comparison of the transcript profiles identified 3,543 differentially expressed genes (DEGs) between the two genotypes, with 2,193 genes downregulated and 1,350 genes upregulated. The largest numbers of DEGs were identified at 55 DAF. The DEGs identified at 25 DAF represented a unique pattern of GO category distributions. KEGG pathway analyses identified 541 altered metabolic pathways in cgy-2-NIL. At 18DAF, 12 DEGs were involved in arginine and proline metabolism. The cgy-2 allele in the homozygous form modified the expression of several Cupin allergen genes. The cgy-2 allele is an alteration of a functional allele that is closely related to soybean protein amino acid quality, and is useful for hypoallergenic soybean breeding programs that aim to improve seed protein quality.
authors.affiliation: Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Song
authors.affiliation: Department of allergy, First Affiliated Hospital, Harbin Medical University, Harbin, China.
authors.forename: Lixin
authors.initials: L
authors.lastname: An
authors.affiliation: Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China.
authors.forename: Yanjing
authors.initials: Y
authors.lastname: Han
authors.affiliation: Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China.
authors.forename: Hongxiu
authors.initials: H
authors.lastname: Gao
authors.affiliation: Inspection and Testing Center for Quality of Cereals and their Products, Ministry of Agriculture China, Harbin 150030, China.
authors.forename: Hongbo
authors.initials: H
authors.lastname: Ren
authors.affiliation: Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China.
authors.forename: Xue
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China.
authors.forename: Xiaoshuang
authors.initials: X
authors.lastname: Wei
authors.affiliation: Plant Genetics Research Unit, Agricultural Research Service (ARS), United States Department of Agriculture, University of Missouri, Columbia, Missouri, 65211, United States of America.
authors.forename: Hari B
authors.initials: HB
authors.lastname: Krishnan
authors.affiliation: Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin 150030, China.
authors.forename: Shanshan
authors.identifier: http://orcid.org/0000-0001-7273-735X
authors.initials: S
authors.lastname: Liu
mesh_terms: D052179:Antigens, Plant / Q000235:genetics*; D001483:Base Sequence; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D005916:Globulins / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D000069600:Plant Breeding; D055314:Seed Storage Proteins / Q000235:genetics*; D012639:Seeds / Q000254:growth & development*; D017423:Sequence Analysis, RNA; D030262:Soybean Proteins / Q000235:genetics*; D013025:Glycine max / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D052179:Antigens, Plant; D005916:Globulins; D055314:Seed Storage Proteins; D030262:Soybean Proteins; C100565:alpha-conglycinin, Glycine max; C013894:beta-conglycinin protein, Glycine max; C011474:glycinin