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.

Mapping Quantitative Trait Loci for Soybean Seedling Shoot and Root Architecture Traits in an Inter-Specific Genetic Population

“…To gain further insight into the expression of genes underlying root trait QTLs we used the publicly available differential gene expression data of Williams 82, a parental line used in developing this inter-specific mapping population. Gene expressions across diverse soybean genetic backgrounds were obtained from Array express ( ) and RNA-sequencing datasets ( Ithal et al, 2007 ; Libault et al, 2010 ; Gong et al, 2014 ; Kour et al, 2014 ; Leisner et al, 2014 ; Lin et al, 2014 ; Shen et al, 2014 ; Valdés-López et al, 2014 ; Wu et al, 2014 ; Zabala and Vodkin, 2014 ; Aghamirzaie et al, 2015 ; Brown and Hudson, 2015 ; Devi et al, 2015 ; Huang and Schiefelbein, 2015 ; Jones et al, 2015 ; Lambirth et al, 2015 ; Lanubile et al, 2015 ; Okamoto et al, 2015 ; Shin et al, 2015 ; Whaley et al, 2015 ; Bellieny-Rabelo et al, 2016 ; Song et al, 2016 ; Cho et al, 2017 ; Dastmalchi et al, 2017 ; Huang et al, 2017 ; Waters et al, 2018 ; Adhikari et al, 2019 ; Li et al, 2019 ; Liu et al, 2019 ; Neupane et al, 2019 ; Wang et al, 2019 ) integrated into Genevestigator database, ( Zimmermann et al, 2014 ). The transcriptome data of the wild soybean parental line, PI 483460B used in this study is not available.…”

Genome-wide analysis of sucrose synthase family in soybean and their expression in response to abiotic stress and seed development

“…Transcriptomic profile of Dongnong47 (DN47) cultivar were compared using Illumina high-throughput RNA-sequencing on samples at 25, 35, 50, and 55 days after flowering (DAF). Seeds at 18 DAF served as the control [48].…”

A cis-Tether Terminator, Linc-GmSTT1, Regulates Transcription Termination via the Linc-GmSTT1-intermolecular Interactome in Soybean 

“…S4). We previously used this population to investigate α-null-related transcription-level changes 8 . Standard farming practices were used to grow the BC 4 F 5 NIL plants in a randomized block design at the Northeast Agricultural University Experimental Station, China.…”

“…The typical inverted repeated (IR) structure is named alpha-IR (AB604030), and a 3.3-kb intergenic region separates the two genes in the cultivar 'Williams 82' 5 . Absence of the α-subunit is inherited independently, which can be incorporated into soybean cultivars and causes no physiological abnormalities 3,7,8 . Alpha-subunit gene expression is controlled at the transcriptional or posttranscriptional levels 6,9 .…”