title: Identification and characterization of large DNA deletions affecting oil quality traits in soybean seeds through transcriptome sequencing analysis.
abstract: Identification and characterization of a 254-kb genomic deletion on a duplicated chromosome segment that resulted in a low level of palmitic acid in soybean seeds using transcriptome sequencing. A large number of soybean genotypes varying in seed oil composition and content have been identified. Understanding the molecular mechanisms underlying these variations is important for breeders to effectively utilize them as a genetic resource. Through design and application of a bioinformatics approach, we identified nine co-regulated gene clusters by comparing seed transcriptomes of nine soybean genotypes varying in oil composition and content. We demonstrated that four gene clusters in the genotypes M23, Jack and N0304-303-3 coincided with large-scale genome rearrangements. The co-regulated gene clusters in M23 and Jack mapped to a previously described 164-kb deletion and a copy number amplification of the Rhg1 locus, respectively. The coordinately down-regulated gene clusters in N0304-303-3 were caused by a 254-kb deletion containing 19 genes including a fatty acyl-ACP thioesterase B gene (FATB1a). This deletion was associated with reduced palmitic acid content in seeds and was the molecular cause of a previously reported nonfunctional FATB1a allele, fap nc . The M23 and N0304-304-3 deletions were located in duplicated genome segments retained from the Glycine-specific whole genome duplication that occurred 13 million years ago. The homoeologous genes in these duplicated regions shared a strong similarity in both their encoded protein sequences and transcript accumulation levels, suggesting that they may have conserved and important functions in seeds. The functional conservation of homoeologous genes may result in genetic redundancy and gene dosage effects for their associated seed traits, explaining why the large deletion did not cause lethal effects or completely eliminate palmitic acid in N0304-303-3.
authors.affiliation: US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Goettel
authors.affiliation: US Department of Agriculture, Agricultural Research Service, Soybean and Nitrogen Fixation Research, 2417 Gardner Hall, Raleigh, NC, 27695, USA.
authors.forename: Martha
authors.initials: M
authors.lastname: Ramirez
authors.affiliation: US Department of Agriculture, Agricultural Research Service, Soybean and Nitrogen Fixation Research, 2417 Gardner Hall, Raleigh, NC, 27695, USA.
authors.forename: Robert G
authors.initials: RG
authors.lastname: Upchurch
authors.affiliation: US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA. yong-qiang.an@ars.usda.gov.
authors.forename: Yong-Qiang Charles
authors.initials: YQ
authors.lastname: An
mesh_terms: D019295:Computational Biology; D018744:DNA, Plant / Q000235:genetics; D020440:Gene Duplication; D020869:Gene Expression Profiling; D015321:Gene Rearrangement; D017343:Genes, Plant; D018745:Genome, Plant; D005838:Genotype; D005810:Multigene Family; D019308:Palmitic Acid / Q000737:chemistry; D012639:Seeds / Q000737:chemistry*; D017384:Sequence Deletion; D013024:Soybean Oil / Q000737:chemistry*; D013025:Glycine max / Q000737:chemistry / Q000235:genetics*; D013869:Thiolester Hydrolases / Q000235:genetics; D059467:Transcriptome
chemical_list: D018744:DNA, Plant; D019308:Palmitic Acid; D013024:Soybean Oil; D013869:Thiolester Hydrolases; C018748:oleoyl-(acyl-carrier-protein) hydrolase