title: Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content.
abstract: BACKGROUND
  Variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement.
  
  
  RESULTS
  In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively.
  
  
  CONCLUSIONS
  As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Goettel
authors.forename: Eric
authors.initials: E
authors.lastname: Xia
authors.forename: Robert
authors.initials: R
authors.lastname: Upchurch
authors.forename: Ming-Li
authors.initials: ML
authors.lastname: Wang
authors.forename: Pengyin
authors.initials: P
authors.lastname: Chen
authors.affiliation: USDA-ARS, Midwest Area, Plant Genetics Research Unit at 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: D032461:Chromosomes, Plant; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D005838:Genotype; D054643:INDEL Mutation; D050356:Lipid Metabolism; D053858:Metabolic Networks and Pathways; D005810:Multigene Family; D009928:Organ Specificity / Q000235:genetics; D010641:Phenotype; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012639:Seeds / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013024:Soybean Oil / Q000737:chemistry*; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D013024:Soybean Oil
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