Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/28/2016
Publication Date: 5/14/2016
Publication URL: http://handle.nal.usda.gov/10113/62763
Citation: Goettel, H.W., Ramirez, M.E., Upchurch, R.G., An, Y. 2016. Identification and characterization of large DNA deletions affecting oil quality traits in soybean seeds through transcriptome sequencing analysis. Theoretical and Applied Genetics. 129(8):1577-1593. doi:10.1007/s00122-016-2725-z.
Interpretive Summary: Soybean seed oil composition is one of the most important agronomic traits for this crop as it determines its nutritional value as well as its utility for biodiesel production and other industrial applications. Understanding the molecular and genetic mechanisms underlying variation in seed composition among different genotypes (varieties) is important for soybean oil quality improvement. ARS scientists designed a bioinformatics approach to compare seed gene expression patterns of 9 soybean genotypes that varied in oil composition and content, and found that the expression of the genes located in two regions of DNA were substantially suppressed in two genotypes, M23 and N0304. They demonstrated that the suppression of the specific genes in M23 were because they were deleted; their location mapping to a previously described deleted region of DNA that was reported to cause an elevation in oleic acid (a preferred fatty acid) in M23. High oleic acid in soybean seed improves its oil shelf life, flavor, and cold flow performance. The suppression of the clustered genes in N0304 was also the result of a deletion of DNA in the genome which was associated with reduced palmitic acid (an undesired fatty acid) in seeds. Consumption of palmitic acid has been shown to increase the risk of developing cardiovascular diseases in humans. The novel identification of the genetic basis underlying reduced palmitic acid in N0304 and knowledge gained from characterization of genes in the two DNA deleted regions enhance our abilities to develop new soybean cultivars with superior oil qualities, and eventually increase the competitiveness of US soybeans.
Technical Abstract: Understanding the molecular and genetic mechanisms underlying variation in seed composition and contents among different genotypes is important for soybean oil quality improvement. We designed a bioinformatics approach to compare seed transcriptomes of 9 soybean genotypes varying in oil composition and content and identified two gene clusters whose expression was substantially suppressed with no or little RNA accumulation in M23 and N0304-303-3 respectively. The suppressed genes in M23 were located in a previously described 164-kb DNA deletion region leading to elevated oleic acid in M23. We demonstrated that the co-suppression of the clustered genes in N0304-303-3 was caused by a 254-kb DNA deletion containing a fatty acyl-ACP thioesterase B gene (FATB1a) and additional 18 genes. Our analysis of lines comprising the pedigree of N0304-303-3 showed that the deletion was associated with reduced palmitic acid content in seeds, and likely responsible for the FATB1a gene deletion at the fapnc locus. The M23 and N0303-304-3 deletions are located in recently duplicated chromosome segments. The genes in the deleted regions shared a strong protein sequence similarity and transcript accumulation levels with their corresponding paralogous genes in soybean and a low Ka/Ks value, suggesting that the genes experienced purifying selection. The functional conservation between paralogous genes may explain the lack of null phenotypes in both deletion mutants.