Wolfgang Goettel, Martha Ramirez, Robert G. Upchurch, Yong-qiang Charles An

Theoretical and Applied Genetics August 2016, Volume 129, Issue 8, pp 1577–1593

Abstract

Key message

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.

Abstract

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.

See: http://link.springer.com/article/10.1007/s00122-016-2725-z

Fig. 1

Identification of a 254-kb deletion on chromosome 5 in N0304-303-3. a This heat map represents expression variation among nine soybean genotypes. The Z score values of all genes arranged by chromosome location were displayed using a color gradient. Please note the red cluster of adjacent genes in N0304-303-3 that appear to be expressed at a significantly lower rate. These genes are listed in Table 2. b An IGV view of the region on chromosome 5, which contains the N0304-303-3 deletion, shows RNA sequence read alignments of soybean genotypes N0304-303-3 and Jack, and corresponding gene models. The deletion breakpoints, which are indicated by green bars, were determined by PCR analysis and sequencing of the amplification product (see below). The deletion in N0304-303-3 is 254,049 bp in size and includes 19 gene models. The FATB1a gene, and the genes located in or next to the breakpoints are marked by red bars. c The deletion in N0304-303-3 generated a fusion gene that consists of the 5′ end of Glyma05g07926 (in red), a small intergenic sequence (in yellow) and Glyma05g08150 (in red). The blue arrows represent both PCR primers used for the amplification across the deletion site (not drawn to scale). d The partial sequence of the PCR product spanning the deletion junction is presented. The primer binding sites are depicted in blue. The 5′ region flanking the deletion site is shown in lower-case letters, while the 3′ region is in upper-case letters (color figure online)