In silico identification and comparative genomics of candidate genes involved in biosynthesis and accumulation of seed oil in plants

Abstract

Genes involved in fatty acids biosynthesis, modification and oil body formation are expected to be conserved in structure and function in different plant species. However, significant differences in the composition of fatty acids and total oil contents in seeds have been observed in different plant species. Comparative genomics was performed on 261 genes involved in fatty acids biosynthesis, TAG synthesis, and oil bodies formation in Arabidopsis, Brassica rapa, castor bean and soybean. In silico expression analysis revealed that stearoyl desaturase, FatB, FAD2, oleosin and DGAT are highly abundant in seeds, thereby considered as ideal candidates for mining of favorable alleles in natural population. Gene structure analysis for major genes, ACCase, FatA, FatB, FAD2, FAD3 and DGAT, which are known to play crucial role in oil synthesis revealed that there are uncommon variations (SNPs and INDELs) which lead to varying content and composition of fatty acids in seed oil. The predicted variations can provide good targets for seed oil QTL identification, understanding the molecular mechanism of seed oil accumulation, and genetic modification to enhance seed oil yield in plants.

Figure 1

In silico transcript abundance (based on matching ESTs available in the database) of oil biosynthesis and accumulation genes in different tissues.

Figure 2

Structure of ACCase gene in Arabidopsis (26 exons), castor bean (31 exons), and soybean (33 exons); thick arrows and thin lines represented exons and introns, respectively. Arabidopsis 1–26 exons showed identity to 6 to 31st and 6 to 33rd exons of castor bean and soybean, respectively; 16th exon of castor bean showed identity to three exons of soybean (16th, 17th, and 18th). A 3 bp deletion (del) in the 8th and 26th exons of castor bean, 3 bp deletion and 3 bp insertion (in) in the 31st and 29th exons of soybean, and a 12 bp insertion in the 24th and 26th exons of castor bean and soybean, respectively. At1g36180: Arabidopsis ACCase gene; 29908.m005991: Castor bean ACCase gene; Glyma04g11550: Soybean ACCase gene.

Figure 3

Structure of FatB (palmitoyl thioesterase) gene in Arabidopsis (At1g08510), castor bean (29848.m004677), and four soybean homologs (Glyma0421910, Glyma05g08060, Glyma17g12940, and Glyma06g23560). The 5th exon of FatB in Arabidopsis showed homology to the 6th exon of one of the homologs of soybean (Glyma04g21910) and last two exons (6th and 7th) of another homolog of soybean (Glyma06g23560), whereas 6th exon of castor bean showed homology to the 6th exons of other two homologs of soybean (Glyma05g08060 and Glyma17g12940).

Figure 4

Structure of FAD 3 (linoleoyl desaturase) gene in Arabidopsis (At2g29980), castor bean (29681.m001360), and two soybean homologs (Glyma01g29630, Glyma07g18350). Exon/intron numbers are conserved in FAD 3 while variation in sizes was observed in the first and last exons. SNP identified in the 6th exon of soybean homolog (Glyma01g29630) was reported to be associated with low linolenic acid content [17].