Zhang D, Zhang H, Hu Z, Chu S, Yu K, Lv L, Yang Y, Zhang X, Chen X, Kan G, Tang Y, An YC, Yu D.

PLoS Genet. 2019 Jul 10;15(7):e1008267. doi: 10.1371/journal.pgen.1008267. [Epub ahead of print]

Abstract

Increasing seed oil content is one of the most important breeding goals for soybean due to a high global demand for edible vegetable oil. However, genetic improvement of seed oil content has been difficult in soybean because of the complexity of oil metabolism. Determining the major variants and molecular mechanisms conferring oil accumulation is critical for substantial oil enhancement in soybean and other oilseed crops. In this study, we evaluated the seed oil contents of 219 diverse soybean accessions across six different environments and dissected the underlying mechanism using a high-resolution genome-wide association study (GWAS). An environmentally stable quantitative trait locus (QTL), GqOil20, significantly associated with oil content was identified, accounting for 23.70% of the total phenotypic variance of seed oil across multiple environments. Haplotype and expression analyses indicate that an oleosin protein-encoding gene (GmOLEO1), colocated with a leading single nucleotide polymorphism (SNP) from the GWAS, was significantly correlated with seed oil content. GmOLEO1 is predominantly expressed during seed maturation, and GmOLEO1 is localized to accumulated oil bodies (OBs) in maturing seeds. Overexpression of GmOLEO1 significantly enriched smaller OBs and increased seed oil content by 10.6% compared with those of control seeds. A time-course transcriptomics analysis between transgenic and control soybeans indicated that GmOLEO1 positively enhanced oil accumulation by affecting triacylglycerol metabolism. Our results also showed that strong artificial selection had occurred in the promoter region of GmOLEO1, which resulted in its high expression in cultivated soybean relative to wild soybean, leading to increased seed oil accumulation. The GmOLEO1 locus may serve as a direct target for both genetic engineering and selection for soybean oil improvement.

See https://www.ncbi.nlm.nih.gov/pubmed/31291251

Fig 1. GWAS for oil content in soybean seeds and candidate gene selection analyses.

A, A Manhattan plot for the BLUP of soybean oil content across six environments by association mapping. A red horizontal line depicts the Bonferroni-adjusted significance threshold (P<4.95×10⁻⁶). The x-axis shows the 20 soybean chromosomes, and the y-axis shows the significance expressed as the -log₁₀P value. B, A zoomed-in Manhattan plot of the 0.2-Mb genomic region on either side of the most significant SNP at the QTL GqOil20 on chromosome 20. The red solid triangle represents the leading SNP (AX-93910018). The color intensity of other SNPs is shown according to their LDs (r² value) with the leading SNP. Gene models within the region are indicated with blue rectangles, and the red rectangle represents the candidate gene Glyma.20G196600. The 50-kb genomic regions on both sides of the leading SNP are highlighted in light yellow. C, The extent of linkage disequilibrium (LD) in the 0.2-Mb genomic region on either side of the leading SNP based on pairwise r² values. The r² values are indicated using the color intensity index. D, Comparisons of seed oil content (%) between cultivated and wild soybeans. E, Comparison of GmOLEO1 expression between cultivated and wild soybeans. F, haplotypes of GmOLEO1 among 38 soybean genotypes. The orange and cyan rectangles on the promoter region indicate the cis-acting regulatory elements involved in ABA response and seed-specific regulation, respectively. G, Comparative analyses of the GmOLEO1 expression and oil content between the six different haplotypes. H, A neighbor-joining tree of the 38 accessions using variants from GmOLEO1. The edge color pattern was the same as that indicated by the six different haplotypes in (G). Black solid dots represent G. soja accessions. I, Ratios of LUC and REN activity in Arabidopsis protoplasts transformed with recombinant plasmids containing the GmOLEO1 promoters from two different haplotypes (Hap1_pro, Hap5_pro) and the control vector. Significance analysis was performed using Fisher’s protected least significant difference (LSD) test. ** indicates a significant difference at the 0.01 level.