Genome-wide association study reveals a patatin-like lipase relating to the reduction of seed oil content in Brassica napus

Abstract

Background Rapeseed (Brassica napus L.) is an important oil crop world-widely cultivated, and seed oil content (SOC) is one of the most important traits for rapeseed. To increase SOC, many efforts for promoting the function of genes on lipid biosynthesis pathway have been previously made. However, seed oil formation is a dynamic balance between lipid synthesis and breakdown. It is, therefore, also reasonable to weaken or eliminate the function of genes involved in lipid degradation for a higher final SOC. Results We applied a genome-wide association study (GWAS) on SOC in a collection of 290 core germplasm accessions. A total of 2,705,480 high-quality SNPs were used in the GWAS, and we identified BnaC07g30920D, a patatin-like lipase (PTL) gene, that was associated with SOC. In particular, six single-nucleotide-polymorphisms (SNPs) in the promoter region of BnaC07g30920D were associated with the significant reduction of SOC, leading to a 4.7–6.2% reduction of SOCs. We performed in silico analysis to show a total of 40 PTLs, which were divided into four clades, evenly distributed on the A and C subgenomes of Brassica napus. RNA-seq analysis unveiled that BnPTLs were preferentially expressed in reproductive tissues especially maturing seeds. Conclusions We identified BnaC07g30920D, a BnPTL gene, that was associated with SOC using GWAS and performed in silico analysis of 40 PTLs in Brassica napus. The results enrich our knowledge about the SOC formation in rapeseed and facilitate the future study in functional characterization of BnPTL genes.

BnIR: a multi-omics database with various tools for Brassica napus research and breeding

“…SOC is one of the most important traits of rapeseed (Wang et al ., 2018; Tang et al ., 2021). Here, the published SOC data of 286 B. napus accessions were used to validate the power of BnIR in identifying new candidate genes associated with traits (Wang et al ., 2021). First, five significant loci were identified using GWAS, among which qOC.C07.1 was the most significant locus.…”

Construction and Genetic Analysis of a Worldwide Core Collection of Rapeseed

“…Undoubtedly, the construction of a worldwide core collection greatly improved the e ciency and was successfully used to identify important genes (Wang et al, 2021;Xuan et al, 2019). For example, patain-like lipase (BnaC07g30920D) was identi ed to regulate seed oil content gene through GWAS using the 300 worldwide core collection of rapeseed (Wang et al, 2021).…”

“…Undoubtedly, the construction of a worldwide core collection greatly improved the e ciency and was successfully used to identify important genes (Wang et al, 2021;Xuan et al, 2019). For example, patain-like lipase (BnaC07g30920D) was identi ed to regulate seed oil content gene through GWAS using the 300 worldwide core collection of rapeseed (Wang et al, 2021). BnaA.GL1.a (BnaA06g31780D), BnaC.SWEET4.a (BnaC07g24860D), BnaC.WAT1.a (BnaC07g24950D) and BnaC.WAT1.b (BnaC07g24960D) were identi ed to be assocatied with the divergence of hairy-and glabrous-leaf genotypes of B. napus through GWAS and transcriptomic studies .…”

Genome-wide exploration of the GDSL-type esterase/lipase gene family in rapeseed reveals several BnGELP proteins active during early seedling development

“…Rapeseed ( Brassica napus L., genome AACC, 2n = 4x = 38) is the third most important oil crop across the world ( Ding et al., 2019a ), and is an allotetraploid derived from an interspecific hybridization between Brassica rapa (genome AA, 2n = 20) and Brassica oleracea (genome CC, 2n = 18), with subsequent chromosomal doubling ( Sun et al., 2017 ; Chen et al., 2021 ). Seed oil content (OC), one of the most important economic and nutritional traits for rapeseed, is mainly determined by a dynamic balance between lipid synthesis and breakdown during seed maturation ( Ding et al., 2019a ; Wang et al., 2021 ). In rapeseed, lipid biosynthesis is initiated just after embryo formation, and its reduction and decomposition occurs during the late maturation stage ( Wang et al., 2021 ).…”

“…Seed oil content (OC), one of the most important economic and nutritional traits for rapeseed, is mainly determined by a dynamic balance between lipid synthesis and breakdown during seed maturation ( Ding et al., 2019a ; Wang et al., 2021 ). In rapeseed, lipid biosynthesis is initiated just after embryo formation, and its reduction and decomposition occurs during the late maturation stage ( Wang et al., 2021 ). Oil bodies, or lipid droplets, are the main reservoir of lipids in seeds of B. napus .…”