Genome Biology: Revealing the Genetic Structure of Seed Coat Content in Brassica

Posted by Ilsa Miller on April 26th, 2022

The rapeseed team at Huazhong Agricultural University, Wuhan, China, published a research paper entitled “Multi-omics analysis dissects the genetic architecture of seed coat content in Brassica napus” in Genome Biology. This study has made important progress in the analysis of the genetic basis of skin shell rate, new gene mining, and regulatory networks for seed carbon source allocation in B. napus.

Rapeseed oil is the third largest edible vegetable oil in the world, and increasing rapeseed oil content is one of the important goals of rapeseed breeding. Rapeseed seeds are mainly composed of seed coat and embryo, which are the main sites for storing nutrients such as oil and protein. Seed coat plays an important role in many biological processes, such as nutrient transport, controlling seed size and resisting biotic and abiotic stresses. Seed coat contains many secondary metabolites such as pigment, lignin, and fiber, and the synthesis of these secondary metabolites is inseparable from the normal development of seed coat, and its content determines the color and thickness of seed coat and affects the skin rate (the proportion of seed coat weight to seed). By regulating seed coat development and reducing seed coat rate, the specific gravity of embryos can be increased, and then the seed oil content can be increased. Therefore, it is important to elucidate the genetic basis of the formation of canopy rate traits in rapeseed and excavate key genes that regulate seed coat development to improve oil content in rapeseed.

The study utilized the genome resequencing data of 382 Brassica napus samples and 257 representative materials selected from them, transcriptome data of two seed developmental stages, through genome-wide association analysis (GWAS) and transcriptome-wide association analysis (TWAS) et al. systematically analyzed the genetic basis of rapeseed husk rate. In this study, more than 700 genes were identified to be significantly associated with shell rate by TWAS analysis, and in combination with the gene module regulatory network, it was found that BnaCCRL and BnaTT8 may play a key role in seed coat development by regulating lignin biosynthesis. Through GWAS analysis, three QTL loci regulating skin-shell rate were mapped, and a hotspot QTL qSCC.A09 was found on the A09 chromosome, which may affect lignin biosynthesis in the seed coat by regulating BnaTT8.

To validate the gene function of BnaCCRL and BnaTT8, the study constructed knockout mutants using gene editing technology. Lignin content, shell rate, as well as seed coat thickness were significantly decreased, while seed oil content was significantly increased in BnaCCRL and BnaTT8 mutants compared to wild type. The analysis suggests that BnaTT8 may indirectly regulate lignin synthesis via the general phenylpropanoid pathway, thereby affecting the skin shell rate. Cinnamoyl-CoA reductase (CCR, cinnamoyl-CoA reductase) is a key enzyme involved in lignin synthesis, while the CCR-like (CCRL) identified in this study is less than 30% identical to CCR, and it was demonstrated for the first time that BnaCCRL also has cinnamoyl-CoA reductase activity by enzyme activity experiments. Genetic, biochemical and metabolic analyses showed that BnaCCRL is directly involved in seed coat lignin biosynthesis to regulate the skin shell rate of rapeseed seeds.

There was a significant negative correlation between seed shell rate and oil content in B. napus, and reducing shell rate was conducive to seed accumulation of more oil. In this study, the significant gene expression of TWAS in oil content and shell rate was analyzed, and a large number of genes involved in the phenylpropanoid pathway and oil synthesis pathway were found to affect the carbon source allocation between rapeseed seed coat and embryo during seed development.

In this study, the genetic basis of the skin shell rate of B. napus was comprehensively analyzed, and two genes regulating lignin content and oil content were cloned. The results have important theoretical significance for elucidating the mechanism of rapeseed seed coat formation, and also provide gene resources and theoretical basis for the cultivation of rapeseed varieties with high oil content.