Petal size in rapeseed: novel QTL and candidate genes detected through genome-wide association study and transcriptome comparison

Petal size determines the value of ornamental plants, and thus their
economic worth. However, the molecular mechanisms controlling petal size
remain unclear in most non-model species. To identify quantitative trait
loci and candidate genes regulating petal size in rapeseed (Brassica
napus), we performed a genome-wide association study (GWAS) using data
from 588 accessions over three consecutive years. We detected 17
significant single nucleotide polymorphisms (SNPs) associated with petal
size, with the most significant SNPs located on chromosomes A05 and C06. A
combination of GWAS and transcriptomic sequencing based on two accessions
with extreme differences in petal size identified 11 differentially
expressed genes (DEGs) that may control petal size variation in rapeseed.
In particular, BnaA05.RAP2.2 homologous to RAP2.2 in rapeseed may be a
critical gene negatively influencing petal size through the ethylene
signaling pathway. In addition, a comparison of petal epidermal cells
indicated that petal size differences between the two extreme accessions
were determined mainly by cell number differences. Finally, we propose a
preliminary model for the control of petal size in rapeseed. Our results
provide insights into the genetic mechanisms regulating petal size, and
also lay the foundation for a better understanding of petal development in
plants.

花瓣大小决定观赏植物的价值，进而影响其经济价值。然而，多数非模式物种中调控花瓣大小的分子机制仍不明确。为鉴定油菜（Brassica napus）中调控花瓣大小的数量性状位点（quantitative trait loci, QTL）及候选基因，我们利用连续三年588份材料的数据开展了全基因组关联分析（genome-wide association study, GWAS）。我们检测到17个与花瓣大小显著关联的单核苷酸多态性位点（single nucleotide polymorphisms, SNPs），其中最显著的SNPs位于A05和C06染色体上。结合GWAS与基于两株花瓣大小差异极端材料的转录组测序（transcriptomic sequencing），我们鉴定出11个可能调控油菜花瓣大小变异的差异表达基因（differentially expressed genes, DEGs）。特别地，与油菜RAP2.2同源的BnaA05.RAP2.2可能是通过乙烯信号通路负调控花瓣大小的关键基因。此外，花瓣表皮细胞的比较分析表明，两株极端材料间的花瓣大小差异主要由细胞数量差异决定。最后，我们提出了油菜花瓣大小调控的初步模型。本研究结果为解析花瓣大小调控的遗传机制提供了见解，也为深入理解植物花瓣发育奠定了基础。