Abstract
BackgroundBrassica napus provides approximately 13–16% of global vegetable oil for human consumption and biodiesel production. Plant height (PH) is a key trait that affects plant architecture, seed yield and harvest index. However, the genetic mechanism of PH in B. napus is poorly understood.ResultsA dwarf mutant df59 was isolated from a large-scale screening of an ethyl methanesulphonate-mutagenized rapeseed variety Ningyou 18. A genetic analysis showed that the dwarfism phenotype was controlled by one semi-dominant gene, which was mapped on C9 chromosome by quantitative trait loci sequencing analysis and designated as BnaDwf.C9. To fine-map BnaDwf.C9, two F2 populations were constructed from crosses between conventional rapeseed cultivars (Zhongshuang 11 and Holly) and df59. BnaDwf.C9 was fine-mapped to the region between single-nucleotide polymorphism (SNP) markers M14 and M4, corresponding to a 120.87-kb interval of the B. napus ‘Darmor-bzh’ genome. Within this interval, seven, eight and nine annotated or predicted genes were identified in “Darmor-bzh”, “Ningyou 7” and “Zhongshuang 11” reference genomes, respectively. In addition, a comparative transcriptome analysis was performed using stem tips from Ningyou 18 and df59 at the stem elongation stage. In total, 3995 differentially expressed genes (DEGs) were identified. Among them, 118 DEGs were clustered in plant hormone-related signal transduction pathways, including 81 DEGs were enriched in auxin signal transduction. Combining the results of fine-mapping and transcriptome analyses, BnaC09g20450D was considered a candidate gene for BnaDwf.C9, which contains a SNP that co-segregated in 4746 individuals. Finally, a PCR-based marker was developed based on the SNP in BnaC09g20450D.ConclusionsThe combination of quantitative trait loci sequencing, fine-mapping and genome-wide transcriptomic analysis revealed one candidate gene located within the confidence interval of 120.87-kb region. This study provides a new genetic resource for semi-dwarf breeding and new insights into understanding the genetic architecture of PH in B. napus.
Highlights
Brassica napus provides approximately 13–16% of global vegetable oil for human consumption and biodiesel production
The aims of the present study were to: (1) fine-map the gene responsible for dwarf architecture in df59 using Quantitative trait locus (QTL) sequencing (QTL-seq) and map-based cloning strategies; (2) elucidate the patterns of gene expression between Ningyou 18 (NY18) and df59 using comparative transcriptomic analyses; and (3) develop a stable single-nucleotide polymorphism (SNP) marker tightly linked to the dwarf gene that could be used for marker-assisted selection
As the Plant height (PH) in A. thaliana and rice were mainly regulated by plant hormones [7,8,9,10,11], we focused on the Differentially expressed gene (DEG) involved in signal transduction pathway (138 genes)
Summary
Brassica napus provides approximately 13–16% of global vegetable oil for human consumption and biodiesel production. Plant height (PH) is a key trait that affects plant architecture, seed yield and harvest index. Rapeseed (Brassica napus, AACC, 2n = 38) is an important oilseed crop worldwide, and an emerging biofuel crop. In China, the cultivated area of rapeseed is ~ 67 million hectares, with an annual seed yield of ~ 4.5 million tons every year [3], and the collectable production of rape straw was 38.17 million tons in 2013 [4]. Plant height (PH) is a key trait that affects the plant architecture, seed yield, dry weight and harvest index [5]. Lodging makes B. napus unsuitable for mechanical harvesting and causes dramatic decreases in yield and seed quality [6]. It is important to understand the genetic bases of PH to breed new cultivars with an ideal plant architecture and to maximize B. napus’ economic benefits as an oil and bioenergy crop
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