Abstract
Plant height is a vital agronomic trait for crops, including oilseed crops such as rapeseed (Brassica napus L.). It affects the crop yield, oil content, and lodging resistance in rapeseed. In this study, we investigated a dwarf trait controlled by a semi-dominant allele in rapeseed. A dwarf line, YA2016-12, was crossed with a tall line, G184-189, and an F2 population was established. Forty of the tallest plants and 40 of the shortest plants from the F2 population were selected and two DNA pools (tall and dwarf) were constructed by the bulked segregant analysis (BSA) method. The two DNA pools and two parental DNAs were then re-sequenced. A sliding window analysis was used to calculate the Δ(SNP-index) and discover an association region on chromosome A03 with a length of 12.4 Mb. Within this region, we found 1225 genes, including 811 genes with non-synonymous or frameshift mutations between YA2016-12 and G184-189. Alignment to known plant height-related orthologs in Arabidopsis thaliana, as well as KEGG pathway and gene ontology annotations, was used to identify nine candidate genes (BnaA03g31770D, BnaA03g37960D, BnaA03g24740D, BnaA03g40550D, BnaA03g26120D, BnaA03g35130D, BnaA03g42350D, BnaA03g25610D, and BnaA03g39850D) involved in gibberellin or cytokinin signaling. Identification of the causal gene for this trait, and of genetic markers linked to favorable alleles, has potential utility for marker-assisted selection to breed rapeseed varieties with improved height.
Highlights
Rapeseed (Brassica naups L.) is a major oil crop globally
We investigated a dwarfism trait controlled by a semi-dominant allele in a rapeseed line, YA2016-12
A total of 811 genes with non-synonymous mutation sites or frameshift mutation sites were found in an association region on ChrA03 identified by bulked segregant analysis (BSA) and whole-genome re-sequencing (WGR)
Summary
Rapeseed (Brassica naups L.) is a major oil crop globally. It is an allotetraploid (AACC, 2n = 38)with a complex genome. Rapeseed (Brassica naups L.) is a major oil crop globally. It is an allotetraploid (AACC, 2n = 38). Plant height is an important yield-related trait; taller plants are more prone to lodging, which results in decreased yield due to grain loss and spoilage, and makes mechanized harvesting difficult [2]. In some crops, such as wheat (Triticum sp.) and rice (Oryza sativa), dwarf or semi-dwarf plant types were introduced in the 1960s and 1970s, resulting in increased yields and the so-called “green revolution” [2]. Breeding rapeseed for dwarfism or semi-dwarfism plant stature could increase lodging resistance, stabilizing production and facilitating mechanized harvesting
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