Rapeseed (Brassica napus L.), also known as rape, or oilseed rape, is a yellow flowering member of the mustard or cabbage family (Brassicaceae) cultivated around the world for its oil-rich seed. Rapeseed was the third-leading source of vegetable oil in the world after soybean and palm oil, and it is the world’s second-leading source of protein meal after soybean. Rapeseed oil can be processed to produce salad oil, shortening, and margarine. In addition to food, rape can also be used as a raw material in several industries and is used to produce soap, paper, and organic fertilizer.
As one of the world’s major producers, China has a thousand-long history of rapeseed cultivation and accounts for more than 50% of the domestic vegetable oil produced every year. As a result, scientists in China have continued to explore ways to increase the yield and quality of the crop produced. This has resulted in the emergence of molecular breeding, shifting from more traditional breeding techniques that rely on experience to focusing on targeted and efficient breeding. This has increased breeding efficiency, improving both the quality and yield of the crop.
A recent study by a team from the Chinese Academy of Agricultural Sciences aimed to understand how molecular breeding improved crop production. To do this, they carried out a comprehensive analysis of the genome of 418 diverse rapeseed accessions, which included 410 accessions from a core collection as well as vegetable-use accessions and a synthetic rapeseed specimen1. The researchers used the information gleaned from the whole-genome resequencing of these accessions to carry out genome variations, genome-wide selections, and genome-wide association studies. They aimed to identify which genes were responsible for 56 agronomic traits that were modified during the rapeseed improvement process., including those associated with morphological characteristics, stress and disease resistance, growth period, yield components, and seed quality.
First, the research team collected young leaves from each rapeseed accession and genomic DNA was extracted. Following this, sequencing was carried out by Novogene using the Illumina HiSeq 4000 platform, generating 150bp paired-end reads. In addition, 135 of the 418 rapeseed accessions were selected for resequencing with high coverage on the Illumina HiSeq X Ten platform. Sequencing yielded 5.6 Tb of data in total. The data was cleaned before the paired-end reads were mapped to a reference genome using BWA software. After alignment, the researchers performed SNP and InDel calling using GATK, and only the high-quality SNPs were retained for subsequent analysis.
The research team carried out a variety of subsequent analyses to identify which possible genes and associated loci are responsible for specific agronomic traits. This included population genetic and LD analysis, introgression analysis, identification of selective sweep signals, GWAS, phylogenetic analysis, Hi-C experiments, expression analysis, gene cloning, and plant transformation. From this, 7,531,945 SNPs and 469,176 InDels were identified. Phylogenetic relationships were established using the SNPs, which showed that the vegetable-use rapeseeds had differentiated from the oil-use accessions. Further, the researchers used this information to classify the 410 oil-use rapeseed accessions into four subclades. The classifications of these accessions did not completely respond to the ecotypes of the accessions that had been observed, demonstrating the occurrence of widespread gene introgressive hybridization between the three ecotypes. This work also identified more than 600 associated loci-related causative candidate genes for the 56 traits they wished to examine. This study provides an important contribution to the research on rapeseed, providing a valuable genomic resource for future breeding programs.
Rapeseed and other crop plants provide important value to human life as a food resource, as well as being of economic value, providing valuable income to people around the world. Studies such as this one demonstrate the value of sequencing as a technique to understand the genetic basis of agronomic traits and provide information that can help us to improve future crop breeding programs. This is of particular importance as we need to feed q rapidly growing population while navigating the problems associated with global climate change, which include significant crop losses due to severe heat and drought2.
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