Dissection Of Genetic Variation Caused By Genomic Fragment Losses In Brassica Napus Germplasm Accessions

Brassica napus is widely distributed all over the world and is one of the important oil crops,which orginated from natural hybridization between B.rapa and B.oleracea and consequent chromosomal doubling 5,000 to 10,000 years ago.B.napus has generated abundant genetic variation in the process of natural and artificial selection.In this study,we constructed an association study population comprising 324 rapeseed accessions collected from major growing regions in the world and identified the deletion variation by high throughput sequencing and bioinformatics.In order to study the relationship between the genetic variation and traits,we conducted whole genome-wide association study(GWAS)in which phenotypic data were collected from multi-environment field assessments.Further study was carried out to analyze the structure variation of the varieties of different ecotypes for dissecting the genetic basis among the different ecotypes.Major results were listed as follows.1.The genomic deletion variation of 324 accessions of B.napus was identified by re-sequencing with a depth of 7X.The bioinformatics results indicated that there are 2,906,978 deletions.Phylogenetic tree was built through these deletions,and the results showed that these varieties could be divided into three subgroups,each mainly consisting of accessions belonging to one of three ecotypes.2.The deletion variation was used as genotype to conduct GWAS with 18 important agronomic characters,and there were 39 deletion association loci found.In comparison with the results from SNP-based GWAS,it was found that there are overlaps between associated regions detected only by deletion and SNP,respectively,and there are also specific regions detected by these deletions.The two traits,thousand seed weight and glucosinonate content,were taken as examples for display of the results.3.Further study on the associated genomic regions with glucosinolate contents showed that the B.napus accessions were divided into the two groups,one with significantly higher glucosinolate contents than the other.It confirmed that the deletion variation is reliable as molecular makers to carry out the whole-genome association analysis.4.Using in depth sequencing of the three ecotype of oilseed rape,we detected a large number of genetic variations including structural variation and copy number variation.These genetic variations involved 6,325,6,413 and 6,443 genes in spring,winter and semi-winter type cultivars,respectively.The GO enrichment analysis showed that they are mainly enriched in the GO categories related to biological metabolism,developmental regulation and environmental adaption etc.For revealing the genes contributed to the formation of different ecotypes of B.napus,we searched the genes with genetic variation on regulatory network related to flowering time,and found that FLC,VRN,GA,SPL3 genes involved in plant vernalization pathway,GA pathway,and senescence pathway carried genetic variation occurred in the genic regions,suggesting that these genes may be responsible for the formation of different ecological adaptations of B.napus.