Genomes And Pedigree Genetic Footprints Of Young Asian Allotetraploid Rapeseed

Brassica napus(AACC,2n=38)is an important oilseed crop grown worldwide.However,little is known about the population evolution of this species,the genomic difference between its major genetic groups,such as European and Asian rapeseed,and the impacts of historical large-scale introgression events on this young tetraploid.In this study.Asian rapeseeds were employed as the model to demonstrate distinctive genomic footprints and deleterious SNP(Single Nucleotide Polymorphism)variants for local adaptation by recent intra-and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop.The major results are as follows:(1)Genome de novo sequencing of an Asian rapeseed and genomeic comparison between Asian and European rapeseedsWe de novo sequenced the genome of the Asian B.napus cultivar Ningyou 7 using a combination of multiply technologies and yielded a genomic assembly of 993 Mb,89.8%(892Mb)can be anchored to chromosomes.A total number of 104.179 protein-coding genes were annotated.Pairwise genome comparisions between Ningyou 7 and each of the two sequenced European cultivars(Darmor-bzh and Tapidor)were carried out and a mass of variations can be observed.Interestingly,a 3.9 Mb deletion in Tapidor’s C03 overlapped with a QTL(es.C3-3)associated with flowering time and seed yield,which may explain the difference of flowering time between European and Asian rapeseeds.(2)Deep sequencing of Ningyou 7 pedigree and its genomic inheritance during breeding process To better understand the inheritance pattern in the breeding process of Asian rapeseeds,we also sequenced four parental lines(Shengliyoucai,Chengduai,Ningyou I and Chuanyou 2)of Ningyou 7 and identity-by-descent(IBD)of Ningyou 7 was estimated through the de novo comparision between the Ningyou 7 genome and its four parental lines.As expected,each parental line has different genetic contribution patterns.Even though the grandparental line B.rapa Chengduai vwas farthest related to Ningyou 7,the genomic region contributed by Chengduai contained favourable QTLs or genes contributing to the regulation of flowering time,which assisted to the shift of primeval Asian rapeseeds to the semi-winter type to adapt to Asian growth environments.(3)Genome-wide selection footprints and deleterious variations in Asian rapeseeds.In the short breeding history,Asian rapeseeds have undergone two important integression events.In the first integression,initial B.napus introducted from Europe through Japan went through interspecific cross with local B.rapa for the local environment adaption in the 1950s.And the second interession,Asian rapeseeds was further significantly improved through intraspecific with European rapeseeds with double-low traits(low seed glucosinolate and low erucic acid)since 1970s.Then Asian rapeseeds can be divided into double-high type and double-low type based on the content of seed glucosinolate and erucic acid.To analyse the genetic differentiation of Asian B.napus cultivars from European cultivars,in addition to 7 Asian double-high accessions genomic data generated in this study,we collected publicly available genomic data of 68 Asian(30 double-low and 38 double-high)and 59 European accessions.Phylogeny and genomic signatures of rapeseed populations showed that Asian rapeseeds originally derived from European rapeseed but subsequently significantly diverged,with rapid genome differentiation after hybridization and intensive local selective breeding.The first historical introgression of B.rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseeds.The second historical introgression of the double-low traits of European rapeseeds(canola)has reshaped Asian rapeseeds into two groups(double-low and double-high),accompanied by an increase in genetic load in the double-low group.This study demonstrates distinctive genomic footprints and deleterious SNP variants for local adaptation by recent intra-and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop.(4)Construction of BnPedigome,a genomic database for the pedigrees and breeding of Brassica napusBased on the assemblies we achieved,we set up a genomic database for the pedigrees and breeding of BraSssica napus,BnPedigome(http://ibi.zju.edu.cn/bnpedigome/).In the BnPedigome.diverse bioinformatics tools are embedded,which allow users to search,visualize and download the information of interest.Genomic resources generated in this study provide not only a better reference genome for B.napus,particularly for the Asian group but also a comprehensive genomic resource for understanding the inheritance of genetic regions underlying important traits related to adaptation of the Asian rapeseeds during its breeding history.