Genomic Polymorphism Analysis And Digital Utilization Of Germplasm Resources In Rapeseed(Brassica Napus L.)

Rapeseed(Brassica napus L.,An An Cn Cn,2n=4x=38)is one of the most important oil crops in the world.It is an allopolyploid crop formed by natural hybridization between two diploid progenitors,Brassica rapa(Ar Ar,2n=2x=20)and Brassica oleracea(Co Co,2n=2x=18)around 7,500 years ago.Despite its relatively short evolutionary history compared to B.rapa and B.oleracea,B.napus has adapted to different climatic zones and latitudes and has formed three main ecotypes,namely winter,semi-winter and spring ecotypes.The genetic basis underlying the divergence of the different B.napus ecotypes is still not fully understood.In this study,we resequenced 991 B.napus germplasm accessions from 39 countries,including 658 winter,145 semi-winter and 188 spring ecotypes.We further constructed an integrated genetic variation map and studied the population structure,genetic diversity and linkage disequilibrium(LD)of 991 B.napus accessions.Our results preliminarily uncovered the genetic basis underlying the divergence of the main ecotypes of B.napus.Further,in order to take full advantage of these genetic variations to identify functional genes,a website for the digital utilization of B.napus germplasm resources was constructed.Our results will contribute to the population genomics studies,identification of functional genes for important agronomic traits,and molecular marker-assisted breeding in B.napus.The main results of this study are summarized as the following three points:1.Construction of genetic variation map of rapeseedWe generated a total of 7.82 Tb of clean reads by whole-genome resequencing of 991 B.napus accessions originating from 39 countries across the world.The average sequencing coverage reached ~6.6×.After SNP and In Del calling,5.56 million SNPs and 1.86 million In Dels were detected by mapping the 991 rapeseed genomes against the reference genome(“Darmor-bzh”),which led to the generation of an integrated genetic variation map.The results revealed a higher frequency of genetic recombination in the A subgenome than that in the C subgenome.This,in turn,broke the linkage disequilibrium in the A subgenome and led to a faster LD decay rate and a higher genetic diversity of the A subgenome.2.Discovery of the genetic basis of rapeseed ecotype divergence The selective sweep analysis among different ecotype groups indicated that FLOWERING LOCUS T(FT)ortholog Bna A02.FT(Bna A02g12130D)and FLOWERING LOCUS C(FLC)ortholog Bna A10.FLC(Bna A10g22080D)were strongly selected during artificial and natural selection in B.napus.Genome-wide association studies(GWAS)of the flowering time in 991 rapeseed accessions showed that Bna A02.FT and Bna A10.FLC were significantly associated with the flowering time.Analysis of SNP distribution in the promoter and coding regions of Bna A02.FT and Bna A10.FLC revealed that the nucleotide sequences of the coding regions of these two genes were relatively conservative across the three ecotypes.However,significant SNP haplotype differences were found in the promoter regions.Moreover,the gene expression levels of Bna A02.FT and Bna A10.FLC were significantly different among the three ecotypes,giving rise to the different flowering times of these three ecotypes.These results indicated that different SNP haplotype in the promoter regions of Bna A02.FT and Bna A10.FLC might be the key genetic basis of the divergence of three main ecotypes in rapeseed.3.Establishment of the website for the utilization of the rapeseed genetic resourcesA SNP database,namely Bna SNPDB(https://bnapus-zju.com/bnasnpdb),was constructed for rapeseed based on the genetic polymorphisms of 991 B.napus germplasm accessions,which provided a series of built-in analysis modules for storing,retrieving,and analyzing SNPs across different germplasm accessions.Moreover,a core germplasm was established by selecting 300 core accessions from the 991 germplasm collections based on the phylogenetic and principal component analysis.A genome-wide association studies(GWAS)platform,namely Bna GWAS(https://bnapus-zju.com/gwas),was built to facilitate GWAS in rapeseed.These two platforms will be of help for the worldwide researchers to carry out various studies such as population genomics,population evolution,development of molecular marker,and molecular marker-assisted breeding,etc.in B.napus.In summary,this study resequenced 991 B.napus germplasm accessions,constructed an integrated genomic variation map of B.napus,revealed the genetic basis of B.napus ecotype divergence,and established a website for the utilization of the B.napus genetic resources.Our results shed new light on the genetic basis underlying the divergence of the main ecotypes of B.napus and lay the foundation for molecular marker-assisted breeding in B.napus,which will promote basic and applied research in B.napus.