Population Genome Variations And Subgenome Asymmetry In Brassica Napus L.

Brassica napus(AACC,2n = 4x = 38)is a young allotetraploid crop formed by the natural hybridization of Brassica rapa(AA,2n = 2x = 20)and Brassica oleracea(CC,2n =2x =18)about 7,500 years ago.Asymmetry is a common phenomenon,in order to study the characteristics and asymmetry of two subgenomes of Brassica napus,we resequenced a natural population containing 1,023 accessions to research their variations and asymmetry,and revealed the effect of the asymmetry in Brassica napus breeding process.Main results were as follows:1.In this study,we used re-sequencing data to detect 4,429,954 SNPs and 645,007 In Dels in the natural population and large fragment deletions and Homeologous exchanges(HEs)in each accession.A high-quality Brassica napus haplotype map containing 57,877 haplotypes,which was 71.93% coverage of genome,was constructed.These results provide important information for revealing the formation basis and QTL mapping of complex traits,mining excellent germplasm resources,the evolution of varieties and genetic improvement.2.By analyzing the genetic structure of Brassica napus by population structure,principal component analysis,phylogenetic tree and population differentiation coefficient,we found that our natural population could be divided into four subgroups,spring type,winter type,semi-winter type and synthetic type,which might be caused by the geographical distribution and ecological adaptability.Further analyses showed that the genetic distance and population differentiation of synthetic type were farther than spring type,winter-type and semi-winter type,their differentiation coefficients were 0.19,0.153 and 0.197,respectively,which might be since synthetic accessions were new allotetraploids.Most of the genome features still retained the original genome of its hybrid parents,Brassica rapa and Brassica oleracea,which results in great differences between the three types of rapeseed in genetic distance and population differentiation.3.We analyzed the genome features of gene density,TEs density,population diversity,large fragmental deletions frequency,HEs frequency,linkage disequilibrium and recombination rate,and found that there were significant differences between the An and Cn subgenomes,especally HEs frequency in An subgenome was 10 times to Cn subgenome.Therefore,we could make full use of the An subgenome with high recombination rate and more polymorphic information to QTL fine mapping and application of elite alleles.Comparing with rapeseed’s parents,Brassica rapa and Brassica oleracea,we speculated that the asymmetry features between two subgenomes might be derived from two parental species.4.Seventy-six(76)and one hundred sixty-two(162)QTL were detected by SNP-GWAS and haplotype-GWAS for 23 traits,respectively.5.We found the asymmetry of two subgenomes played an important role in the breeding process of rapeseed by analyzing two vertical pedigrees of "Zhongyou821".Therefore,we proposed to use the hybridization of Brassica oleracea and Brassica napus or the technology of molecular biology to balance the asymmetry of two subgenomes,which could create more genetic variations for genetic improvement in rapeseed.