Resequencing Analysis And QTL Mapping For Two Genetic Mapping Populations Of Brassica Napus L.

Brassica napus(A~nA~nC~nC~n)is an important oil seed crop in China and even in the world.It is a relatively young allotetraploid species formed by the cross of diploid ancestor B.rapa(A~rA~r)and B.oleracea(C~oC~o),and its genetic basis is relatively narrow because of the short domestication and cultivation history and intense artificial selection.To broaden the genetic basis of B.napus,our research group had massively introduced the A~rgenome of B.rapa and the C~c genome of B.carinata into B.napus.New-type B.napus with exogenous introgression components close to the genome constitution of A~rA~rC~cC~c was established.They have significant genetic differences with conventional B.napus,and there are a large number of new genetic variations in their genomes.In order to further study these new genetic variants and their profound effects on agronomic traits improvement and rapeseed genome evolution.In this study,the two mapping populations derived from the hybridization of new-type B.napus and two sequencing varieties and their parents were used as research materials,the genotypic analysis and construction and comparison of high-density genetic maps based on genome-wide sequencing were carried out,and the yield trial and QTL mapping of NG3 DH population were carried out.The results in details are as following:1)Using the obtained genome-wide sequencing data of the two mapping populations,SNP calling was performed using Ningyou7 genome sequence as the reference,which obtained 2.28 million and 2.61 million polymorphic markers,respectively.The markers were divided into three types:normal,pav,and hemi.According to the differences between parental genotypes and populational genotypes,the total markers were divided into two big groups:1)parental and populational genotype consistent markers and 2)parental and populational genotype inconsistent markers.The marker density map of parental and populational genotype consistent markers was displayed.The results showed that different types of markers exhibit a non-uniform distribution on the chromosome,Overall,the normal,pav,and hemi markers that conformd to the chi-square separation ratio of 1:1 could cover the entire genome.2)The NG3 DH population adopted normal markers,and pav?hemi markers of A02and C02.13024 bin markers were obtained after screening and bin collection.The genetic map was constructed and named as NG3mapV1 which containing 3798 bin markers and19 linkage groups.For the pav and hemi markers of the parental and populational genotype consistent markers with separation ratio of 1:1,11433 bin markers were obtained after screening and bin collection.The pav/hemi genetic map was constructed and named as NG3mapV2 which containing 404 bin markers and 12 linkage groups.The two maps were integrated as NG3mapV3 which contained 4080 bin markers.The TG3 DH population adopted normal markers,and pav?hemi markers of A02 and C02.11905 bin markers were obtained after screening and bin collection.The genetic map of TG3 DH population was constructed and named as TG3mapV1,and contained3813 bin markers and 19 linkage groups.No genetic maps were constructed for the pav and hemi markers on other linkage groups in the TG3 population.Through collinearity analysis of NG3mapV1,Ningyou7 genome,and TG3mapV1,using the genomic sequence of Ningyou7 as reference,we found 6 possible translocations that were detected in both NG3 DH and TG3 DH populations,and some potential inversions on three linkage groups(A06,A09 and C09)in both of the two populations.3)We conducted yield trials of the NG3 DH population in Wuhan and Gansu,and examined 14 and 4 traits,respectively.Combined with the NG3mapV3,QTL mapping was performed for each trait using the composite interval mapping method.A total of 96“QTLs”controlling these traits were detected,and the phenotypic variation variances that they each explain range from 2.7%to 17.7%.Among them,3 QTLs are located in the pav and hemi marker regions in the genetic map.57 QTLs and 39 QTLs were detected in the semi-winter environment of Wuhan and the spring environment of Gansu,respectively.The results can provide a basis for the subsequent optimization of the genetic maps,comparison of genetic map,and QTL mapping between these groups,capturing the structural variation between the three parents and their effects on trait variation.