Genetic Properties And Flowering Time QTL Analysis Of A Nested Association Mapping Population In Rapeseed

Rapeseed?Brassica napus L.?is one of the most important oil crops in the world.In rapeseed,the genetic architecture of complex traits has been dissected by traditionally QTL mapping using segregating populations derived from biparental crosses,and more recently by GWAS using cultivars or breeding lines.Recently,The Nested association mapping?NAM?population,which simultaneously has the advantages of both joint linkage analysis and association mapping,has been widely applied to dissect the genetic basis of complex quantitative traits in numerous crops.NAM population includes both historic and recent recombination events,and has the advantages of low marker density requirements,high allele richness,high mapping resolution,and high statistical power.In this study,we firstly developed a rapeseed NAM?BN-NAM?population and analyzed the genetic properties and flowering time QTLs as followed.1.Genetic properties of the B.napus nested association mapping populationThe BN-NAM population contained 15 RIL families?NAM01-NAM15?and a total of2,425 F₆ recombinant inbred lines?RILs?,ranging from 117 to 213 lines per RIL family.All RILs were genotyped by the reduced representation library sequencing and the 16parents were genotyped by the re-sequencing.We constructed three types of genotypic maps.Firstly,fifteen high-density linkage map?LM?were constructed and had a total of94,701 redundant SNP markers.The length of LM ranged from 1,564.7 to 2,446.2centiMorgans?cM?,with an average length of 1,989.7 cM.The number of bins for LM ranged from 1,308 in NAM11 to 2,805 in NAM05,with an average of 1,834 bins across all RIL families.Then,we constructed a joint linkage map?JLM?for the BN-NAM,which contained 30,209 non-redundant markers and 10,182 bins.Furthermore,an ultra-density whole-genome variation map?WVM?was constructed by projecting4,444,309 high-quality variants of parents to the fifteen LMs.Analyses of population structure and principal components revealed that the BN-NAM population could be divided into three groups with weak stratification.A total of 88,386 unique recombination events?REs?were identified in the BN-NAM population,and the number of REs in each RIL family varied from 4,109 in NAM14 to 8,603 in NAM07.The mean number of REs per line varied from 32.6 in NAM11 to 50.7 in NAM03,with an average 41.4 REs per line in the BN-NAM population.The recombination rate along chromosomes is positively correlated with the densities of genes and markers,but negatively correlated with the density of transposable elements and linkage disequilibrium?LD?.The LD decay distance across the 19 chromosomes in whole genome varied from 170 to 2,400 Kb.The mean LD decay distance in the A and C genome was 280 Kb and 950 Kb,varying from 170 to 450 Kb and from 360 to 2,400 Kb,respectively.LD decays in the A genome was much faster than in the C genome,might be due to that the LD blocks in pericentromeric regions of C genome is larger than A genome.2.QTL analysis of flowering time for BN-NAM populationBN-NAM population was planted with a randomized complete block design in eight natural environments at five different locations over a period of four years.The eight different environments included six winter environments and two spring environments.The genetic bases of flowering time were dissected using all three types of genotypic maps of the BN-NAM population.A total of 42 QTLs were identified by each linkage mapping in the whole genome across the 15 RIL populations.Among these QTLs,15QTLs were co-located across multiple environments and RIL families and 45%of them could explain more than 10%of the phenotypic variance.In joint linkage mapping analysis,34 and 30 QTLs were identified for flowering time in the winter and spring environments,respectively.Moreover,63 and 79 QTLs were detected through GWAS analysis in the winter and spring environments,respectively.All QTLs detected by the three methods were integrated,with 20.3%and 46.5%of the loci detected by JLM and GWAS were co-located within the QTL interval of LM,respectively.A total of non-redundant 169 QTLs were identified,with lots of repeated QTLs in the whole genome,particularly on the chromosomes A2,C2,A10 and C08.To gain further insights into flowering time of rapeseed,we tried to find the candidate genes underlying each QTL.A total of 125 candidate genes,one-tenth of the total number of flowering-time genes in the genome,were found in the 84 QTLs.These candidates contained many important flowering-time genes,including FLC,FT,VIN3,CRY2,FLD,AP1,CO,SOC1.It is worth noting that three homologous genes of FLC are the most likely candidates underlying the three major QTLs detected by GWAS analysis on chromosome A2,A10 and C2?BnaA02.FLC,BnaA10.FLC and BnaC02.FLC?.Taken together,the BN-NAM population displays a high resolution and accuracy for the QTL mapping of important traits with an example of flowering-time.