| Rapeseed is an important oil crop of traditional superiority in China. Genetic dissection of yield traits, seed-quality traits and other traits of agronomic value in rapeseed holds special attention for rapeseed breeders all the time. Bi-parents populations and natural populations have been widely used for gene discovery while the development of second generation mapping populations breaks out this pattern. C urrently, reports on the newly developed mapping population MAGIC, which represents Multi-parent Advanced Generation Inter-cross, could be hardly read in genetic research of Brassica napus.In this study, Genetic diversity and genetic distance of the Brassica napus MAGIC composed of 545 MAGIC lines were initially illustrated by SSR markers; Based on these results, 204 MAGIC lines were selected to form a subset MAGIC. 60 K SNP microarray were then adopted to study the extensive linkage disequilibrium and event ually,we conduct genome-wide association study for quality-related traits in MAGIC. Main results are as follows:1.Among 60 SSR markers adopted to study the genetic diversity of MAGIC, 261 alleles in total were amplified, with 4.35 alleles per marker, 2 to 8 alleles per marker, and 38.33% markers with 4 alleles, which is the largest frequency. Average PIC value for each marker was 0.48.2.Analysis of genetic distance between 8 parents, between line groups and within line groups indicated that, the genetic diversity between 8 parents was broader than the diversity between line groups, and diversity between line groups was broader than that within the line groups.On criteria of a sum total maximum of all genetic distances,3-4 representative lines in each of the 63 line groups were selected to form a new subset population of MAGIC, which were applied in further association mapping study.3.60 K SNP microarray were applied to get genotypes of the subset MAGIC making up of 204 lines and 8 parents. The filteration of SNP data mainly include two steps: 10979 SNPs with a heterogeneity rate over 20% and 5997 SNPs with MAF below 0.05 were removed. Last but not least, by blasting the rest SNPs onto the reference genome sequence of Brassica napus reported by French, 16583 SNPs with known position in linkage groups were obtained4.16583 SNPs described above were used for analysis of genetic diversity o f the subset MAGIC. In the genome-wide scale, the average PIC for each SNP was 0.40.While genome A had a average PIC of 0.39, genome C got a average PIC of 0.41, a bit higher than genome A. There were 12785 SNPs with a PIC value exceeding 0.3, which took up 77.1% of the total number.5.Results of the extensive linkage disequilibrium in MAGIC showed that, on the whole, r2 decayed to 0.20 when the mean distance between SNP markers was about 4Mb. LD-decay rates between the genome A and the genome C in MAGIC were quite different, decay rate for the genome A was considerably faster than the genome C. r2 decayed to 0.2 when the average distance was 700 kb and to 0.1 when it was 2.1Mb in the genome A; whereas, r2 decayed to 0.2 when the average distance was 6.6 Mb and to 0.1 when it was 7.7 Mb in the genome C.6.In association study, 17 SNPs significantly associated with erucic acid were detected, peak SNP on A8 is only 385 Kb away from the Bna A.FAE1. 18 glucosinolate SNPs,with the peak 186 Kb away from the Bna A.HAG1,could explain 30% of the total phenotypic variance. 3 palmitic acid SNPs,34 oleic acid SNPs and 5 linoleic acid SNPs were detected respectively and all these 43 SNPs were on the A8 linkage group. |
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