Genome-wide Association Analysis Of Plant-type Related Traits In Rapeseed (Brassica Napus L.)

Rapeseed(Brassica napus L.) is widely cultivated oil crop in the world, and it’s one of the most important oil crops in China. Yields as well as mechanized production have been the primary task in breeding and cultivations. It has been reported seed yield is directly determined by silique number per plant, seeds number per silique, thousand-seed weight, and it’s also influenced by plant-type traits such an plant height, the first branch height, branch angel, branch numbers etc. Futhermore, rapeseed production mechanization depends on special plant type. In this study, a population of 529 oilseed rape (Brassica napus L.) accessions were collected from different breeding institutions. Firstly, the natural population were used to assess population structure, relative kinship and linkage disequilibrium. Secondly, we used association mapping to detect SNP markers linked to seven plant-type traits and three yield-related traits using 34103 SNPs. The main results are summarized as follows:1. Phenotypic analysis of plant-type traits and yield-related traits:In our association mapping, extensive phenotypic variations were observed for all traits, highly phenotypic correlations were observed between almost all the traits. Three traits i.e. the plant height, branch angle and the effective height of branch showed the effects of genotype and environment effects significantly, silique length only showed the effects of genotype and genotype and the environment interaction effect, the remaining six plant-type and yield-related traits showed extremely significant level of genotype, environment and the effects of genotype and environment interactions.2. Analysis of population structure and relative kinship:The natural population could be divided into PI and P2 groups by a model-based population structure analysis using 11368 SNP markers. Most of the lines in group P1 were from China and belong to semi-winter oilseed rape, most of the lines in group P2 were from European, Qinghai and Gansu province, and belong to winter or spring oilseed rape. In the association panel, about 55% kinship between any two lines is 0, and about 14% is between 0-0.05. These results indicate that the little influence caused by the population structure is due to the weak relationship.3. Linkage disequilibrium:By calculating the r2 value of pairwise markers in the same chromosome, we simulate the trend lines of LD found that r2 value declined rapidly while the physical distance increased. When the cut off value of r2 was setted to 0.2, it was found that the decay of the LD in A genome is about 150 Kb, and approximately 750 Kb in C genome, indicating that Brassica rapa.was widely used in breeding.4. Association mapping of seven plant-type traits and three yield-related traits: Using Q+K model, association analyses were carried out with 34103 SNP markers for seven plant-type traits and three yield-related traits. A total of 360 SNP markers linked to 10 traits were detected in two years (P<1/34103).Of these,13 SNPs were detected in both two years,19 SNPs were associated with two or more traits simultaneously.5. Candidate genes:In this study, the homologous genome sequences of B. napus associated with SNP markers were annotated according to the genome informations of Arabidopsis thaliana, one gene i.e. AT5G14090 (AtLAZY1) was found to be related to branch angle phenotype, twenty genes such as AT2G34555(ATGA2ox3), AT5G17490(RGL3), AT4G33430(BAK1), AT4G18710 (BIN2), AT4G39400(BRIl) and AT2G36800(D0GT1) were found to be related to plant height phenotype, four genes i.e. AT5G17690(TFL2), AT1G69120(AP1), AT4G32980(ATH1) and AT2G19520(FVE) were found to be related to major inflorescence length phenotype and one gene i.e. AT5G60690 (REV) was found to be related to silique nuber of major inflorescence phenotype, one gene i.e.AT5G54650(FH5) was found to be related to seeds yield, and one gene i.e. AT3G59900(ARGOS) was found to be related to silique length involved in organ size. In summary, these identified genes and SNPs will offer essential information for cloning plant-type and yield-related genes in rapeseed.