Correlation Analysis Between Heterosis and Genetic Distance Evaluated by Genome-Wide SNP Chip in Brassica napus

【Objective】 To investigate the feasibility of heterosis prediction by single nucleotide polymorphism (SNP) markers in rapeseed, the 60K SNP chip covering the whole genome of Brassica napus was used to estimate the genetic distance (GD) of elite parental lines of B. napus, and the correlation between GD and heterosis was analyzed for the guidance of hybrid development of rapeseed. 【Method】 Forty-six F1 hybrids were produced using six maintainer lines (1019B, 1055B, 6098B, 8908B, 6019B and ZS11B) and eight restorer lines (R1, R2, R3, R6, R9, R10, R11 and OR1) of Polima cytoplasmic male sterility (CMS) in an incomplete diallel cross design. All the parents and F1s were grown in three different ecological conditions which are located in Wuhan, Guiyang, and Chaohu. Ten yield-related traits including plant height (PH), branch height (BH), number of effective primary branches (NEPB), silique density (SD), effective length of main inflorescence (ELMI), number of effective siliques on main inflorescence (ESMI), number of effective siliques per plant (ESPP), seed per silique (SPS), 1 000-seed weight (TSW) and yield per plant (YPP) were investigated for mid-parent heterosis and high-parent heterosis. The 14 parental lines were genotyped by 60K SNP chip of Brassicas. GD based on SNP genotyping was estimated with MEGA5.0 software, and cluster analysis was carried out using unweighted pair group method arithmetic averages (UPGMA) method. Correlation analysis between GD and heterosis was conducted by SAS9.1 statistical analysis software.【Result】There were 40 201 loci selected from 52 157 SNP loci as being effective for genetic distance calculation and cluster analysis after quality determination. GDs of the 14 parental lines ranged from 0.1883 to 0.8811, with an average of 0.5217. The GD between 6098B and 6019B was the smallest and that between ZS11B and R6 was the largest. The parental lines were divided into four groups, with six maintainers in one big group, four restorer lines R2, R6, R9 and R10 in a second group, three restorer lines R1, R3 and R11 in the third group, and the remaining one restorer OR1 in the fourth group. This cluster results indicate that the genetic variation in the restorers is greater than that in the maintainers, which is in accordance with their pedigree relationships. The average mid-parent heterosis of the 10 traits ranged from -0.07%-38.78%, and the average high-parent heterosis ranged from -7.74%-20.78%. Except for NEPB, all other nine yield-related traits showed significant heterosis in F1 hybrids. Especially for PH, SPS, BH and YPP, the average mid-parent heterosis was 6.83%, 15.31%, 16.13% and 38.78%, respectively, with the number of F1s having positive mid-parent heterosis was 45, 41, 46 and 46; and the average high-parent heterosis reached 3.18%, 5.19%, 7.85% and 20.78%, respectively, with the number of F1s having positive high-parent heterosis was 41, 31, 42 and 44. A significant positive correlation between heterosis and SNP estimated GD was detected for PH, BH and YPP, with the correlation coefficients between SNP estimated GD and mid-parent heterosis were 0.3884, 0.4051 and 0.4038, respectively. The correlation between heterosis and SNP estimated GD for other traits was not significant. 【Conclusion】The genome-wide 60K SNP chip of Brassicas has significant advantages for genotyping, genetic distance estimation and cluster analysis. The GD estimated by genome-wide SNP makers has a very significantly positive correlation with heterosis for traits with high and universal heterosis, including plant yield. Thus, the genome-wide 60K SNP chip of Brassicas can be used to well predict heterosis in rapeseed.