利用全基因组SNP芯片分析油菜遗传距离与杂种优势的关系

doi:10.3864/j.issn.0578-1752.2015.12.020

摘要/Abstract

摘要： 【目的】利用单核苷酸多态性（single nucleotide polymorphism，简称SNP）标记估算油菜优异亲本间的遗传距离，分析其与杂种优势间的关系，探讨利用SNP标记预测油菜杂种优势的可行性，为油菜杂种优势利用育种提供指导。【方法】将油菜波里马细胞质雄性不育系的6个保持系（1019B、1055B、6098B、8908B、6019B、ZS11B）和8个恢复系（R1、R2、R3、R6、R9、R10、R11、OR1）采用不完全双列杂交试验设计配制得到的46个F₁杂种及其亲本，在湖北武汉、贵州贵阳和安徽巢湖3种生态环境下考察株高、分枝部位高度、一次有效分枝数、结角密度、主花序有效长、主花序有效角果数、单株有效角果数、每角粒数、千粒重及单株产量共10个产量相关性状，统计各性状在每个F₁组合中的杂种优势，包括中亲优势和超亲优势。利用油菜全基因组60K SNP芯片对14个亲本进行基因型分型，对分型得到的SNP标记经质控后利用MEGA5.0软件估算亲本间的遗传距离，采用非加权类平均法（unweighted pair group method arithmetic averages，UPGMA）对亲本进行聚类分析，利用SAS9.1软件进行遗传距离与性状杂种优势的相关性分析。【结果】14个亲本经油菜全基因组60K SNP芯片进行基因型分型后共得到52 157个SNP位点，经质量控制后，最终筛选出40 201个SNP有效位点用于亲本遗传距离计算及聚类分析。14个亲本中以6098B与6019B的遗传距离最小，ZS11B与R6的遗传距离最大，所有亲本间的遗传距离介于0.1883—0.8811，平均为0.5217。14个亲本被分成4个主群，6个保持系为一个主群，8个恢复系中OR1单独为一个主群，R1、R3、R11为一个主群，R2、R6、R9、R10为一个主群，证明恢复系群体的遗传变异大于保持系，分群结果与实际系谱相符。所考察的10个性状的中亲优势均值变幅为-0.07%—38.78%，超亲优势均值变幅为-7.74%—20.78%。10个性状中除了一次有效分枝数外，其他性状的杂种优势效应显著，尤其是株高、每角粒数、分枝部位高度和单株产量，平均中亲优势分别达到6.83%、15.31%、16.13%和38.78%，正向中亲优势组合数分别有45、41、46和46个；平均超亲优势分别达到3.18%、5.19%、7.85%和20.78%，正向超亲优势的组合数分别有41、31、42和44个。10个性状中株高、分枝部位高度和单株产量的杂种优势与遗传距离的相关系数达到极显著正相关水平，该3个性状的中亲优势与遗传距离的相关系数分别为0.4200、0.5033和0.4711，超亲优势与遗传距离的相关系数分别为0.3884、0.4051和0.4038，而其他性状的杂种优势与遗传距离的相关性不显著。【结论】SNP标记在油菜基因型分型、遗传距离估算及聚类分析的研究中优势明显，基于全基因组SNP标记估算的遗传距离与油菜株高、分枝部位高度和单株产量的杂种优势相关性极显著，说明基于油菜60K SNP芯片分析亲本的遗传关系预测油菜杂种优势的效果显著。

关键词: 甘蓝型油菜, SNP标记, 遗传距离, 杂种优势预测

Abstract: 【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.

Key words: oilseed rape, SNP marker, genetic distance, heterosis prediction

桑世飞，王会，梅德圣，刘佳，付丽，王军，汪文祥，胡琼. 利用全基因组SNP芯片分析油菜遗传距离与杂种优势的关系[J]. 中国农业科学, 2015, 48(12): 2469-2478.

SANG Shi-fei, WANG Hui, MEI De-sheng, LIU Jia, FU Li, WANG Jun, WANG Wen-xiang, HU Qiong. Correlation Analysis Between Heterosis and Genetic Distance Evaluated by Genome-Wide SNP Chip in Brassica napus[J]. Scientia Agricultura Sinica, 2015, 48(12): 2469-2478.

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