Theoretical and Applied Genetics

, Volume 129, Issue 6, pp 1203–1215 | Cite as

A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus

  • Sheng Liu
  • Chuchuan Fan
  • Jiana Li
  • Guangqin Cai
  • Qingyong Yang
  • Jian Wu
  • Xinqi Yi
  • Chunyu Zhang
  • Yongming ZhouEmail author
Original Article


Key message

A set of additive loci for seed oil content were identified using association mapping and one of the novel loci on the chromosome A5 was validated by linkage mapping.


Increasing seed oil content is one of the most important goals in the breeding of oilseed crops including Brassica napus, yet the genetic basis for variations in this important trait remains unclear. By genome-wide association study of seed oil content using 521 B. napus accessions genotyped with the Brassica 60K SNP array, we identified 50 loci significantly associated with seed oil content using three statistical models, the general linear model, the mixed linear model and the Anderson–Darling test. Together, the identified loci could explain approximately 80 % of the total phenotypic variance, and 29 of these loci have not been reported previously. Furthermore, a novel locus on the chromosome A5 that could increase 1.5–1.7 % of seed oil content was validated in an independent bi-parental linkage population. Haplotype analysis showed that the favorable alleles for seed oil content exhibit cumulative effects. Our results thus provide valuable information for understanding the genetic control of seed oil content in B. napus and may facilitate marker-based breeding for a higher seed oil content in this important oil crop.


Quantitative Trait Locus Mixed Linear Model Double Haploid Double Haploid Line Favorable Allele 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The work was financially supported by the funding from the Ministry of Science and Technology of China (2015CB150200, 2014DFA32210), Ministry of Agriculture of China (nycytx-00503 and 948 project (2011-G23)).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The authors declare that this study complies with the current laws of the country in which the experiments were performed.

Supplementary material

122_2016_2697_MOESM1_ESM.tif (3 mb)
Figure S1 Clustering strategy improves genotyping efficiency. (a) Automatic SNP calling using GenomeStudio software. (b) Corrected SNP calling according to parent/F1 triads. P1, P2, and F1 indicate representative samples with parent/F1 relationships. The three highlighted clusters denote the areas where the three different genotypes, homozygous allele AA (red), heterozygous AB (purple) and homozygous allele BB (blue), are called. Allele calls that are ambiguously located in the lighter colored areas between these areas are scored as “no call” (black) (TIFF 3052 kb)
122_2016_2697_MOESM2_ESM.tif (1.5 mb)
Figure S2 Principal component analysis (PCA) of 521 rapeseed accessions based on (a) 31,090 SNPs without manual editing and (b) 4,595 SNPs recovered by manual editing. Each individual is represented by one dot and different color are corresponding to the population structure inferred by STRUCTURE (TIFF 1542 kb)
122_2016_2697_MOESM3_ESM.tif (4.2 mb)
Figure S3 Principal component analysis (PCA) of 521 rapeseed accessions based on 25,870 SNPs. The first two principal components are shown. Each individual is represented by one dot and the color label corresponding to their classification: (a) the population structure inferred by STRUCTURE, (b) different growth type and (c) different geographic distribution (TIFF 4290 kb)
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Figure S4 Neighbor-joining phylogenetic tree based on Nei’s genetic distance (TIFF 5706 kb)
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Figure S5 Distribution of pairwise relative kinship estimates between rapeseed accessions (TIFF 468 kb)
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Figure S6 Linkage disequilibrium (LD) decay across the 19 chromosomes of B. napus (TIFF 1997 kb)
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Figure S7 Comparison of seed oil content of three environments. The two environments are plotted against each other, with their Pearson’s coefficients indicated (TIFF 1129 kb)
122_2016_2697_MOESM8_ESM.tif (1.1 mb)
Figure S8 Box plots of seed oil content in the association panel grouped by population structure. The middle line indicates the median, the plus sign indicates the mean, the box indicates the range of the 25th to 75th percentiles of the total data, and the whiskers indicate the minimum and maximum values (TIFF 1138 kb)
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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Sheng Liu
    • 1
  • Chuchuan Fan
    • 1
  • Jiana Li
    • 2
  • Guangqin Cai
    • 1
  • Qingyong Yang
    • 1
  • Jian Wu
    • 1
  • Xinqi Yi
    • 1
  • Chunyu Zhang
    • 1
  • Yongming Zhou
    • 1
    Email author
  1. 1.National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
  2. 2.College of Agronomy and BiotechnologySouthwest UniversityChongqingChina

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