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

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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.

Abstract

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.

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Acknowledgments

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)).

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Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Sheng Liu, Chuchuan Fan, Guangqin Cai, Qingyong Yang, Jian Wu, Xinqi Yi, Chunyu Zhang & Yongming Zhou

  2. College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China

    Jiana Li

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  1. Sheng Liu
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Correspondence to Yongming Zhou.

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Communicated by I. Parkin.

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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)

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)

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)

Figure S4

Neighbor-joining phylogenetic tree based on Nei’s genetic distance (TIFF 5706 kb)

Figure S5

Distribution of pairwise relative kinship estimates between rapeseed accessions (TIFF 468 kb)

Figure S6

Linkage disequilibrium (LD) decay across the 19 chromosomes of B. napus (TIFF 1997 kb)

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)

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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Liu, S., Fan, C., Li, J. et al. A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus . Theor Appl Genet 129, 1203–1215 (2016). https://doi.org/10.1007/s00122-016-2697-z

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