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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (9): 1311-1319.doi: 10.3724/SP.J.1006.2018.01311

• RESEARCH PAPERS • Previous Articles     Next Articles

Genome-wide Association Study on Seed Oil Content in Rapeseed and Construction of Integration System for Oil Content Loci

Da-Yong WEI1,2,3(),Yi-Xin CUI3,4,Jia-Qin MEI3,4,Qing-Lin TANG1,2,Jia-Na LI3,4,Wei QIAN3,4,*()   

  1. 1 College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
    2 Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing 400715, China
    3 College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    4 Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
  • Received:2018-01-30 Accepted:2018-06-09 Online:2018-09-10 Published:2018-09-12
  • Contact: Wei QIAN E-mail:swuwdy@swu.edu.cn;qianwei666@hotmail.com
  • Supported by:
    This study was supported by the Doctoral Fund of Southwest University(SWU118010);the National Natural Science Foundation of China(31601333);the National Basic Research Program of China(973 Program 2015CB150201);the Fundamental Research Funds for Central Universities(XDJK2017B036)


Genetic loci for oil content, one of the most important traits of rapeseed (Brassica napus L.), have been widely studied, however, comparisons were difficult to be carried out among studies due to different mapping populations and molecular marker systems. In the present study, a 60K Brassica SNP array was applied in the genome-wide association study (GWAS) using a natural rapeseed population which was comprised of 308 accessions and grown for four consecutive years to identify loci for seed oil content. An integration system was built by anchoring the present loci and previous loci that identified onto the rapeseed genome in other studies using ten segregation populations and two natural populations. A total of eight SNPs significantly associated with seed oil contents of rapeseed were detected in our study, explaining 3.22%-5.13% of the phenotypic variance each SNP. Combining the data from other 12 populations, 193 integrated loci were identified, spreading on all 19 chromosomes of B. napus with more loci distributed on A subgenome (13 loci/chromosome) than C subgenome (seven loci/chromosome). Seven integrated intervals from A subgenome (chromosome A01, A02, A03, A06, A08, A09, and A10) were identified in at least three populations, of which three were homologous to intervals on C subgenome, with 26 known genes associated with seed oil metabolism. The 193 loci were anchored to the reference genome of B. napus var. Darmor-Bzh, resulting in a visualized genome-wide integrated system for seed oil content loci. This study is helpful to determine the important seed oil content loci and to make the optimal breeding strategy to increase oil content in rapeseed.

Key words: Brassica napus, seed oil content, genome-wide association study, QTL, integrated system

Table 1

Phenotypic variation of seed oil contents in a natural population with 308 accessions"

年份 Year 范围 Range (%) 平均值±标准偏差 Mean±SD (%) 变异系数CV (%)
2013 24.50-48.46 37.01±3.79 10.24
2014 27.47-47.35 36.82±3.45 9.37
2015 25.27-44.43 34.99±3.07 8.79
2016 25.21-49.91 38.54±3.88 10.06

Fig. 1

Frequency distribution of seed oil content"

Table 2

Results of GWAS and predicted candidate genes"

Position (bp)
R2 (%)
Candidate gene
Arabidopsis homologue
Gene annotation
A02 20818388 3.22 3.85E-05 BnaA02g28280D AT3G26790 B3类转录因子
B3 transcription factor
A03 6727279 4.56 3.18E-05 BnaA03g14670D AT2G31690 三酰甘油酯的降解
Involved in the degradation of triacylglycerol
A05 15959252 3.51 3.45E-05
A05 18730739 4.29 2.44E-05 BnaA05g25260D AT3G14205 磷酸肌醇磷酸酯酶家族蛋白
Phosphoinositide phosphatase family protein
A05 19407850 3.26 7.52E-06 BnaA05g26510D AT3G12680 C3H类转录因子
C3H transcription factor
A05 19483554 5.13 6.52E-06 BnaA05g26900D AT3G12120 bZIP类转录因子
bZIP transcription factor
C02 45446662 3.71 2.46E-05
C02 45458214 4.22 1.65E-05 BnaC02g43130D AT5G64440 肪酸酰胺水解酶
Fatty acid amide hydrolase

Fig. 2

GWAS of seed oil contenta: Manhattan plot of seed oil content, the horizontal dashed black line represents the significant threshold (1/23490, -lg P = 4.37); b: Q-Q plot of estimated threshold."


Fig. 3

Genome-wide level display of the sites of seed oil content in different rapeseed populations (a) chromosome number; (b) heat map of all genes in reference genome (window size is 500 kb); (c) 1663 known oil metabolic genes; (1) DY-DH population; (2) RNSL-DH population; (3) GP-RIL population; (4) RC-F2 population; (5) SG-DH population; (6) Z5-DH population; (7) KN-DH population; (8) TN-DH population; (9) PT-DH population; (10) 521 natural population 1; (11) 521 natural population 2; (12) 521 natural population 3; (13) ES-DH population; (14) 142 natural population 4; (15) 308 natural population 5. Lines in the middle indicate the homology of integrated loci between the A and the C subgenomes."

Table 4

Distribution of stable sites of seed oil content and the known genes related to oil metabolism"

Region (Mb)
Known genes related to oil metabolism1)
A01 3, 4, 5, 8 7.23-7.49 BnaA01g14400D, BnaA01g14480D
A02 6, 8, 11 8.09-10.25 BnaA02g14460D, BnaA02g15090D, BnaA02g15290D, BnaA02g15690D, BnaA02g15770D, BnaA02g16020D, BnaA02g16070D, BnaA02g16200D, BnaA02g16260D, BnaA02g16470D, BnaA02g16520D, BnaA02g16570D, BnaA02g17050D
A03 1, 2, 8, 9 16.53-17.65 BnaA03g34340D, BnaA03g34830D, BnaA03g34980D, BnaA03g35170D,
A06 1, 10, 14 21.5-21.7 BnaA06g32660D
A08 2, 3, 4, 7, 8 10.85-12.17 BnaA08g12720D, BnaA08g12780D, BnaA08g12850D, BnaA08g13370D, BnaA08g13410D, BnaA08g13530D, BnaA08g13870D, BnaA08g14190D
A09 8, 10, 11, 12, 13 30.49-31.23 BnaA09g44630D, BnaA09g44650D, BnaA09g44980D, BnaA09g45010D, BnaA09g45250D, BnaA09g45720D
A10 10, 11, 12, 13, 14 14.35-16.06 BnaA10g20920D, BnaA10g21350D, BnaA10g21780D, BnaA10g22070D, BnaA10g23290D, BnaA10g23670D, BnaA10g23790D, BnaA10g23950D, BnaA10g24440D, BnaA10g24560D
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