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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (01): 147-153.doi: 10.3724/SP.J.1006.2020.94060

• RESEARCH NOTES • Previous Articles    

Genome-wide association study of seed number per silique in rapeseed (Brassica napus L.)

SUN Cheng-Ming1,2,CHEN Feng1,CHEN Song1,PENG Qi1,ZHANG Wei1,YI Bin2,*(),ZHANG Jie-Fu1,*(),FU Ting-Dong2   

  1. 1 Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210014, Jiangsu, China
    2 National Key Laboratory of Crop Genetic Improvement/College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China;
  • Received:2019-04-15 Accepted:2019-08-09 Online:2020-01-12 Published:2019-09-11
  • Contact: Bin YI,Jie-Fu ZHANG E-mail:yibin@mail.hzau.edu.cn;jiefu_z@163.com
  • Supported by:
    The study was supported by the National Key Research and Development Program of China(2018YFD0100602);Earmarked Fund for China Agriculture Research System(CARS-12);Jiangsu Agriculture Science and Technology Innovation Fund(CX(19)3055-12);Natural Fund Project of Jiangsu Basic Research Program(BK20190260);Fundamental Research Funds for the Central Universities(2662016PY063)


Seed number per silique (SSN) is a key component of seed yield in rapeseed, increasing SSN can improve the seed yield of plants. A collection of 496 representative rapeseed accessions was genotyped by the Illumina 60K SNP array and phenotyped for SSN in two environments. The genome-wide association study (GWAS) of SSN was performed via the MLM (Mixed linear model) and GLM (General linear model). The broad-sense heritability of SSN was 57.7%. Nine and twenty loci were detected with MLM and GLM, respectively, and all loci detected by MLM were included those by GLM. Six loci were overlapped with reported QTLs, and two of them were validated by two independent researches, and the rest 14 loci were new. We identified plausible candidate genes nearby seven loci, and the reported rapeseed SSN gene BnaC9.SMG7b was found near the locus Bn-scaff_15576_1-p74980 on C09 chromosome detected in this study. Besides, six candidates orthologous to documented Arabidopsis SSN genes, like GRDP1, SPATULA, HVA22D, and DA2, were found near our GWAS loci. The results provide an insight into the genetic basis of seed number per silique and lay a foundation for further mechanism exploration and breeding for this trait in B. napus.

Key words: Brassica napus L., yield, seed number per silique, GWAS, SNP

Table 1

Statistical analysis of seed number per silique of the association panel"

Mean ± SD
2014/2015 Taizhou 8.83 27.73 21.45±2.36 0.11
2015/2016 Taizhou 11.00 26.24 20.56±1.99 0.10

Fig. 1

Distribution of seed number per silique of the association panel in two environments"

Table 2

Significant GWAS loci of seed number per silique in MLM"

-lg (P) 表型变异
R2 (%)
Reported QTL
Bn-A01-p3904495 A01 3,530,446 5.01 0.03832 16TZ [5]
Bn-A04-p10393460 A04 11,537,744 5.15 0.03946 15TZ
Bn-A07-p22251229 A07 23,650,401 4.78 0.03896 15TZ
Bn-A08-p14749618 A08 12,312,967 4.37 0.03265 15TZ [7]
Bn-scaff_15936_1-p270915 C01 36,405,870 4.66 0.03521 BLUP [5-6]
Bn-scaff_15712_6-p1336179 C02 38,045,422 4.33 0.04469 15TZ, 16TZ
Bn-scaff_23954_1-p220801 C03 11,576,750 4.49 0.03371 15TZ
Bn-scaff_16027_1-p367097 C04 1,254,637 4.52 0.03698 15TZ
Bn-scaff_23907_1-p3780 C04 7,268,977 5.09 0.04605 BLUP

Fig. 2

Genome-wide association study of rapeseed seed number per silique (MLM) A: Manhattan plot of MLM based on BLUP value; B: Manhattan plot of MLM in15TZ; C: Manhattan plot of MLM in 16TZ. The dashed horizontal line depicts the Bonferroni significance threshold."

Table 3

Significant GWAS loci of seed number per silique in GLM"

-lg (P) 表型变异
R2 (%)
Reported QTL
Bn-A01-p3904495 A01 3,530,446 5.05 0.0357 16TZ [5]
Bn-A04-p10393460 A04 11,537,744 5.79 0.0408 15TZ
Bn-A07-p9916502 A07 11,196,091 4.50 0.0404 BLUP
Bn-A07-p22251229 A07 23,650,401 4.41 0.0322 15TZ
Bn-A08-p14749618 A08 12,312,967 4.74 0.0327 15TZ [7]
Bn-scaff_15838_1-p1554155 C01 1,926,096 4.41 0.0437 16TZ [8]
Bn-scaff_15936_1-p270915 C01 36,405,870 5.13 0.0353 BLUP [5-6]
Bn-scaff_15712_6-p1336179 C02 38,045,422 4.66 0.0435 16TZ
Bn-scaff_23954_1-p635109 C03 11,205,203 4.78 0.0330 15TZ
Bn-scaff_16027_1-p367097 C04 1,254,637 4.62 0.0365 15TZ
Bn-scaff_23907_1-p3780 C04 7,268,977 5.59 0.0483 15TZ,BLUP
Bn-scaff_19253_1-p524524 C04 15,606,945 4.29 0.0290 BLUP
Bn-scaff_15936_1-p357665 C05 9,508,115 4.78 0.0453 BLUP
Bn-scaff_16064_1-p1144443 C06 24,511,029 4.74 0.0327 15TZ
Bn-scaff_17484_1-p132976 C07 5,857,563 4.60 0.0317 15TZ
Bn-scaff_20084_1-p104549 C07 9,638,283 5.36 0.0375 15TZ
Bn-scaff_16069_1-p1651456 C07 38,070,340 5.23 0.0365 15TZ
Bn-scaff_16069_1-p3780494 C07 40,184,749 4.35 0.0302 16TZ
Bn-scaff_15808_1-p420800 C09 37,129,614 5.15 0.0365 16TZ [5]
Bn-scaff_15576_1-p74980 C09 41,126,168 4.35 0.0303 16TZ [5,19]

Fig. 3

Genome-wide association study of rapeseed seed number per silique (GLM) A: Manhattan plot of GLM based on BLUP value; B: Manhattan plot of GLM in 15TZ; C: Manhattan plot of GLM in 16TZ. The dashed horizontal line depicts the Bonferroni significance threshold."

Table 4

Information of candidate genes of seed number per silique GWAS loci"

Rapeseed gene
Ar. homolog
Bn-A04-p10393460 BnaA04g13080 A04 11,015,882 GRDP1
Bn-A07-p9916502 BnaA07g13170 A07 11,744,966 GLE1
Bn-A08-p14749618 BnaA08g15580 A08 12,923,783 SPATULA
Bn-scaff_23954_1-p635109 BnaC03g21140 C03 11,367,292 DA2
Bn-scaff_16069_1-p3780494 BnaC07g39210 C07 40,210,953 HVA22D
Bn-scaff_15808_1-p420800 BnaC09g33680 C09 36,922,347 MSI1
Bn-scaff_15576_1-p74980 BnaC09g38310 C09 41,208,383 SMG7b
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