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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (11): 2099-2110.doi: 10.3724/SP.J.1006.2021.04245

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide association study of seed density and its related traits in Brassica napus L.

LEI Wei1,2(), WANG Rui-Li1, WANG Liu-Yan1, YUAN Fang1,2, MENG Li-Jiao1,2, XING Ming-Li1,2, XU Lu1,2, TANG Zhang-Lin1,2, LI Jia-Na1,2, CUI Cui1,*(), ZHOU Qing-Yuan1,2,*()   

  1. 1College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    2Chongqing rape Engineering Technology Research Center, Chongqing 400715, China
  • Received:2020-10-17 Accepted:2021-03-19 Online:2021-11-12 Published:2021-04-01
  • Contact: CUI Cui,ZHOU Qing-Yuan E-mail:1305600171@qq.com;cuicui@swu.edu.cn;qingyuan@swu.edu.cn
  • Supported by:
    National Key Research and Development Program of China(2018YFD0100500);China Agriculture Research System(CARS-12);Chongqing Technology Innovation and Application Development Project(cstc2019jscx-msxmX0383)

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Abstract:

Seed density reflects the accumulation characteristics of crop photosynthetic products in the grains, which plays an important role in the thousand-seed weight of rape. Selecting high seed density germplasm resources and studying the genetic characteristics of seed density are very important in the breeding of rapeseed. A natural population containing 187 Brassica napus L. varieties (lines) with different genetic backgrounds was used as plant materials to determine the seed density and its related traits (thousand-seed weight and seed volume) in the two environments. Genome-wide association study was carried out based on the optimal model and the candidate genes associated with seed density, thousand-seed weight, and seed volume was predicted. In the two years, there were significant differences in the seed density and its related traits among 187 materials at P < 0.05, and three materials with high seed density or thousand-seed weight were selected. A total of 24 SNP loci, that were significantly associated with seed density, seed weight, and seed volume, were identified by GWAS, which explained the phenotypic variation of 8.21%-10.40%. Haplotype analysis was used to determine the block interval of the SNP sites. The blocks containing 11 SNPs covered 12 candidate genes, which mainly encoded transcription factors such as WOX8, HAIKU1, AP2/ERF transcription factors, Dof family-zinc finger superfamily, BZR1 transcription factors, enzymes such as BKI1, KAT2, CEL1, UBP15, DNA binding proteins, and hormone response proteins such as ARF2 and J3. These results provide the theoretical basis for the development of high seed density rape varieties and the functional research of subsequent genes.

Key words: Brassica napus L., seed density, thousand-seed weight, seed volume, genome-wide association study (GWAS)

Fig. 1

Frequency distribution of seed density, 1000-seed weight, and seed volume in two environments"

Table 1

Phenotypic statistics of seed density, thousand-seed weight, and seed volume in 187 Brassica napus L."

性状
Trait		 年份
Year		 最大值
Max.		 最小值
Min.		 均值
Average		 标准差
SD		 变异系数
CV (%)
籽粒容重Seed density (kg m-3) 2018-2019 969.05 527.31 859.96** 61.16 7.11
2019-2020 946.00 433.93 804.35** 99.47 12.37
体积Seed volume (×10-9 m3) 2018-2019 7.30 2.58 4.60** 0.89 19.38
2019-2020 11.97 1.28 3.52** 1.27 35.93
千粒重Thousand-seed weight (×10-3 kg) 2018-2019 5.75 1.73 3.95** 0.76 19.24
2019-2020 7.39 0.70 2.80** 0.89 31.79

Table 2

Phenotypic statistics of the thousand-seed weight and seed volume of 81 high test density in Brassica napus L."

性状
Trait		 年度
Year		 最大值
Max.		 最小值
Min.		 均值
Average		 标准差
SD		 变异系数
CV (%)
籽粒容重Seed density (kg m-3) 2018-2019 969.05 860.09 901.76** 26.41 2.93
2019-2020 946.00 806.90 875.16** 31.35 3.58
体积Seed volume (×10-9 m3) 2018-2019 6.36 2.69 4.51** 0.78 17.30
2019-2020 6.01 1.28 3.19** 0.87 27.26
千粒重Thousand-seed weight (×10-3 kg) 2018-2019 5.75 2.36 4.06** 0.69 16.87
2019-2020 5.01 1.16 2.78** 0.74 26.54

Table 3

Correlation analysis of three traits of rape seeds"

性状
Trait		 容重
Seed density		 体积
Seed volume		 千粒重
Thousand-seed weight
容重Seed density 1 -0.29** 0.1
体积Seed volume -0.03 1 0.90**
千粒重Thousand-seed weight 0.31** 0.93** 1

Fig. 2

Quantile-Quantile plot for six models of association analysis using the optimal model for seeds density and its component trait in two years A: seed density in 2018 and 2019; B: seed density in 2019 and 2020; C: thousand-seed weight in 2018 and 2019; D: thousand-seed weight in 2019 and 2020; E: seed volume in 2018 and 2019; F: seed volume in 2019 and 2020."

Fig. 3

Manhattan plot of seeds density and its component trait in two years A: seed density in 2018 and 2019; B: seed density in 2019 and 2020; C: thousand-seed weight in 2018 and 2019; D: thousand-seed weight in 2019 and 2020; E: seed volume in 2018 and 2019; F: seed volume in 2019 and 2020."

Table 4

Summary of significant SNPs for seed density, thousand-seed weight, and seed volume"

性状
Trait		 环境
Environment		 模型
Model		 位点
SNP		 染色体
Chr.		 位置
Position		 阈值
-log10(P)		 贡献率
R2 (%)		 基因型
Loci
容重
Seed density		 2018-2019 K+PCA Bn-A01-p6774837 A01 6194252 5.12 9.52 T/C
Bn-scaff_17067_1-p175366 C02 27613356 5.06 8.64 T/C
Bn-A03-p8112016 C03 9899295 4.64 8.43 A/G
Bn-scaff_16069_1-p1916253 C07 38327703 4.59 9.39 A/G
Bn-scaff_21269_1-p313587 C08 37159594 4.53 8.54 A/G
2019-2020 K+PCA Bn-scaff_16394_2-p777469 C03 50479817 5.58 10.36 T/C
Bn-scaff_16394_2-p510062 C03 50830988 4.95 9.20 T/C
体积
Seed volume		 2018-2019 K+PCA Bn-A10-p9973634 C09 40023501 4.41 8.22 A/C
2019-2020 K+PCA Bn-Scaffold000232-p58128 A07 826353 5.32 9.88 A/G
性状
Trait		 环境
Environment		 模型
Model		 位点
SNP		 染色体
Chr.		 位置
Position		 阈值
-log10(P)		 贡献率
R2 (%)		 基因型
Loci
Bn-A07-p3618045 A07 5593584 5.32 9.88 T/C
Bn-A10-p5210204 A10 4798717 4.43 8.25 T/G
Bn-A10-p12933288 A10 12981101 4.88 9.07 A/C
Bn-scaff_15838_5-p603655 C01 3432942 5.03 9.34 T/C
Bn-scaff_17731_1-p749457 C01 7033263 4.41 8.21 A/C
Bn-scaff_17731_1-p979512 C01 7260158 4.76 8.84 A/G
Bn-scaff_21186_1-p36313 C04 43747053 4.65 8.65 A/G
Bn-scaff_21566_1-p5088 C04 43859433 4.60 8.56 A/C
Bn-scaff_16770_1-p306276 C05 35633542 5.26 9.78 T/C
Bn-scaff_20270_1-p1211632 C05 41648492 5.04 9.37 T/C
Bn-scaff_18439_1-p633449 C06 12752920 5.22 9.70 T/C
Bn-scaff_15763_1-p595094 C06 20165181 4.65 8.64 T/G
Bn-A07-p16045526 C06 26606197 4.63 8.62 A/C
千粒重Thousand-seed weight 2018-2019 K —
2019-2020 K Bn-scaff_21186_1-p36313 C04 43747053 4.55 8.43 A/G
Bn-scaff_21566_1-p5088 C04 43859433 5.62 10.40 A/C

Fig. 4

Blocks including significant SNP markers and their candidate genes"

Table 5

Summary of candidate genes associated with seed density and related traits in Brassica napus L."

性状
Trait		 物理区间
Physical interval		 甘蓝型油菜基因编号
Gene ID in B. napus		 拟南芥基因
Arabidopsis gene		 基因
Gene		 参考文献
Reference
SD 26393356-28833356 BnaC02g28720D AT5G42750 BKI1 [35]
9439295-10359295 BnaC03g18470D AT2G33150 KAT2 [36]
BnaC03g18850D AT5G45980 WOX8 [37]
BnaC03g19320D AT2G35230 IKU1 [38]
BnaC03g19550D AT2G35700 ERF38 [39]
37927703-38727703 BnaC07g36540D AT4G21030 ATDOF4.2 [40-41]
TSW 43147053-44459433 BnaC04g43460D AT1G70710 CEL1 [42]
SV 2632942-4232942 BnaC01g06800D AT1G17110 UBP15 [43]
6233263-7833263 BnaC01g11380D AT1G75080 BZR1 [35]
43147053-44459433 BnaC04g43460D AT1G70710 CEL1 [42]
12082920-13422920 BnaC06g10480D AT1G54060 ASIL1 [44]
39083501-40963501 BnaC09g35740D AT3G61830 ARF2 [45]
BnaC09g36560D AT3G44110 J3 [46]
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