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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (6): 818-828.doi: 10.3724/SP.J.1006.2019.84133


Detection of stem height QTL and integration of the loci for plant height- related traits in B. napus

Li-Juan WEI1,2,*,Rui-Ying LIU1,2,*,Li ZHANG1,2,Zhi-You CHEN1,2,Hong YANG1,2,Qiang HUO1,2,Jia-Na LI1,2,*()   

  1. 1 College of Agronomy and Biotechnology, Southwest University / Chongqing Engineering Research Center for Rapeseed, Chongqing 400715, China
    2 Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
  • Received:2018-10-23 Accepted:2019-01-19 Online:2019-06-12 Published:2019-06-12
  • Contact: Li-Juan WEI,Rui-Ying LIU,Jia-Na LI E-mail:ljn1950@swu.edu.cn
  • Supported by:
    This study was supported by the China Postdoctoral Science Foundation Funded Project(2017M622945);National Postdoctoral Program for Innovative Talents(BX201700201);National Postdoctoral Program for Innovative Talents(Chongqing Graduate Student Research Innovation Project CYS17078);the National Basic Research Program of China(973 Program 40203917);National Natural Science Foundation of China (31701460).


Stem height (SH) is important for the plant architecture and yield in Brassica napus. To date, the research about stem height in B. napus is very less. In the study, QTL mapping of stem height in B. napus was performed using the high density SNP genetic map constructed from the recombinant inbred lines (RIL) population with Illumina 60K SNP array. Totally 11 QTLs were detected in two years on A04, A06, C04, A08, and C01, which explained 7.25%-19.61% of the phenotypic variation. In addition, genome-wide association analysis (GWAS) of stem height in the 455 B. napus genotyped by resequencing was performed, and five significantly associated SNP loci on A08, A10, C02, and C06 were identified. And the candidate genes involved in photomorphogenesis, plant growth and development, and hormone pathway such as auxin, gibberellin and brassinosteroid were identified. We also integrated the loci for plant height-related traits including plant height (PH), main inflorescence length (MIL), branch segment (BS) and branch initiation height (BIH) in B. napus, in which four loci for PH on A01, A03, A07, C03, and C06 were identified in at least four populations, one locus for MIL on A10 and two loci for BIH on A02 and C03 were identified in two populations. The loci for stem height in our study were consistent with pervious QTL mapping results for plant height, branch initiation height and main inflorescence length. This study lays a foundation for the breeding of plant architecture in B. napus.

Key words: Brassica napus, stem height, QTL mapping, GWAS, loci integration

Table 1

Phenotypic variation of stem height in RIL population and natural population"

Mean±SD (cm)
Range (cm)
CV (%)
父本ZY821 Male parent ZY821 2016 138.00±5.51
2017 131.90±12.30
母本GH06 Female parent GH06 2016 159.60±6.46
2017 145.60±8.77
重组自交系RIL 2016 150.64±11.49 119.00-174.25 7.63
2017 148.53±10.91 114.40-175.00 7.34
自然群体 Natural population 2016 156.58±17.11 93.86-200.10 10.93
2017 143.01±21.20 62.00-202.60 14.82

Fig. 1

Frequency distribution of stem height in RIL (a) and natural population (b)"

Table 2

Correlation coefficients of stem height with plant architecture and yield traits in B. napus"

重组自交系 RIL 自然群体 Natural population
2016SH 2017SH 2016SH 2017SH
主花序长度 Main infloresences length (cm) -0.403** -0.355** -0.089 -0.306**
株高 Plant height (cm) 0.738** 0.617** 0.865** 0.865**
结荚高度 Height of podding (cm) 0.638** 0.581** 0.745** 0.850**
结荚厚度 Thickness of pod canopy (cm) 0.089 0.024 0.185 0.101
一次有效分枝起点 Branch initiation height (cm) 0.610** 0.589** 0.621** 0.772**
经济产量 Yield (g) 0.341** 0.037 0.255** 0.286**

Table 3

QTL related to stem height in B. napus"

LOD score
SNP interval
Additive effect
R2 (%)
Physical position (bp)
q2016SH-A04-1 A04 3.72 SNP42542-SNP9367 6.21 13.70
q2016SH-A04-2 5.61 SNP9354-SNP9343 7.17 19.52 18264803-18455956
q2016SH-A04-3 2.90 SNP42544-SNP9263 5.61 10.78 17846583-18115323
q2016SH-A06-1 A06 4.33 SNP13035-SNP13048 -4.72 14.46 1469838-1480581
q2016SH-A06-2 5.50 SNP13263-SNP34194 -5.45 19.61 1860393-2106757
q2016SH-A06-3 4.56 SNP12979-SNP13009 -4.88 15.07 1360428-1442742
q2016SH-A06-4 2.83 SNP14849-SNP14835 3.65 8.88 6967630-7274382
q2016SH-C04 C04 3.29 SNP49157-SNP49146 3.85 9.97 7352388-7867004
q2017SH-A08 A08 3.94 SNP18566-SNP18577 2.95 7.25 18081289-18861275
q2017SH-C01-1 C01 6.11 SNP2398-SNP37156 3.80 11.86
q2017SH-C01-2 6.02 SNP37161-SNP38210 3.79 11.70 12068324-12309768

Fig. 2

Chromosomal locations of QTL for stem height in RIL population Grey boxes indicated the 99% confidence interval of the QTL; “T” on the boxes indicated the 95% confidence interval of the QTL."

Fig. 3

Population structure of 455 B. napus"

Fig. 4

Manhattan and quantile-quantile plot for stem height in 2016 and 2017"

Table 4

Markers with significant association for stem height"

-lg (P)
2016SH-1 2016 Naive S8_12459044 A08 12459044 5.90 15.90
2016SH-2 S10_16428321 A10 16428321 5.62 15.64
2017SH-1 2017 K+PCA S12_13075515 C02 13075515 7.62 10.08
2017SH-2 S12_13075493 C02 13075493 5.64 6.91
2017SH-3 S16_28288339 C06 28288339 5.70 6.86

Fig. 5

Integration of the loci for plant height-related traits in B. napus PH: plant height; MIL: main inflorescence length; BS: branch segment; BIH: branch initiation height; SH: stem height."

Table 5

Identification of candidate genes for stem height"

Physical position
Homologs in A. thaliana
Functional annotation
q2016SH-A04-2 BnaA04g25550D A04: 18331184-18331589 AT2G44080/ARL 调控细胞大小
Regulated cell expansion
q2016SH-A04-3 BnaA04g24760D A04: 18025141-18026983 AT2G43010/PIF4 编码转录因子bHLH, 参与生长素生物合成, 调控下胚轴伸长
Encoded the bHLH transcription factor, involving in the auxin biosynthesis and regulating hypocotyl elongation
BnaA04g24770D A04: 18030030-18033008 AT2G43020/PAO2 参与ABA介导的植物生长
Involved in plant development mediated by ABA
BnaA04g24970D A04: 18140559-18140805 AT2G43280/FAR1 调控光敏色素信号传导
Involved in phytochrome A signaling
BnaA04g24980D A04: 18141000-18144940 AT2G43280/FAR1 调控光敏色素信号传导
Involved in phytochrome A signaling
q2016SH-A06-2 BnaA06g03090D A06: 1869158-1871192 AT1G49770/RGE1 编码转录因子bHLH,影响植物生长发育
Encoded the bHLH transcription factor, regulating plant growth and development
q2016SH-A06-4 BnaA06g13320D A06: 6972730-6976892 AT1G19220/ARF19 参与生长素和乙烯信号传导过程
Involved in auxin and ethylene signaling
q2016SH-C04 BnaC04g10190D C04: 7847368-7848334 AT2G35150/EXL7 调控植物生长发育
Regulated plant growth and development
q2017SH-A08 BnaA08g28200D A08: 18580209-18583117 AT1G05180/AXR1 参与生长素抵抗反应
Involved in auxin resistance
q2017SH-C01-2 BnaC01g17440D C01: 12009590-12010572 AT4G25560/MYB18 调控光形态建成
Regulated photomorphogenesis in the light
2016SH-1 BnaA08g15400D A08: 12809202-12810946 AT4G36730/GBF1 调控光形态建成
Regulated photomorphogenesis in the light
2016SH-2 BnaA10g24860D A10: 16153991-16157850 AT5G05690/CPD 编码CP90A蛋白, 参与油菜素内酯生物合成
Encoded a member of the CP90A family, and involved in the brassinosteroid biosynthesis
2017SH-1 BnaC02g17570D C02: 13199941-13200513 AT5G13790/AGL15 MADS家族成员, 参与赤霉素代谢
Encoded a member of the MADS family, and involved in the gibberellin metabolic process
2017SH-2 BnaC06g27170D C06: 28615555-28619464 AT5G37020/ARF8 参与生长素稳态
Involved in auxin homeostasis
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