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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (9): 1320-1333.doi: 10.3724/SP.J.1006.2018.01320

• RESEARCH PAPERS • Previous Articles     Next Articles

QTL Mapping for Yield, Growth Period and Plant Height Traits Using MAGIC Population in Upland Cotton

Cong HUANG1(),Xiao-Fang LI2,Ding-Guo LI2,*(),Zhong-Xu LIN1,*()   

  1. 1 National Key Laboratory of Crop Genetic Improvement / College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
    2 Institute of Crop Genetic and Breeding, Yangtze University, Jingzhou 434025, Hubei, China
  • Received:2018-02-08 Accepted:2018-06-12 Online:2018-09-10 Published:2018-07-02
  • Contact: Ding-Guo LI,Zhong-Xu LIN E-mail:huangcong@webmail.hzau.edu.cn;361113214@qq.com;linzhongxu@mail.hzau.edu.cn
  • Supported by:
    This study was supported by the National Natural Science Foundation of China (31371674)


The yield, growth period and plant height are important agronomic traits that decide the economic value and planting pattern of cotton (Gossypium spp.). In order to dissect the genetic basic of these traits, an 8-way upland cotton MAGIC (multi-parent advanced generation inter-cross) population and SSR markers were used for association mapping. Eight traits of this MAGIC population were phenotyped in five environments (three years and three locations), showing wider variations than these of the founder parents. The broad-sense heritability (H 2) of the eight traits ranged from 0.17 to 0.71. Association analysis based on mix linear model was performed using 284 polymorphic SSR markers. There were 51, 27, and 9 markers significantly associated with yield, growth period and plant height traits respectively. All identified loci had minor effect for controlling the phenotypic variations, showing a higher powerful ability of the MAGIC population in association mapping. Furthermore, 20 loci were found to be associated with multiple traits acting as pleiotropism. In addition, chromosome hot spots were found for effective boll number, lint weight, first fruit spur branch number and plant height, which provided references for deeply genetically studying these loci. The elite MAGIC lines and the valuable SSR loci lay a foundation for the genetic improvement of upland cotton.

Key words: upland cotton, MAGIC population, yield, growth period, plant height, SSR, association mapping

Table 1

Eight parents for upland cotton MAGIC population"

Parent code
Cross code
Agronomic trait
Material sources
PM1 A GY5 鄂棉15选系
Emian 15 inbred lines
优质, 高产
High yield and fibre quality
College of Agriculturel, Yangtze
PM2 B KB10 鄂抗棉10号
Ekangmian 10
Fusarium wilt-resistant and Verticillium wilt-tolerance
Cotton Research Institute of Chinese Academy of Agricultural Sciences
PM3 C GY2 苏棉16
Sumian 16
High yield and fibre quality
Taicang City Cotton Seed Farm in
Jiangsu province
PM4 D KC9 DP410B 抗虫
Hubei Province Seed Management Station
PM5 E CQ13 GK-12 抗虫
Cotton Research Institute of Chinese Academy of Agricultural Sciences
PM6 F GY6 鄂棉15
Emian 15
High yield and fibre quality
College of Agriculture, Yangtze
PM7 G CQ2 KC160 抗虫
Hubei Province Seed Management Station
PM8 H GY4 鄂荆1号选系
Ejing 1 inbred lines
High yield and fibre quality
College of Agriculture, Yangtze

Table 2

ANOVA (analysis of variance) results of the eight traits"

平方和 Sum of squares 均方 Mean of square P值显著性 Significance by P-value
开花期FT 28792 276730 9815 30 138365 7 ***
第一果枝节位FFSBN 27900 19 11088 29.12 18.92 15.73
株高PH 212681 770794 100555 222 770794 145 ***
单株有效铃数EBN 44434 78050 68598 46 39025 37 * ***
单铃籽棉重BW 672.5 1949.1 460.3 0.7 974.6 0.3 *** *** ***
单铃皮棉重LW 129.5 435.3 108.8 0.13 217.67 0.06 *** *** ***
衣分LP 14719 3611 10178 15.3 1805.4 5.7 *** *** *
籽指SI 1679.2 321.9 502.3 1.7 321.9 0.6 *** ***

Table 3

Statistics description of phenotypic variations after BLUP"

CV (%)
开花期FT (d) 76.52 77.93 74.41-78.39 76.71-80.44 0.55 0.70 0.93 1.35 0.87 0.46
第一果枝节位FFSBN 6.03 5.59 5.68-6.32 5.44-5.76 0.06 1.07 0.35 -0.37 0.45 0.20
株高PH (cm) 102.04 104.36 98.22-103.61 98.44-108.96 1.32 1.26 -0.23 0.88 0.59 0.29
单株有效铃数EBN 27.75 24.77 25.16-29.41 23.71-26.29 0.39 1.56 0.37 0.44 0.57 0.17
单铃籽棉重BW (g) 5.04 5.46 4.84-5.36 4.73-6.34 0.21 3.88 -0.02 0.23 0.66 0.64
单铃皮棉重LW (g) 2.17 2.23 2.15-2.20 1.90-2.50 0.08 3.48 -0.21 0.59 0.22 0.54
衣分LP (%) 43.14 40.74 42.34-43.87 35.31-44.49 1.04 2.54 -0.55 2.00 0.56 0.60
籽指SI (g) 10.87 10.63 10.60-11.35 9.23-12.07 0.48 4.48 0.18 0.01 0.62 0.71

Fig. 1

Phenotype histograms of eight traits after BLUP A: flowering time (FT); B: first fruit spur branch number (FFSBN); C: plant height (PH); D: effective boll number (EBN); E: boll weight (BW); F: lint weight (LW); G: lint percentage (LP); H, seed index (SI)."

Fig. 2

Pearson’s correlation coefficients among eight traits* and ** indicate the significant correlation at P < 0.05 and P < 0.01, respectively. FT: flowering time; FFSBN: first fruit spur branch number; PH: plant height; EBN: effective boll number; BW: boll weight; LW: lint weight; LP: lint percentage; SI: seed index."

Fig. 3

Comparison between GLM and MLM by Quantile-quantile (Q-Q) plots in association mappingA: flowering time; B: first fruit spur branch number; C: plant height; D: effective boll number; E: boll weight; F: lint weight; G: lint percentage; H: seed index."

Table 4

Significant SSR markers associated with the eight traits"

SSR marker
Position (cM)
R2 (%)
开花期 NBRI_HQ527566 1 150.22 4.24E-03 (*, #) 1.45 BLUP
FT MON_CGR5525 6 49.08 3.91E-03 (*, #) 1.20 BLUP
MON_DC20094 8 101.49 1.33E-03 (**) 1.12 BLUP
MON_CER0167 10 101.22 9.83E-03 (*, #) 0.81 BLUP
MON_CGR5113 11 10.25 1.38E-03 (**, #) 5.44 BLUP
MON_CGR5390 13 55.20 7.07E-03 (*, #) 1.10 BLUP
MON_DPL0522 21 16.34 1.35E-03 (**, #) 1.52 BLUP
MON_DC30015 23 85.25 1.04E-05 (**, #) 7.23 BLUP
DPL0461 24 63.21 6.98E-03 (*, #) 0.78 BLUP, E5
MON_SHIN0607 26 137.12 2.09E-03 (**, #) 1.52 BLUP
第一果枝节位 NBRI_HQ527566 1 150.22 5.85E-03 (*) 1.28 BLUP
FFSBN MON_CGR5534 2 17.30 5.68E-03 (*, #) 1.24 BLUP
SSR marker
Position (cM)
R2 (%)
NAU2858 2 133.14 1.64E-03 (**, #) 2.03 BLUP
MON_CER0086b 6 106.70 5.23E-05 (**, #) 2.48 BLUP
MON_CGR5001b 7 22.05 8.69E-03 (*, #) 0.73 BLUP
MON_DC20094 8 101.49 6.08E-03 (*, #) 0.80 BLUP, E2
BNL3442 11 31.48 6.41E-03 (*, #) 0.79 BLUP
HAU2489 15 44.81 5.03E-03 (*) 0.84 BLUP
MUSS422b 15 115.63 2.58E-08 (**, #) 3.33 BLUP
MON_CGR5001a 16 39.66 1.26E-03 (**, #) 1.10 BLUP
HAU3069 19 206.66 3.92E-03 (*, #) 1.18 BLUP, E3
NAU7153 21 59.03 9.20E-05 (**, #) 1.97 BLUP
BNL3171 21 72.70 4.07E-03 (*) 1.89 BLUP
MON_DC30015 23 85.25 8.21E-08 (**, #) 7.27 BLUP
MON_CGR5423 24 10.95 2.18E-03 (**, #) 1.43 BLUP
HAU3812 24 43.09 5.18E-03 (*, #) 1.12 BLUP
MON_CER0086a 25 86.68 1.69E-03 (**, #) 1.49 BLUP
株高 miR393-Me4 8 67.26 9.45E-03 (*) 0.71 BLUP
PH MON_CGR5113 11 10.25 8.72E-03 (*, #) 4.02 BLUP
MON_CGR6580a 11 78.45 7.93E-03 (*, #) 1.21 BLUP
MON_SHIN1343 17 40.41 6.26E-03 (*, #) 1.11 BLUP
HAU3069 19 206.66 7.38E-03 (*, #) 1.04 BLUP, E3
MON_DPL0522 21 16.34 1.61E-03 (**, #) 1.40 BLUP
DPL0461 24 63.21 7.63E-05 (**, #) 1.66 BLUP
MON_DC20035 24 198.85 1.49E-03 (**, #) 1.36 BLUP
MON_DPL0811a 25 113.14 6.02E-03 (*, #) 0.79 BLUP
单株有效铃数 MON_DC40052 1 51.96 5.92E-03 (*, #) 1.69 BLUP
EBN NBRI_HQ527566 1 150.22 2.93E-03 (**) 1.52 BLUP
CIR381 2 38.87 3.97E-04 (**, #) 1.68 BLUP
CCRI523 5 39.95 9.49E-03 (*) 0.72 BLUP
BNL584 6 17.52 7.51E-03 (*, #) 1.26 BLUP
MON_CER0086b 6 106.70 1.34E-03 (**, #) 1.61 BLUP
HAU2147 10 4.91 4.40E-03 (*) 0.87 BLUP
BNL511 10 59.83 9.83E-03 (*, #) 0.71 BLUP
HAU3909 10 63.97 6.86E-06 (**, #) 2.63 BLUP
MON_CGR5352b 13 22.19 9.17E-04 (**, #) 1.85 BLUP
MON_CGR5390 13 55.20 2.17E-03 (**, #) 1.36 BLUP
MON_DC30178 13 90.51 6.32E-03 (*) 0.80 BLUP
MON_DPL0535 13 97.44 2.52E-03 (**, #) 2.01 BLUP
MON_CER0157 13 148.92 1.41E-03 (**, #) 1.09 BLUP
MON_CGR5001a 16 39.66 7.63E-03 (*) 0.76 BLUP
HAU0197 17 61.97 5.67E-04 (**, #) 2.04 BLUP
BNL3875 19 125.78 3.76E-03 (*, #) 1.45 BLUP
MON_CGR5845 19 177.05 1.72E-05 (**, #) 4.55 BLUP
NAU7153 21 59.03 6.31E-05 (**, #) 2.05 BLUP
SSR marker
Position (cM)
R2 (%)
HAU2959 21 107.97 3.53E-03 (*, #) 0.89 BLUP
MUSS298 23 29.08 3.94E-03 (*, #) 0.86 BLUP, E5
MON_DPL0524 23 31.92 4.30E-03 (*) 1.44 BLUP, E3
MON_DC30015 23 85.25 6.46E-07 (**, #) 6.19 BLUP
HAU4497 24 185.64 5.50E-05 (**, #) 2.05 BLUP
MON_DC40117 26 62.97 6.25E-03 (*, #) 1.05 BLUP, E2
单铃籽棉重 HAU1619a 1 168.64 3.66E-03 (*) 0.92 BLUP
BW CIR381 2 38.87 9.59E-04 (**, #) 1.48 BLUP
HAU0800a 2 142.99 9.39E-03 (*) 0.73 BLUP
MON_CER0086b 6 106.70 1.74E-03 (**, #) 1.74 BLUP
MUSB0812 8 107.81 7.25E-03 (*, #) 1.42 BLUP
HAU0119 17 0.00 4.71E-03 (*, #) 1.75 BLUP
HAU3986 17 100.50 3.67E-03 (*, #) 1.68 BLUP
MUSB1135a 18 140.00 5.50E-05 (**, #) 1.73 BLUP
MON_CGR5845 19 177.05 2.16E-03 (**) 3.63 BLUP
MON_DC40103 20 60.87 3.84E-03 (*, #) 1.17 BLUP
单铃皮棉重 HAU2959 21 107.97 3.16E-03 (**, #) 0.91 BLUP
LW NAU5418 21 108.18 8.76E-04 (**, #) 1.63 BLUP
HAU3640 24 175.90 6.59E-03 (*, #) 1.09 BLUP
HAU0800a 2 142.99 6.07E-03 (*) 0.79 BLUP
BNL3034 14 66.47 5.81E-03 (*, #) 1.67 BLUP
MUSB1135a 18 140.00 2.51E-03 (**, #) 0.95 BLUP
HAU3640 24 175.90 1.62E-03 (**, #) 1.37 BLUP
MON_DPL0811a 25 113.14 1.75E-03 (**, #) 1.02 BLUP
衣分 MON_CGR5707 9 61.36 2.37E-03 (**, #) 1.32 BLUP
LP MON_DPL0095b 17 78.11 3.67E-03 (*, #) 1.34 BLUP
MON_DC30015 23 85.25 8.92E-03 (*, #) 3.60 BLUP
籽指 CIR381 02 38.87 5.35E-06 (**, #) 2.60 BLUP
SI HAU1321 12 29.33 7.26E-03 (*) 2.12 BLUP
MON_SHIN1558 13 54.09 9.94E-03 (*) 0.71 BLUP
MON_C2-0118 14 135.20 7.01E-03 (*, #) 0.78 BLUP
NAU6468 16 28.49 8.77E-04 (**, #) 2.51 BLUP

Fig. 4

Distribution of the loci identified by association analysis on the published genetic mapThe identified markers significantly associated with traits are indicated by red and underlined font. * and ** indicate the significant association at P < 0.05 and P < 0.00352, respectively. FT: flowering time; FFSBN: first fruit spur branch number; PH: plant height; EBN: effective boll number; BW: boll weight; LW: lint weight; LP: lint percentage; SI: seed index."

Table 5

The markers associated with multi-traits"

Multi-effect SSR marker
Position (cM)
NBRI_HQ527566 1 150.22 单株有效铃数, 第一果枝节位, 开花期 EBN, FFSBN, FT
CIR381 2 38.87 单铃籽棉重, 单株有效铃数, 籽指 BW, EBN, SI
HAU0800a 2 142.99 单铃籽棉重, 单铃皮棉重 BW, LW
MON_CER0086b 6 106.70 单铃籽棉重, 单株有效铃数, 第一果枝节位 BW, EBN, FFSBN
MON_DC20094 8 101.49 第一果枝节位, 开花期 FFSBN, FT
MON_CGR5113 11 10.25 开花期, 株高 FT, PH
MON_CGR5390 13 55.20 单株有效铃数, 开花期 EBN, FT
MON_CGR5001a 16 39.66 单株有效铃数, 第一果枝节位 EBN, FFSBN
MUSB1135a 18 140.00 单铃籽棉重, 单铃皮棉重 BW, LW
MON_CGR5845 19 177.05 单铃籽棉重, 单株有效铃数 BW, EBN
HAU3069 19 206.66 第一果枝节位, 株高 FFSBN, PH
MON_DPL0522 21 16.34 开花期, 株高 FT, PH
NAU7153 21 59.03 单株有效铃数, 第一果枝节位 EBN, FFSBN
HAU2959 21 107.97 单铃籽棉重, 单株有效铃数 BW, EBN
MON_DC30015 23 85.25 单株有效铃数, 第一果枝节位, 开花期, 衣分 EBN, FFSBN, FT, LP
DPL0461 24 63.21 开花期, 株高 FT, PH
HAU3640 24 175.90 单铃籽棉重, 单铃皮棉重 BW, LW
MON_DPL0811a 25 113.14 单铃皮棉重, 株高 LW, PH
MON_CGR5390 13 55.20 单株有效铃数, 开花期 EBN, FT
HAU2959 21 107.97 单铃籽棉重, 单株有效铃数 BW, EBN

Table 6

Comparison of the loci in this study with these in previously reported studies"

SSR marker
Associated traits in this study
Identified traits in reported studies
BNL3034 单铃皮棉重LW 籽壳比重, 籽指, 纤维舒适度, 纤维2.5%跨距长度, 株高 HP, SI, WF, SL2.5, PH
BNL3171 第一果枝节位FFSBN 纤维50%跨距长度, 纤维2.5%跨距长度, 纤维长度, 纤维强度 SL50, SL2.5, FL, FS
BNL3442 第一果枝节位FFSBN 纤维50%跨距长度, 纤维2.5%跨距长度, 纤维长度 SL50, SL2.5, FL
单株籽棉产量, 单株有效铃数 SY, EBN
BNL3875 单株有效铃数EBN 纤维长度, 纤维强度, 纤维伸长率, 纤维整齐度FL, FU, FE, FS
BNL584 单株有效铃数EBN 衣指, 马克隆值LI, MV
单铃籽棉重, 单株有效铃数,
籽指 LW, EBN, SI
纤维周长, 纤维舒适度, 纤维2.5%跨距长度, 纤维强度 PER, WF, SL2.5, FS
HAU0119 单铃籽棉重BW 纤维强度, 耐盐性 FS, ST
HAU1321 籽指SI 单株铃数, 棉籽含油量 EBN, OC
HAU1619a 单铃籽棉重BW 马克隆值 MV
HAU2147 单株有效铃数BW 籽指, 纤维长度 SI, FL
HAU2489 第一果枝节位FFSBN 纤维伸长率, 纤维整齐度 FE, FU
SSR marker
Associated traits in this study
Identified traits in reported studies
第一果枝节位, 株高
单铃籽棉重, 籽指, 根系面积 BW, SI, RSA
MON_CGR5001a 单株有效铃数EBN 棉籽含油量, 棉籽蛋白含量 OC, PC
MON_CGR5423 第一果枝节位FFSBN 主根长 RL
MON_CGR5525 开花期FT 果枝长度 FBL
MON_CGR5534 第一果枝节位FFSBN 衣分, 株高, 果枝数, 籽指, 第一果枝长度 LP, PH, FSBN, SI, BFBL
MON_CGR5707 衣分LP 单铃种子数, 衣分 BSN, LP

单株有效铃数, 第一果枝节位,
开花期, 衣分
籽指 SI

MON_DC30178 单株有效铃数EBN 籽指 SI
MON_DC40052 单株有效铃数EBN 棉籽棕榈酸含量 PAC
MON_DC40117 单株有效铃数EBN 腺体 Gl
MON_DPL0095b 衣分LP 衣分, 籽棉产量, 籽指 LP, SY, SI
MON_DPL0522 开花期, 株高FT, PH 第一果枝节位 FFSBN
MON_DPL0524 单株有效铃数EBN 开花期, 果枝始节高 FT, FFSH
MON_DPL0535 单株有效铃数EBN 根系面积, 根系体积 RSA, RV
MUSB0812 单铃籽棉重EBN 枯萎病抗性 FW
MUSS298 单株有效铃数EBN 棉仁蛋白含量, 纤维马克隆值, 纤维强度 EPP, MV, FS
MUSS422b 第一果枝节位FFSBN 株高, 果枝数, 秋桃数, 纤维长度, 纤维强度 PH, FSBN, AB, FL, FS
NAU5418 单铃籽棉重EBN 棉籽含油量 OC
NAU6468 籽指SI 果枝数, 纤维长度 FSBN, FL
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