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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (10): 1517-1525.doi: 10.3724/SP.J.1006.2020.02008


QTL detection and stability analysis of rice grain shape and thousand-grain weight based on chromosome segment substitution lines

WANG Xiao-Lei1(), LI Wei-Xing1, ZENG Bo-Hong2, SUN Xiao-Tang1, OU-YANG Lin-Juan1, CHEN Xiao-Rong1, HE Hao-Hua1,*(), ZHU Chang-Lan1,*()   

  1. 1 Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education / Jiangxi Super Rice Engineering Technology Research Center, Nanchang 330045, Jiangxi, China
    2 Jiangxi Super Rice Research and Development Center of Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
  • Received:2020-02-13 Accepted:2020-06-02 Online:2020-10-12 Published:2020-06-23
  • Contact: Hao-Hua HE,Chang-Lan ZHU E-mail:wxl0vip@163.com;hhhua64@163.com;zhuchanglan@163.com
  • Supported by:
    National Natural Science Foundation of China(31860373);National Major Project for Developing New GM Crops(2016-ZX08001-002);“5511” Superior Science and Technology Innovation Team Project of Jiangxi Province, China(2016-5BCB19005)


Grain shape and 1000-grain weight are the important factors affecting rice yield. Discovering the excellent genes of these traits is of great significance for super high yield rice breeding. In this study, a set of chromosome segment substitute lines (CSSLs), derived from a cross between Koshihikari (a japonica cultivar, as donor patent) and Changhui 121 (an indica restorer line, as a background patent), were used to quantitative trait locus (QTLs) detection and stability analysis in three environments. The results showed that a total of 59 QTLs were identified on chromosomes 1, 2, 3, 4, 5, 6, 7, 10, 11, and 12, respectively, whose contribution rate was 0.77%-36.26%. Among them, 10 pleiotropic QTLs were found, and qGW2-1, qGW2-2, qGW3-1, qGW3-2, qGL3, and qGL12 could all be detected in three environments. Furthermore, qGW3-1 is a novel identified QTL locus. These results lay a foundation for further fine mapping, cloning and marker-assisted breeding of grain shape genes.

Key words: rice, chromosome segment substitution lines (CSSLs), grain shape, 1000-grain weight, quantitative trait locus (QTL)

Fig. 1

Location of QTL traits of rice grain shape and thousand grain weight on the chromosomes GL: grain length; GW: grain width; TGW: thousand grain weight."

Table 1

Traits of CSSLs and its parents Changhui 121 and Koshihikari"

亲本Parents 置换系群体CSSL
Changhui 121a
Mean ± SD
CV (%)
粒长GL (mm) E1 9.30±0.48** 7.30±1.56 8.58±0.22 7.60-10.10 0.03
E2 9.84±0.08** 7.40±0.14 9.18±0.34 7.80-9.80 0.04
E3 9.04±0.14** 7.09±0.60 8.91±0.34 7.60-9.82 0.04
粒宽GW (mm) E1 2.40±0.12* 3.30±0.56 2.73±0.13 2.20-3.20 0.05
E2 2.48±0.12* 3.20±0.00 2.58±0.17 2.40-3.26 0.07
E3 2.33±0.19** 3.24±0.60 2.48±0.16 2.22-3.30 0.06
千粒重TGW (g) E1 21.20±1.02** 18.78±0.32 22.36±0.34 16.50-26.80 0.02
E2 20.18±0.09** 18.66±0.36 22.51±1.53 16.90-26.62 0.07
E3 21.91±0.09** 18.89±0.60 21.32±1.46 16.90-26.40 0.07

Table 2

QTL of rice grain shape and thousand grain weight identified by 208 CSSLs"

Marker interval
LOD值LOD value 贡献率PVE (%) 加性效应Additive effect
E1 E2 E3 E1 E2 E3 E1 E2 E3
千粒重TGW (g) qTGW1 1 RM6292-RM5362 5.26 6.75 1.36
qTGW2-1 2 RM1358-RM5812 8.34 8.47 2.11
qTGW2-2 2 RM8030-RM1092 28.21 13.67 36.26 19.34 2.56 1.55
qTGW2-3 2 RM1092-RM208 8.52 8.67 -1.85
qTGW3-1 3 RM3646-RM3513 4.41 4.28 -1.17
qTGW3-2 3 RM3513-RM2334 3.68 3.61 7.07 4.55 1.02 0.80
qTGW4 4 RM6089-RM5503 7.73 4.31 7.80 8.35 -1.08 -0.95
qTGW5 5 RM3295-RM3476 3.01 5.37 2.88 6.91 1.23 1.58
qTGW6 6 RM5371-RM7641 5.96 5.89 -1.16
qTGW7 7 RM3186-RM3404 3.92 2.66 7.56 3.31 -0.76 -0.49
qTGW11 11 RM6894-RM5731 5.00 6.39 -0.60
GW (mm)
qGW1-1 1 RM312-RM5638 3.24 0.77 0.08
qGW1-2 1 RM5389-RM6696 9.70 2.49 -0.06
qGW2-1 2 RM1358-RM5812 46.92 3.23 27.80 18.99 1.26 11.21 0.31 0.10 0.29
qGW2-2 2 RM8030-RM1092 14.21 26.45 58.34 3.84 13.64 35.01 -0.10 -0.29 -0.30
qGW3-1 3 RM5748-RM6676 16.43 3.91 5.02 4.56 1.55 1.54 0.13 0.07 0.08
qGW3-2 3 RM3513-RM2334 19.31 9.43 9.82 5.54 3.98 3.19 0.11 0.11 0.10
qGW4-1 4 RM5412-RM3471 12.33 3.26 0.06
qGW4-2 4 RM6089-RM5503 30.53 4.03 10.04 1.59 -0.12 -0.06
qGW5-1 5 RM3295-RM3476 11.98 3.15 0.10
qGW5-2 5 RM7423-RM1054 12.36 3.27 -0.16
qGW6 6 RM8258-RM2615 10.64 4.93 2.75 1.97 0.09 0.09
qGW10 10 RM5271-RM2125 9.72 4.11 0.13
qGW11 11 RM6272-RM287 7.99 2.01 -0.08
qGW12 12 RM8216-RM6288 12.85 3.04 3.41 0.92 -0.09 -0.04
GL (mm)
qGL1-1 1 RM1220-RM259 7.90 7.36 0.19
qGL1-2 1 RM5389-RM6696 10.47 10.04 0.41
qGL2 2 RM1358-RM5812 5.39 4.88 -0.33
qGL3 3 RM3646-RM3513 12.86 16.33 18.19 12.68 18.82 23.05 -0.41 -0.48 -0.53
qGL5 5 RM7444-RM3328 14.75 12.09 14.87 13.61 -0.32 -0.30
qGL6 6 RM8258-RM2615 8.65 3.28 8.12 3.34 -0.30 -0.19
qGL7-1 7 RM5711-RM8263 5.10 4.60 -0.19
qGL7-2 7 RM3186-RM3404 3.85 3.84 -0.13
qGL10-1 10 RM5271-RM2125 4.94 4.46 4.44 4.49 -0.22 -0.22
qGL10-2 10 RM1375-RM6704 2.67 2.7 -0.17
qGL12 12 RM19-RM6296 6.04 5.38 4.85 5.51 5.47 5.02 -0.14 -0.13 -0.13

Table 3

Pleiotropic regional analysis in rice"

Marker interval
Pleiotropic QTL
Cloned gene
1 RM5389-RM6696 GW, GL qGL1-2, qGW1-2 _ _
2 RM1358-RM5812 TGW, GW, GL qTGW2-1, qGL2, qGW2-1 LG1/OsUBP15, GW2 Shi et al.[25]; Song et al.[8]
2 RM8030-RM1092 TGW, GW qTGW2-2, qGW2-2 _ _
3 RM3646-RM3513 TGW, GL qTGW3-1, qGL3 GS3 Fan et al.[11]
3 RM3513-RM2334 TGW, GW qTGW3-2, qGW3-2 _ _
4 RM6089-RM5503 TGW, GW qGW4-2, qTGW4 _ _
5 RM3295-RM3476 TGW, GW qTGW5, qGW5-1 gW5 Weng et al.[9]
6 RM8258-RM2615 GW, GL qGL6, qGW6 _ _
7 RM3186-RM3404 TGW, GL qTGW7, qGL7-2 BG2/CYP78A13 Xu et al.[26]
10 RM5271-RM2125 GW, GL qGW10, qGL10-1 _ _

Fig. 2

Differences of phenotypic values of rice grain shape traits between genetic background parent Changhui 121 and the CSSLs harboring the QTL alleles. NC and HN represent Nanchang and Hainan, respectively. ** means significant differences by Student’s t-test (P < 0.01) between rice grain shape traits of Changhui 121 and the CSSLs harboring the QTL alleles."

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