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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (8): 1472-1480.doi: 10.3724/SP.J.1006.2021.02056


Mapping and identification QTLs controlling grain size in rice (Oryza sativa L.) by using single segment substitution lines derived from IAPAR9

ZHANG Bo(), PEI Rui-Qing, YANG Wei-Feng, ZHU Hai-Tao, LIU Gui-Fu, ZHANG Gui-Quan, WANG Shao-Kui*()   

  1. Guangdong Provincial Key Laboratory of Plant Molecular Breeding/State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/South China Agricultural University, Guangzhou 510642, Guangdong, China
  • Received:2020-08-17 Accepted:2021-01-13 Online:2021-08-12 Published:2021-02-25
  • Contact: WANG Shao-Kui E-mail:zhangboscau@163.com;shaokuiwang@scau.edu.cn
  • Supported by:
    National Key Research and Development Program of China(2016YFD0100406);Key Projects of Basic Research and Applied Basic Research of Guangdong Province(2019B030302006);Special Support Program of Guangdong Province for High-level Talents(2016TX03N224)


Rice grain size is a complex quantitative trait controlled by multiple genes. Grain size is an important factor affecting rice yield and quality. The mapping and genetic analysis of genes controlling rice grain size are essential for the concurrent improvement of rice yield and quality. Here 13 QTLs for grain size were detected using 153 rice single-segment substitution lines in rice, which were derived from HJX74 as the receptor parent, and IAPAR9 as the donor parent. One-way ANOVA and Duncan’s multiple comparison were employed to detect the genetic bases of rice grain size in two consecutive years. Based on the substitution mapping using overlapped substitution-fragment in the SSSLs, a total of 13 grain size-related QTLs were detected on chromosomes 1, 2, 4, 5, 6, 7, 9, and 11, including nine QTLs controlling grain length, one QTL controlling grain width, and three QTLs controlling 1000-grain weight. Furthermore, qGL1-2, qTGW1-2, and qGL11 were novel identified QTLs. This study provided new basis for cloning and functional analysis of genes regulating grain size.

Key words: rice, single segment substitution line, grain size, QTL mapping

Fig. 1

Grain size of IAPAR9 and HJX74 a, b: the grain shape of HJX74 and IAPAR9, Bar: 5 mm; c: the grain length of HJX74 and IAPAR9; d: the grain width of HJX74 and IAPAR9; e: the grain weight of HJX74 and IAPAR9. ** means significant difference in grain length, grain width and grain weight between HJX74 and IAPAR9 by Student’s t-test (P < 0.01)."

Table S1

Primers and the sequence of the primers"

Sequence (5′-3′)
Sequence (5′-3′)

Fig. 2

DNA marker polymorphism of grain size between HJX74 and IAPAR9 The white lines indicate the target bands obtained by PCR, and the other bands are non-specific amplifications."

Fig. 3

Coverage of substitution fragments on rice chromosomes The genetic distance (cM) is shown as rulers on the left margin. Filled and open bars represent chromosomal segments homozygous for IAPAR9 and HJX74 alleles, respectively. The cloned genes are shown in blue font."

Table S2

The distribution of the substitution segment in the SSSLs"

No. of SSSLs
TL (cM)
CL (cM)
CP (%)
Chr. 1 30 571.00 19.03 59.16
Chr. 2 22 526.00 23.91 78.31
Chr. 3 4 112.40 28.10 35.21
Chr. 4 14 380.70 27.19 43.90
Chr. 5 12 179.30 14.94 53.98
Chr. 6 24 541.40 22.56 73.55
Chr. 7 7 75.20 10.74 19.27
Chr. 8 8 181.40 22.68 66.91
Chr. 9 9 256.70 28.52 85.03
Chr. 10 6 160.60 26.77 55.93
Chr. 11 16 320.60 20.04 60.04
Chr. 12 1 6.90 6.90 3.15
平均Mean 12.75 276.02 20.95 52.87

Fig. 4

Frequency distribution of grain length, width and 1000-grain weight in SSSLs and the parents in two seasons a-c: the frequency distribution of grain length, width, and 1000-grain weight in SSSLs and the parents in later season of 2018; d-f: the frequency distribution of grain length, width, and 1000-grain weight in SSSLs and the parents in early season of 2019."

Fig. 5

Chromosome location of 13 QTLs for grain shape and 1000-grain weight in rice The genetic distance is shown as rulers on the left margin. Black bars on the right of each chromosome are the location intervals of QTLs for grain size with their names on the right."

Table 1

Detection of the QTLs and additive effects for grain size in the SSSLs"

Marker interval
加性效应Additive effect PP-value
2018 2019 2018 2019
粒长Grain length qGL1-1 1 PSM13-RM84 -0.19 -0.11 0.0025 0.0188
qGL1-2 1 OSR23-RM104 0.30 0.31 0.0001 0.0005
qGL2 2 RM250-RM166 -0.19 -0.15 <0.0001 0.0029
qGL4 4 RM317-PSM110 -0.23 -0.15 0.0002 0.0081
qGL5 5 RM164-RM161 -0.19 -0.12 0.0002 0.0289
qGL6 6 PSM136-RM275 -0.22 -0.15 <0.0001 0.0227
qGL7 7 RM505-PSM432 0.37 0.43 0.0003 <0.0001
qGL9 9 PSM399-RM105 -0.20 -0.15 <0.0001 0.0084
qGL11 11 RM209-RM21 -0.17 -0.16 0.0005 0.0023
粒宽Grain width qGW2 2 RM263-RM525 0.09 0.08 0.0003 0.0039
千粒重1000-grain weight qTGW1-1 1 PSM13-RM84 -1.46 -1.32 <0.0001 0.0016
qTGW1-2 1 OSR23-RM104 0.65 1.25 0.0003 0.0011
qTGW4 4 RM127-RM280 -1.31 -1.45 <0.0001 <0.0001
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