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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (3): 731-743.doi: 10.3724/SP.J.1006.2023.12081

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

Identification and pyramid analysis of QTLs for grain size based on rice long-large-grain chromosome segment substitution line Z66

XIANG Si-Qian(), LI Ru-Xiang, XU Guang-Yi, DENG Ke-Li, YU Jin-Jin, LI Miao-Miao, YANG Zheng-Lin, LING Ying-Hua, SANG Xian-Chun, HE Guang-Hua, ZHAO Fang-Ming()   

  1. Rice Research Institute, Southwest University / Academy of Agricultural Sciences, Southwest University / Transgenic Plants and Safety Control, Chongqing Key Laboratory, Chongqing 400715, China
  • Received:2021-11-30 Accepted:2022-06-07 Online:2023-03-12 Published:2022-07-07
  • Contact: ZHAO Fang-Ming E-mail:969937373@qq.com;zhaofangming2004@163.com
  • Supported by:
    National Natural Science Foundation of China(32072039);Germplasm Creation for Southwest University

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Abstract:

Rice grain size is a complex agronomic trait, controlled by multiple genes. Chromosome segment substitution lines are an effective method for creating natural occurring variations and are as the ideal materials for exploring the complex traits. In this study, a novel rice long-large grain chromosome segment substitution line Z66 was developed. Z66 contained 12 substitution segments from R225 (average substitution length was 3.32 Mb) based on the genetic backgrounds of Nipponbare. Then, 12 QTLs for rice grain size were identified by the secondary F2 population from Nipponbare/Z66, and 5 novel single-segment substitution lines (SSSLs, S1-S5), and 4 novel double-segment substitution lines (DSSLs, D1-D4) harboring target QTL were developed. Among them, 9 QTLs (qGL3, qGL7, qGL10, qGW6, qGW10, qRLW3, qRLW10, qGWT3, and qGWT10) could be verified by the SSSLs, indicating that these QTLs were genetically stable. In addition, 6 novel QTLs (qGL9-2, qGW9-2, qRLW6, qRLW7, qRLW9-2, and qGWT7) were detected by the SSSLs. Among 18 QTLs, 5 QTLs (qGL9-2, qRLW9-1, qRLW9-2, qGW9-2, and qGWT9-2) might be novel. Target QTLs pyramiding showed that the pyramid of different QTLs had various epistasis effects. For example, the pyramids of qRLW3 (a=0.21) and qRLW9-2 (a=0.08) produced an epistasis effect of 0.10, which made the ratio of grain length to width in D2 significantly larger than that in Nipponbare, S1 (qRLW3), and S4 (qRLW9-2). The pyramid of qGWT3 (a=3.99) and qGWT10 (a=3.98) yielded an epistasis effect of -5.35, and its genetic effects in D3 (2.62 g) significantly increased 1000-grain weight of D3 than in Nipponbare, but significantly decreased than that in S1 (qGWT3) and S5 (qGWT10). Understanding the interaction effects between target QTLs can predict the phenotype of futural QTL pyramid genotypes, which is important for intelligent design breeding in rice.

Key words: rice, grain shape, QTLs, chromosome segment substitution line, additive effect, epistasis effect

Fig. 1

Process of development of CSSL including Z66 MAS: molecular marker assisted selection; CSSL: chromosome segment substitution lines."

Fig. 2

Epistasis of Q1 on the “i” substitution segment and Q2 on the “j” substitution segment of the double-segment substitution line DSSLij Dij represents the double-segment substitution line containing the “i” substitution segment and the “j” substitution segment. The additive effects of QTLs (Q1 and Q2) for a certain trait were detected by the according SSSLi (containing single “i” substitution segment) and SSSLj (containing single “j” substitution segment). The epistasis effect between Q1 and Q2 is detected by (Nipponbare+DSSLij) and (SSSLi+SSSLj). Chr. represents 2 rice chromosomes carrying Q1 and Q2, respectively. Black region represents the genetic background of the recipient Nipponbare, the genotypes of markers are represented by “(-1, -1)”, the red region represents the substitution region from the donor R225, the genotypes of marker are represented by “(1, 1)”, and if there is QTL for a trait in the substitution regions, they are showed as Q1 and Q2, respectively. The connecting between Q1 and Q2 shows existing epistasis effect at P < 0.05."

Fig. 3

Chromosomes substitution segments of Z66 Physical distances (Mb) and mapped QTL are marked at the left of each chromosome; substitution length (black arrow direction) are displayed at the right of each chromosome. GL: grain length; GW: grain width; RLW: ratio of grain length to width; GWT: 1000-grain weight."

Fig. 4

Statistical analysis of grain size of Nipponbare and Z66 A: plant type; B: grain length; C: grain width; D-G: the statistics analysis of grain length, grain width, ratio of length to width, and 1000-grain weight. ** indicate significant difference between the traits of Nipponbare and Z66 at P < 0.01, respectively."

Fig. 5

Frequency distribution of grain size related traits in F2 secondary population from Nipponbare/Z66 A-D: the frequency distribution of grain length, grain width, ratio of and length to width, and 1000-grain weight in F2 population in sequence, respectively."

Table 1

QTL for rice grain size detected in secondary F2 population from Nipponbare/Z66"

性状
Trait		 QTL 染色体
Chr.		 连锁标记
Linked marker		 加性效应
Additive effect		 贡献率
R2 (%)		 P值
P-value
粒长
Grain length		 qGL3 3 RM5928 0.21 8.95 0.0028
qGL7 7 RM5481 0.10 2.61 0.0360
qGL10 10 RM6673 0.13 4.62 0.0210
粒宽
Grain width		 qGW6 6 RM3183 -0.11 30.78 0.0005
qGW9-1 9 RM5657 -0.10 14.87 0.0018
qGW10 10 RM6673 0.12 39.18 0.0003
长宽比
Ratio of length to width		 qRLW3 3 RM5928 0.09 14.78 0.0440
qRLW9-1 9 RM5657 0.25 44.93 0.0220
qRLW10 10 RM6673 0.049 6.40 0.0200
千粒重
1000-grain weight		 qGWT3 3 RM5928 1.14 9.48 0.0250
qGWT9-2 9 RM2144 -0.79 6.05 0.0360
qGWT10 10 RM6673 0.73 5.14 0.0430

Fig. 6

Development of secondary single segment substitution lines and double segment substitution lines and analysis of additive and epistasis effects of QTLs for grain size A: sketch map of developed SSSLs (S1-S5), DSSLs (D1-D4). N: Nipponbare; S: SSSL; D: DSSL. B: grain length (GL); C: grain width (GW); D: ratio of length to width (RLW); E: 1000-grain weight (GWT). Different lowercase letters indicate significant difference at P < 0.05 as determined by Duncan’s multiple comparisons. μ is the mean value of each line, ai denotes the additive effect of QTLs, I denotes the additive × additive epistasis effect between QTLs. The P-value for a SSSL indicates the probability of a significant difference between the SSSL and Nipponbare, and the SSSL carried a QTL (Student’s t-test, P < 0.05). The P-value for a DSSL indicates the probability of an epitasis effect between QTLs in the DSSLij. (Nipponbare + DSSLij) and (SSSLi and SSSLj) (Student’s t-test, P < 0.05). S1: Chr3, RM3766-RM2917; S2: Chr6, RM3330-RM3567; S3: Chr7, RM1186-RM3826; S4: Chr9, RM1553-End of long arm; S5: Chr10, RM4477-End of long arm; D1: Chr3, RM3766-RM2917; Chr6, RM3330-RM3567; D2: Chr3, RM3766-RM2917; Chr9, RM1553-RM205; D3: Chr3, RM3766-RM2917; Chr10, RM4477-RM6673; D4: Chr6, RM3330-RM3567; Chr9, RM1553-RM205; Hyphenated internal tokens indicate alternative segments from the donor."

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