Scientia Agricultura Sinica ›› 2025, Vol. 58 ›› Issue (3): 401-415.doi: 10.3864/j.issn.0578-1752.2025.03.001

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

Construction of Single and Dual-Segment Substitution Lines from Rice CSSL-Z492 and Genetic Dissection of QTL for Grain Size

LI Lu(), XIE Zhuang, XIE KeYing, ZHANG Han, ZHAO ZhuoWen, XIANG AoNi, LI QiaoLong, LING YingHua, HE GuangHua, ZHAO FangMing()   

  1. Rice Research Institute, Southwest University/Academy of Agricultural Sciences, Southwest University/Chongqing Key Laboratory of Crop Molecular Improvement, Chongqing 400715
  • Received:2024-07-12 Accepted:2024-08-14 Online:2025-02-01 Published:2025-02-11
  • Contact: ZHAO FangMing

Abstract:

【Objective】Rice grain size is a quantitative trait controlled by multiple genes. They can be dissected into a single segment substitution line (SSSL), which is of great significance for their genetic mechanism study and breeding by design. 【Method】Z492, a chromosome segment substitution line in the genetic background of Nipponbare, was used as material to dissect QTL for rice grain size by mixed linear model (MLM) method. 【Result】The F2 population was constructed from Nipponbare/Z492 to identify four QTL for grain size, including qGL6 and qGL7 for grain length and qRLW7 and qRLW12 for rate of grain length to width. Then three single-segment substitution lines (SSSL, S1-S3) and 3 dual-segment substitution lines (DSSL, D1-D3) carrying these QTL were further constructed. And the SSSL were then used to detect eight QTL for grain size, including qGL6, qGL7 and six newly identified QTL (qGW6, qRLW6, qGW7, qGWT7, qGL12, qGW12). Simultaneously, the genetic model of different QTL in 3 DSSL were analyzed. The results showed that interaction of qGL6 (a=0.26 mm) and qGL7 (a=0.21 mm) produced -0.21 mm of grain length epistatic effect, which resulted in the genetic effect (0.26 mm) of D1 equal to the additive effect of each QTL. Thus, the grain length (7.98 mm) of D1 displayed no difference from those (7.89 and 7.98 mm) of S2 with qGL7 and S1 containing qGL6, while significantly longer than that (7.47 mm) of Nipponbare. The result indicated that it is not necessary to pyramid qGL6 and qGL7 in breeding by design for increasing grain length. qGW6 (a=0.07 mm) and qGW12 (a=0.06 mm) belonged to independent inheritance in D2, thus, the genetic effect (0.13 mm) after pyramiding of qGW6 and qGW12 caused the grain width (3.65 mm) of D2 broader significantly than any of the SSSL with the single QTL. So, qGW6 and qGW12 can be selected to increase grain width in breeding by design. Interaction of qGW7 (a=0.11 mm) and qGW12 (a=0.06 mm) yielded -0.10 mm of epistatic effect, causing the grain width genetic effect (0.07 mm) of D3 parallel to the additive effect of qGW12. Thus, the grain width (3.59 mm) of D3 exhibited no difference with that (3.56 mm) of S3 carrying qGW12, while wider significantly than that (3.44 mm) of Nipponbare and narrower significantly than that (3.66 mm) of S2. 【Conclusion】It is very necessary for breeding by design to identify QTL for different important traits using SSSL and DSSL. Pyramiding different QTL produce various genetic models. Some display independent inheritance, and others exhibit various epistatic effects. In addition, to cross with S1 and S3 can realize the goal of longer, wider and heavier rice grain, and to cross with S1 and S2 can reach the target of heavier grain weight, while to cross with S2 and S3 have no any effects in grain size.

Key words: rice, grain size, QTL, single segment substitution lines, QTL interaction

Fig. 1

Substitution segments and detected QTLs in Z492 GL: Grain length; RLW: Rate of the length to width"

Fig. 2

Plant type and grain size of Nipponbare and Z492 A: Plant type; B: Panicle length C: Grain length; D: Grain width; E-H: The statistics analysis of grain length, rate of length to width, grain width, and 1000-grain weight. *: Existing significant difference between the traits of Nipponbare and Z492 at P<0.05, respectively; NS: No significant difference between them"

Fig. 3

Frequency distribution of grain size traits in secondary F2 population from Nipponbare/Z492 A: Grain length; B: Grain width; C: 1000 grain weight; D: Rate of length to width"

Table 1

QTL for rice grain size detected in F2 population from Nipponbare/Z492"

性状
Trait
QTL 染色体
Chr.
连锁标记
Linked marker
估计效应
Estimated effect
贡献率
Var. (%)
P
P value
粒长Grain length (mm) qGL6 6 RM494 0.07 4.97 0.0314
粒长Grain length (mm) qGL7 7 RM5672 0.15 24.16 <0.0010
长宽比Rate of length to width qRLW7 7 RM5672 0.03 6.24 0.0208
长宽比Rate of length to width qRLW12 12 RM491 0.03 4.57 0.0400

Fig. 4

Sketch of developed SSSL (S1-S3) and DSSL (D1-D3) S: Single segment substitution line (SSSL); D: Dual segment substitution line (DSSL); GL: Grain length; GW: Grain width; GWT: 1000-grain weight ; RLW: Rate of length to width; S1 (Chr.6, RM439--RM494--RM20769); S2 (Chr.7, RM6081--RM5672--RM1186); S3 (Chr.12, RM6288--RM491-RM3455-- RM7119); D1 (Chr.6, RM439--RM494--RM20769; Chr.7, RM6081--RM5672--RM1186); D2 (Chr.6, RM439--RM494--RM20769; Chr.12, RM6288--RM491- RM3455--RM7119); D3(Chr.7, RM6081--RM5672--RM1186; Chr.12, RM6288--RM491-RM3455--RM7119)"

Fig. 5

Analysis of additive and epistatic effects of QTL for grain type in secondary single segment substitution lines and dual segment substitution lines A: Grain length; B: Grain width; C: 1000 grain weight; D: Rate of length to width; Different letters indicate significant differences each other at P<0.05 level. μ: The average value of each line, ai: Additive effect of QTL, I: Additive×additive epistasis effect between QTLs, S1 (Chr.6, RM439--RM494--RM20769); S2 (Chr.7, RM6081--RM5672--RM1186); S3 (Chr.12, RM6288--RM491-RM3455--RM7119); D1 (Chr.6, RM439--RM494--RM20769; Chr.7, RM6081-- RM5672--RM1186); D2 (Chr.6, RM439--RM494--RM20769; Chr.12, RM6288--RM491-RM3455--RM7119); D3 (Chr.7, RM6081--RM5672--RM1186; Chr.12, RM6288--RM491-RM3455--RM7119)"

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