QTL Analysis of Z414, a Chromosome Segment Substitution Line with Short, Wide Grains, and Substitution Mapping of qGL11 in Rice

Juan Li; Hongxia Yang; Guangyi Xu; Keli Deng; Jinjin Yu; Siqian Xiang; Kai Zhou; Qiuli Zhang; Ruxiang Li; Miaomiao Li; Yinghua Ling; Zhenglin Yang; Guanghua He; Fangming Zhao

doi:10.1186/s12284-022-00571-7

QTL Analysis of Z414, a Chromosome Segment Substitution Line with Short, Wide Grains, and Substitution Mapping of qGL11 in Rice

Rice (N Y). 2022 May 9;15(1):25. doi: 10.1186/s12284-022-00571-7.

Authors

Juan Li^#¹, Hongxia Yang^#¹, Guangyi Xu¹, Keli Deng¹, Jinjin Yu¹, Siqian Xiang¹, Kai Zhou¹, Qiuli Zhang¹, Ruxiang Li¹, Miaomiao Li¹, Yinghua Ling¹, Zhenglin Yang¹, Guanghua He¹, Fangming Zhao²

Affiliations

¹ Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
² Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China. zhaofangming2004@163.com.

^# Contributed equally.

Abstract

Most agronomic traits of rice (Oryza sativa), such as grain length, are complex traits controlled by multiple genes. Chromosome segment substitution lines (CSSLs) are ideal materials for dissecting these complex traits. We developed the novel rice CSSL 'Z414', which has short, wide grains, from progeny of the recipient parent 'Xihui 18' (an indica restorer line) and the donor parent 'Huhan 3' (a japonica cultivar). Z414 contains four substitution segments with an average length of 3.04 Mb. Z414 displays seven traits that significantly differ from those of Xihui 18, including differences in grain length, width, and weight; degree of chalkiness; and brown rice rate. We identified seven quantitative trait loci (QTL) that are responsible for these differences in an F₂ population from a cross between Xihui 18 and Z414. Among these, six QTL (qPL3, qGW5, qGL11, qRLW5, qRLW11, and qGWT5) were detected in newly developed single-segment substitution lines (SSSLs) S1-S6. In addition, four QTL (qGL3, qGL5, qCD3, and qCD5) were detected in S1 and S5. Analysis of these SSSLs attributed the short, wide grain trait of Z414 to qGL11, qGL3, qGL5, and qGW5. Substitution mapping delimited qGL11 within an 810-kb interval on chromosome 11. Sequencing, real time quantitative PCR, and cell morphology analysis revealed that qGL11 might be a novel QTL encoding the cyclin CycT1;3. Finally, pyramiding qGL3 (a = 0.43) and qGL11 (a = - 0.37) led to shorter grains in the dual-segment substitution line D2 and revealed that qGL11 is epistatic to qGL3. In addition, S1 and D2 exhibited different grain sizes and less chalkiness than Z414. In conclusion, the short grain phenotype of the CSSL Z414 is controlled by qGL11, qGL3, and qGL5. qGL11 might be a novel QTL encoding CycT1;3, whose specific role in regulating grain length was previously unknown, and qGL11 is epistatic to qGL3. S1 and D2 could potentially be used in hybrid rice breeding.

Keywords: Chromosome segment substitution line; Grain size; Quantitative trait locus; Rice; Substitution mapping; qGL11.

Abstract

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