Dissection of three quantitative trait loci for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.)

Yu-Jun Zhu; Zhi-Chao Sun; Xiao-Jun Niu; Jie-Zheng Ying; Ye-Yang Fan; Tong-Min Mou; Shao-Qing Tang; Jie-Yun Zhuang

doi:10.7717/peerj.6966

Dissection of three quantitative trait loci for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.)

PeerJ. 2019 May 16:7:e6966. doi: 10.7717/peerj.6966. eCollection 2019.

Authors

Yu-Jun Zhu^{1

2}, Zhi-Chao Sun¹, Xiao-Jun Niu¹, Jie-Zheng Ying¹, Ye-Yang Fan¹, Tong-Min Mou², Shao-Qing Tang¹, Jie-Yun Zhuang¹

Affiliations

¹ State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
² State Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China.

Abstract

Background: Thousand grain weight is a key component of grain yield in rice, and a trait closely related to grain length (GL) and grain width (GW) that are important traits for grain quality. Causal genes for 16 quantitative trait loci (QTL) affecting these traits have been cloned, but more QTL remain to be characterized for establishing a genetic regulating network. A QTL controlling grain size in rice, qGS10, was previously mapped in the interval RM6100-RM228 on chromosome 10. This study aimed to delimitate this QTL to a more precise location.

Method: A total of 12 populations were used. The ZC9 population comprised 203 S _1:2 families derived from a residual heterozygous (RH) plant in the F ₉ generation of the indica rice cross Teqing (TQ)/IRBB52, segregating the upper region of RM6100-RM228 and three more regions on chromosomes 1, 9, and 11. The Ti52-1 population comprised 171 S ₁ plants derived from one RH plant in F ₇ of TQ/IRBB52, segregating a single interval that was in the lower portion of RM6100-RM228. The other ten populations were all derived from Ti52-1, including five S ₁ populations with sequential segregating regions covering the target region and five near isogenic line (NIL) populations maintaining the same segregating pattern. QTL analysis for 1,000-grain weight, GL, and GW was performed using QTL IciMapping and SAS procedure GLM.

Result: Three QTL were separated in the original qGS10 region. The qGL10.1 was located in the upper region RM6704-RM3773, shown to affect GL only. The qGS10.1 was located within a 207.1-kb interval flanked by InDel markers Te20811 and Te21018, having a stable and relatively high effect on all the three traits analyzed. The qGS10.2 was located within a 1.2-Mb interval flanked by simple sequence repeat markers RM3123 and RM6673. This QTL also affected all the three traits but the effect was inconsistent across different experiments. QTL for grain size were also detected in all the other three segregating regions.

Conclusion: Three QTL for grain size that were tightly linked on the long arm of chromosome 10 of rice were separated using NIL populations with sequential segregating regions. One of them, qGS10.1, had a stable and relatively high effect on grain weight, GL, and GW, providing a good candidate for gene cloning. Another QTL, qGS10.2, had a significant effect on all the three traits but the effect was inconsistent across different experiments, providing an example of genotype-by-environmental interaction.

Keywords: Grain size; Grain weight; Quantitative trait locus; Rice; Tightly-linked.

Grants and funding

This work was supported by the National Key R&D Program of China (2016YFD0101104), the National Natural Science Foundation of China (31521064), and a project of the China National Rice Research Institute (2017RG001-2). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.