Fine-mapping of qTGW2, a quantitative trait locus for grain weight in rice (Oryza sativa L.)

Hui Zhang; Yu-Jun Zhu; An-Dong Zhu; Ye-Yang Fan; Ting-Xu Huang; Jian-Fu Zhang; Hua-An Xie; Jie-Yun Zhuang

doi:10.7717/peerj.8679

Fine-mapping of qTGW2, a quantitative trait locus for grain weight in rice (Oryza sativa L.)

PeerJ. 2020 Mar 4:8:e8679. doi: 10.7717/peerj.8679. eCollection 2020.

Authors

Hui Zhang^{1

2

3}, Yu-Jun Zhu², An-Dong Zhu², Ye-Yang Fan², Ting-Xu Huang³, Jian-Fu Zhang³, Hua-An Xie^{1

3}, Jie-Yun Zhuang²

Affiliations

¹ College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.
² State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.
³ Rice Research Institute and Fuzhou Branch of the National Center for Rice Improvement, Fujian Academy of Agricultural Sciences, Fuzhou, China.

Abstract

Background: Grain weight is a grain yield component, which is an integrated index of grain length, width and thickness. They are controlled by a large number of quantitative trait loci (QTLs). Besides major QTLs, minor QTLs play an essential role. In our previous studies, QTL analysis for grain length and width was performed using a recombinant inbred line population derived from rice cross TQ/IRBB lines. Two major QTLs were detected, which were located in proximity to GS3 and GW5 that have been cloned. In the present study, QTLs for grain weight and shape were identified using rice populations that were homozygous at GS3 and GW5.

Method: Nine populations derived from the indica rice cross TQ/IRBB52 were used. An F_10:11population named W1, consisting of 250 families and covering 16 segregating regions, was developed from one residual heterozygote (RH) in the F₇generation of Teqing/IRBB52. Three near isogenic line (NIL)-F₂ populations, ZH1, ZH2 and ZH3 that comprised 205, 239 and 234 plants, respectively, were derived from three RHs in F_10:11. They segregated the target QTL region in an isogenic background. Two NIL populations, HY2 and HY3, were respectively produced from homozygous progeny of the ZH2 and ZH3 populations. Three other NIL-F₂ populations, Z1, Z2 and Z3, were established using three RHs having smaller heterozygous segments. QTL analysis for 1000-grain weight (TGW), grain length (GL), grain width (GW), and length/width ratio (LWR) was conducted using QTL IciMapping and SAS procedure with GLM model.

Result: A total of 27 QTLs distributed on 12 chromosomes were identified. One QTL cluster, qTGW2/qGL2/qGW2 located in the terminal region of chromosome 2, were selected for further analysis. Two linked QTLs were separated in region Tw31911-RM266. qGL2 was located in Tw31911-Tw32437 and mainly controlled GL and GW. The effects were larger on GL than on GW and the allelic directions were opposite. qTGW2 was located in Tw35293-RM266 and affected TGW, GL and GW with the same allelic direction. Finally, qTGW2 was delimited within a 103-kb region flanked by Tw35293 and Tw35395.

Conclusion: qTGW2 with significant effects on TGW, GL and GW was validated and fine-mapped using NIL and NIL-F₂ populations. These results provide a basis for map-based cloning of qTGW2 and utilization of qTGW2 in the breeding of high-yielding rice varieties.

Keywords: Fine-mapping; Grain length; Grain weight; Grain width; Minor effect; Quantitative trait loci; Rice.

Grants and funding

This work was supported by the Science and Technology Innovation Program of the Fujian Academy of Agricultural Sciences (STIT 2017-1-1), the National Research and Development Program (2016YFD0101801), the Special Foundation of Non-Profit Research Institutes of Fujian Province (2018R1101013-4) and the National Natural Science Foundation of China (31521064). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.