Abstract
Leaf pigment content is a complicated quantitative trait which results from the cooperation of multiple related genes or quantitative trait loci (QTL) in rice. So far, more than 600 QTL for leaf pigment content has been reported. However, most QTL positions could not be directly compared with each other. In this study, our goal was to analyze consistent QTL regions affecting leaf pigment content by applying a genome wide QTL meta-analysis approach. 20 QTL related to leaf pigment content were detected at 5 different growth periods in 134 recombinant inbred lines (RILs) from a typical Indica-Japonica cross derived from PA64s and 9311 (two parents of super hybrid rice Liangyoupei 9). There was a candidate gene GLTP in the region of 3 QTL (qFS_Chla4, qFS_Chla+b4, and qFS_Car4), which related to component of chloroplast thylakoid membranes. After sequencing and qRT-PCR analysis, the gene showed significant difference in parents of the RILs. Meta-analysis was performed on 618 QTL collected from 38 previous studies. Consequently, a total of 64 MQTL (Meta-QTL) were obtained, of which 58.95% confidence intervals (CI) were smaller than the average Cl of the original QTL. In addition, 64 MQTL covered 6 of 20 QTL detected. Among them, four main QTL were included in 3 MQTL, and phenotypic variation of 21 MQTL was greater than 20%. The traits with higher number of QTL had higher number of MQTL, and candidate genes in overlapping MQTL include multiple effects. 7 candidate genes related to leaf pigment content were found in 4 MQTL spanning physical intervals < 0.5 Mb. These findings are not only anticipated to help molecular marker-assisted selection and pyramiding, but also contribute to determine candidate genes that regulate pigment content.
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Acknowledgments
The authors would like to thank Qian Qian who provide the RIL population in this research. We would also like to thank the reviewers who provided suggestions to improve this paper.
Funding
This research was funded by the National Natural Science Foundation of China (32001491), the Genetically Modified Organisms Breeding Major Projects of China (2016ZX08001-002), the National Key R&D Program of China (2017YFD0100201), the Educational Commission of Sichuan Province, China (18ZA0507).
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LL, YP, and ST conducted the phenotypic experiment. ST, DY, FG, GY and LL measured the physiological traits and collected QTL information. LL, MT, YP, XW and YH performed the bioinformatics analysis and statistical analysis. LL and ST wrote the draft of manuscript, and YP revision of the manuscript. YP and YH were involved in designing the entire experiment and providing critical advices on the manuscript. All authors approved the final manuscript.
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Li, L., Peng, Y., Tang, S. et al. Mapping QTL for leaf pigment content at dynamic development stage and analyzing Meta-QTL in rice. Euphytica 217, 90 (2021). https://doi.org/10.1007/s10681-021-02820-0
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DOI: https://doi.org/10.1007/s10681-021-02820-0