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Mapping for yield related traits in rice reveals major effect QTL qFLA1.1 from Oryza nivara increases flag leaf area

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Abstract

A stable back cross introgression line IL65 (IET22161) (Swarna/O. nivara-BC2F6) of rice was used to map flag leaf related traits in F2 and F3 populations. A total of 12 QTLs were mapped on two chromosomes with each QTL explaining 3 to 21% phenotypic variance (PV). Interestingly, a novel 12 Mb QTL cluster (RM8094—RM9) that controls 7 traits was identified on long arm of chromosome 1 where QTLs qSPAD1.2, qSPAD1.3 for SPAD, qFLL1.1, qFLL1.2 for flag leaf length, qFLW1.1, qFLW1.2 for flag leaf width, qFLA1.1, qFLA1.2 for flag leaf area, qPH1.1, qPH1.2 for plant height, qDTF1.2, qDTF1.3 for days to flowering and qHI1.2, qHI1.3 for harvest index were co-located. Among these, one major effect QTL qFLA1.1 for flag leaf area explaining 12.7% PV was identified in a 9 Mb region between RM8094 and RM5638. There was an adjacent minor effect QTL qFLA1.2 with 7% PV in a 3 Mb region between RM5638 and RM9. Together, these two QTLs from O. nivara explained 19.7% PV of leaf area. The QTL for flag leaf related traits can be fine mapped and considered for breeding rice varieties with higher flag leaf area, photosynthetic rate and grain yield.

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Data availability

All datasets generated for this study are included in this article and its supplementary files.

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Acknowledgements

We thank staff of Department of Genetics, Osmania University, and Director, IIRR for support for the research work of GH.

Funding

This research and GH was supported by funds from Department of Biotechnology, Government of India (DBT No. BT/PR13357/AGR/02/695/2009) and (BT/AB/FG -2 (PHII) (IA/2009).

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Contributions

NS and GH designed the study. GH developed the mapping populations. GH, ChG and MSB performed the field experiments under the supervision of NS. GH, ChG, MSB and BK phenotyped and genotyped the mapping populations. DB analyzed the data, statistical analysis of phenotypic data and detection of CSSLs. RM carried out construction of linkage map and QTL mapping analysis. GH did in-silico analysis of genes within major QTL. GH and NS wrote the manuscript. NS, RM and DB revised the manuscript. All authors read and approved the final submission. This is part of PhD work of GH submitted to Osmania University, Hyderabad.

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Correspondence to Sarla Neelamraju.

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Guttikonda, H., Chandu, G., Munnam, S.B. et al. Mapping for yield related traits in rice reveals major effect QTL qFLA1.1 from Oryza nivara increases flag leaf area. Euphytica 220, 53 (2024). https://doi.org/10.1007/s10681-024-03297-3

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