Abstract
Panicle architecture directly affects the grain yield of rice; meanwhile, crop domestication has increased the complexity of rice panicle size and branching pattern. Genome-wide association study (GWAS) was performed to investigate the genetic basis underlying panicle architecture using 183 rice accessions from around the world and a 7 K SNP array. Phenotyping was conducted at Texas A&M AgriLife Research Center in Beaumont, TX. GWAS was performed using MLM (Q + K) model using GAPIT software. At p-value < 0.001, a total of 49 GWAS QTLs controlling various panicle architecture traits were mapped. Considering the recurring and linked SNPs across the panicle architecture traits, 42 independent QTL regions were identified. Among these, 27 QTL regions co-localized with known genes or previously reported QTLs or significant SNP markers, while 15 were potentially novel QTL regions. The results of our study offer useful information on genetic bases controlling panicle architecture in rice, which could be further validated and utilized for designing markers for use in markers assisted selection (MAS) in rice breeding programs.
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22 April 2021
A Correction to this paper has been published: https://doi.org/10.1007/s10722-021-01185-6
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Acknowledgments
We thank Chersty Harper and the members of the Rice Genetics Lab of 2016/2017 for technical assistance on seed multiplication and post-harvest processes; and Susan McCouch at Cornell University for developing the 7K SNP chip.
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This work was supported by the Texas A&M AgriLife Research and the NIFA-USDA Hatch project # 1009300.
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RT and ES designed the experiment; ES conceived the project; RET and RT performed seed multiplication and post-harvest processes; RT performed the experiment; RT and ES analyzed data; RT wrote the first draft of the manuscript; ES reviewed and edited the manuscript; all read and approved the manuscript.
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Thapa, R., Tabien, R.E. & Septiningsih, E.M. Genome-wide association study to identify chromosomal regions related to panicle architecture in rice (Oryza sativa). Genet Resour Crop Evol 68, 2849–2865 (2021). https://doi.org/10.1007/s10722-021-01159-8
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DOI: https://doi.org/10.1007/s10722-021-01159-8