@article{5dcfbac789ef4f4a8f67e29de61c833a,
title = "Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice",
abstract = "Manual phenotyping of rice tillers is time consuming and labor intensive, and lags behind the rapid development of rice functional genomics. Thus, automated, non-destructive methods of phenotyping rice tiller traits at a high spatial resolution and high throughput for large-scale assessment of rice accessions are urgently needed. In this study, we developed a high-throughput micro-CT-RGB imaging system to non-destructively extract 739 traits from 234 rice accessions at nine time points. We could explain 30\% of the grain yield variance from two tiller traits assessed in the early growth stages. A total of 402 significantly associated loci were identified by genome-wide association study, and dynamic and static genetic components were found across the nine time points. A major locus associated with tiller angle was detected at time point 9, which contained a major gene, TAC1. Significant variants associated with tiller angle were enriched in the 3ʹ-untranslated region of TAC1. Three haplotypes for the gene were found, and rice accessions containing haplotype H3 displayed much smaller tiller angles. Further, we found two loci containing associations with both vigor-related traits identified by high-throughput micro-CT-RGB imaging and yield. The superior alleles would be beneficial for breeding for high yield and dense planting.",
keywords = "dyamic phenotyping, GWAS, high throughput, longitudinal traits, micro-CT-RGB, plant phenomics, rice tiller, tiller traits, Dynamic phenotyping, Longitudinal traits, Tiller traits, Rice tiller, High throughput, Plant phenomics, Micro-CT-RGB, Genome-Wide Association Study, Edible Grain/growth \& development, Oryza/genetics, Biomass, Genome, Plant, X-Ray Microtomography, Droughts",
author = "Di Wu and Zilong Guo and Junli Ye and Hui Feng and Jianxiao Liu and Guoxing Chen and Jingshan Zheng and Dongmei Yan and Xiaoquan Yang and Xiong Xiong and Qian Liu and Zhiyou Niu and Alan Gay and John Doonan and Lizhong Xiong and Wanneng Yang",
note = "Funding Information: This work was supported by grants from the National Key Research and Development Program of China (2016YFD0100101-18), the National Natural Science Foundation of China (31770397), the Fundamental Research Funds for the Central Universities (2662017PY058), and UK grants supported by the Biotechnology and Biological Sciences Research Council (BB/J004464/1, BB/CAP1730/1, BB/CSP1730/1 and BB/R02118X/1). Publisher Copyright: {\textcopyright} The Author(s) 2018.",
year = "2019",
month = jan,
day = "7",
doi = "10.1093/jxb/ery373",
language = "English",
volume = "70",
pages = "545--561",
journal = "Journal of Experimental Botany",
issn = "0022-0957",
publisher = "Oxford University Press",
number = "2",
}