Rice co-expression network analysis identifies gene modules associated with agronomic traits

Y Zhang, E Han, Y Peng, Y Wang, Y Wang… - Plant …, 2022 - academic.oup.com
Identifying trait-associated genes is critical for rice (Oryza sativa) improvement, which
usually relies on map-based cloning, quantitative trait locus analysis, or genome-wide …

Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice

L Xia, D Zou, J Sang, X Xu, H Yin, M Li, S Wu… - Journal of Genetics and …, 2017 - Elsevier
Rice is one of the most important stable food as well as a monocotyledonous model
organism for the plant research community. Here, we present RED (Rice Expression …

Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

K Yano, E Yamamoto, K Aya, H Takeuchi, P Lo, L Hu… - Nature …, 2016 - nature.com
A genome-wide association study (GWAS) can be a powerful tool for the identification of
genes associated with agronomic traits in crop species, but it is often hindered by population …

CARMO: a comprehensive annotation platform for functional exploration of rice multi‐omics data

J Wang, M Qi, J Liu, Y Zhang - The Plant Journal, 2015 - Wiley Online Library
High‐throughput technology is gradually becoming a powerful tool for routine research in
rice. Interpretation of biological significance from the huge amount of data is a critical but …

Identification of key genes for the ultrahigh yield of rice using dynamic cross-tissue network analysis

J Hu, T Zeng, Q Xia, L Huang, Y Zhang… - Genomics …, 2020 - academic.oup.com
Significantly increasing crop yield is a major and worldwide challenge for food supply and
security. It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the …

[HTML][HTML] Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

K Zhao, CW Tung, GC Eizenga, MH Wright… - Nature …, 2011 - nature.com
Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's
population. Understanding the genetic basis of diverse physiological, developmental, and …

Analysis of trait heritability in functionally partitioned rice genomes

J Wei, W Xie, R Li, S Wang, H Qu, R Ma, X Zhou, Z Jia - Heredity, 2020 - nature.com
Abstract Knowledge of the genetic architecture of importantly agronomical traits can speed
up genetic improvement in cultivated rice (Oryza sativa L.). Many recent investigations have …

[HTML][HTML] Rice functional genomics research: past decade and future

Y Li, J Xiao, L Chen, X Huang, Z Cheng, B Han… - Molecular plant, 2018 - cell.com
Rice (Oryza sativa) is a major staple food crop for more than 3.5 billion people worldwide.
Understanding the regulatory mechanisms of complex agronomic traits in rice is critical for …

[HTML][HTML] A pangenome analysis pipeline provides insights into functional gene identification in rice

J Wang, W Yang, S Zhang, H Hu, Y Yuan, J Dong… - Genome Biology, 2023 - Springer
Background A pangenome aims to capture the complete genetic diversity within a species
and reduce bias in genetic analysis inherent in using a single reference genome. However …

RiceFREND: a platform for retrieving coexpressed gene networks in rice

Y Sato, N Namiki, H Takehisa, K Kamatsuki… - Nucleic acids …, 2013 - academic.oup.com
Similarity of gene expression across a wide range of biological conditions can be efficiently
used in characterization of gene function. We have constructed a rice gene coexpression …