MaizeNet: a co-functional network for network-assisted systems genetics in Zea mays

Tak Lee, Sungho Lee, Sunmo Yang, Insuk Lee

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Maize (Zea mays) has multiple uses in human food, animal fodder, starch and sweetener production and as a biofuel, and is accordingly the most extensively cultivated cereal worldwide. To enhance maize production, genetic factors underlying important agricultural traits, including stress tolerance and flowering, have been explored through forward and reverse genetics approaches. Co-functional gene networks are systems biology resources useful in identifying trait-associated genes in plants by prioritizing candidate genes. Here, we present MaizeNet (http://www.inetbio.org/maizenet/), a genome-scale co-functional network of Z. mays genes, and a companion web server for network-assisted systems genetics. We describe the validation of MaizeNet network quality and its ability to functionally predict molecular pathways and complex traits in maize. Furthermore, we demonstrate that MaizeNet-based prioritization of candidate genes can facilitate the identification of cell wall biosynthesis genes and detect network communities associated with flowering-time candidate genes derived from genome-wide association studies. The demonstrated gene prioritization and subnetwork analysis can be conducted by simply submitting maize gene models based on the commonly used B73 RefGen_v3 and the latest B73 RefGen_v4 reference genomes on the MaizeNet web server. MaizeNet-based network-assisted systems genetics will substantially accelerate the discovery of trait-associated genes for crop improvement.

Original languageEnglish
Pages (from-to)571-582
Number of pages12
JournalPlant Journal
Volume99
Issue number3
DOIs
Publication statusPublished - 2019 Aug

Fingerprint

Zea mays
Genes
genes
Gene Regulatory Networks
corn
prioritization
Genome
Reverse Genetics
Sweetening Agents
Plant Genes
Systems Biology
Biofuels
Genome-Wide Association Study
flowering
Starch
Zea
Cell Wall
genome
sweeteners
food animals

All Science Journal Classification (ASJC) codes

  • Genetics
  • Plant Science
  • Cell Biology

Cite this

Lee, Tak ; Lee, Sungho ; Yang, Sunmo ; Lee, Insuk. / MaizeNet : a co-functional network for network-assisted systems genetics in Zea mays. In: Plant Journal. 2019 ; Vol. 99, No. 3. pp. 571-582.
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MaizeNet : a co-functional network for network-assisted systems genetics in Zea mays. / Lee, Tak; Lee, Sungho; Yang, Sunmo; Lee, Insuk.

In: Plant Journal, Vol. 99, No. 3, 08.2019, p. 571-582.

Research output: Contribution to journalArticle

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