Proceedings of the Korean Society of Crop Science Conference (한국작물학회:학술대회논문집)

The Korean Society of Crop Science (한국작물학회)
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Global Transcriptome-Wide Association Studies (TWAS) Reveal a Gene Regulation Network of Eating and Cooking Quality Traits in Rice

  • Weiguo Zhao (Department of Plant Resources, College of Industrial Sciences, Kongju National University) ;
  • Qiang He (Department of Plant Resources, College of Industrial Sciences, Kongju National University) ;
  • Kyu-Won Kim (Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University) ;
  • Feifei Xu (Department of Plant Resources, College of Industrial Sciences, Kongju National University) ;
  • Thant Zin Maung (Department of Plant Resources, College of Industrial Sciences, Kongju National University) ;
  • Aueangporn Somsri (Department of Plant Resources, College of Industrial Sciences, Kongju National University) ;
  • Min-Young Yoon (Department of Plant Resources, College of Industrial Sciences, Kongju National University) ;
  • Sang-Beom Lee (Department Crop Foundation Division, National Institute of Crop Science, Rural Development Administration) ;
  • Seung-Hyun Kim (Department of Applied Bioscience, Konkuk University) ;
  • Joohyun Lee (Department of Applied Bioscience, Konkuk University) ;
  • Soon-Wook Kwon (Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University) ;
  • Gang-Seob Lee (National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Bhagwat Nawade (Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University) ;
  • Sang-Ho Chu (Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University) ;
  • Wondo Lee (SEEDPIA Inc.) ;
  • Yoo-Hyun Cho (SEEDPIA Inc.) ;
  • Chang-Yong Lee (Department of Industrial and Systems Engineering, Kongju National University) ;
  • Ill-Min Chung (Department of Applied Bioscience, Konkuk University) ;
  • Jong-Seong Jeon (Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University) ;
  • Yong-Jin Park (Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Published : 2022.10.13
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Abstract

Eating and cooking quality (ECQ) is one of the most complex quantitative traits in rice. The understanding of genetic regulation of transcript expression levels attributing to phenotypic variation in ECQ traits is limited. We integrated whole-genome resequencing, transcriptome, and phenotypic variation data from 84 Japonica accessions to build a transcriptome-wide association study (TWAS) based regulatory network. All ECQ traits showed a large phenotypic variation and significant phenotypic correlations among the traits. TWAS analysis identified a total of 285 transcripts significantly associated with six ECQ traits. Genome-wide mapping of ECQ-associated transcripts revealed 66,905 quantitative expression traits (eQTLs), including 21,747 local eQTLs, and 45,158 trans-eQTLs, regulating the expression of 43 genes. The starch synthesis-related genes (SSRGs), starch synthase IV-1 (SSIV-1), starch branching enzyme 1 (SBE1), granule-bound starch synthase 2 (GBSS2), and ADP-glucose pyrophosphorylase small subunit 2a (OsAGPS2a) were found to have eQTLs regulating the expression of ECQ associated transcripts. Further, in co-expression analysis, 130 genes produced at least one network with 22 master regulators. In addition, we developed CRISPR/Cas9-edited glbl mutant lines that confirmed the role of alpha-globulin (glbl) in starch synthesis to validate the co-expression analysis. This study provided novel insights into the genetic regulation of ECQ traits, and transcripts associated with these traits were discovered that could be used in further rice breeding.

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Acknowledgement

This work was supported by National Research Foundation of Korea (NRF) grants by the Korean government (MSIT) (Nos. NRF-2022R1A4A1030348 and NRF-2017R1E1A1A01075282), "Cooperative Research Program for Agriculture Science and Technology Development" (Project No. PJ015935) of the Rural Development Administration, and Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET), Ministry of Agriculture, Food and Rural Affairs (MAFRA)(322060031HD020).