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Genomic investigation of 18,421 lines reveals the genetic architecture of rice

Affiliations
  • 1Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
  • 2State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.
  • 3CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
  • 4State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
  • 5Key Laboratory of Plant Functional Genomics of Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
  • 6Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.

Published on:

July 4, 2024

Abstract

Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced population structure. We generated reference-level genome assemblies of the founders and genotyped all 18K-rice lines through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to variation in 16 traits were identified, including and verified as causal genes for panicle number and heading date, respectively. We identified epistatic QTL pairs and constructed a genetic interaction network with 19 genes serving as hubs. Overall, 170 masking epistasis pairs were characterized, serving as an important factor contributing to genetic background effects across diverse varieties. The work provides a basis to guide grain yield and quality improvements in rice.

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