Journal
G3-GENES GENOMES GENETICS
Volume 11, Issue 7, Pages -Publisher
OXFORD UNIV PRESS INC
DOI: 10.1093/g3journal/jkab130
Keywords
epistasis; RILs; GWAS; rice; modeling
Categories
Funding
- Project of the NARO Bio-oriented Technology Research Advancement Institution (research program on development of innovative technology)
- JSPS KAKENHI [15H05779, 20H00421, 17H03752, 20H02962]
- Grants-in-Aid for Scientific Research [15H05779, 17H03752, 20H00421, 20H02962] Funding Source: KAKEN
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Characterizing epistatic gene interactions is crucial for understanding complex traits, and using recombinant inbred lines can provide a simple and interpretable method for detecting such interactions.
Characterizing epistatic gene interactions is fundamental for understanding the genetic architecture of complex traits. However, due to the large number of potential gene combinations, detecting epistatic gene interactions is computationally demanding. A simple, easy-to-perform method for sensitive detection of epistasis is required. Due to their homozygous nature, use of recombinant inbred lines excludes the dominance effect of alleles and interactions involving heterozygous genotypes, thereby allowing detection of epistasis in a simple and interpretable model. Here, we present an approach called RIL-StEp (recombinant inbred lines stepwise epistasis detection) to detect epistasis using single-nucleotide polymorphisms in the genome. We applied the method to reveal epistasis affecting rice (Oryza sativa) seed hull color and leaf chlorophyll content and successfully identified pairs of genomic regions that presumably control these phenotypes. This method has the potential to improve our understanding of the genetic architecture of various traits of crops and other organisms.
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