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Title: RIL-StEp: epistasis analysis of rice recombinant inbred lines (RILs) reveals candidate interacting genes that control seed hull color and leaf chlorophyll content
Authors: Sakai, Toshiyuki  kyouindb  KAKEN_id  orcid https://orcid.org/0000-0003-2737-3299 (unconfirmed)
Abe, Akira
Shimizu, Motoki
Terauchi, Ryohei
Author's alias: 堺, 俊之
寺内, 良平
Keywords: epistasis
RILs
GWAS
rice
modeling
Issue Date: Jul-2021
Publisher: Oxford University Press (OUP)
Genetics Society of America
Journal title: G3 Genes|Genomes|Genetics
Volume: 11
Issue: 7
Thesis number: jkab130
Abstract: 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.
Rights: © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.
This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence, which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited.
URI: http://hdl.handle.net/2433/276530
DOI(Published Version): 10.1093/g3journal/jkab130
PubMed ID: 33871605
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