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Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice

dc.contributor.authorShujun Wei
dc.contributor.authorRyokei Tanaka
dc.contributor.authorTaiji Kawakatsu
dc.contributor.authorShota Teramoto
dc.contributor.authorNobuhiro Tanaka
dc.contributor.authorMatthew Shenton
dc.contributor.authorYusaku Uga
dc.contributor.authorShiori Yabe
dc.contributor.otherInstitute of Crop Sciences, National Agriculture & Food Research Organization
dc.contributor.otherInstitute of Crop Sciences, National Agriculture & Food Research Organization
dc.contributor.otherInstitute of Agrobiological Sciences, National Agriculture & Food Research Organization
dc.contributor.otherInstitute of Crop Sciences, National Agriculture & Food Research Organization
dc.contributor.otherInstitute of Crop Sciences, National Agriculture & Food Research Organization
dc.contributor.otherInstitute of Crop Sciences, National Agriculture & Food Research Organization
dc.contributor.otherInstitute of Crop Sciences, National Agriculture & Food Research Organization
dc.contributor.otherInstitute of Crop Sciences, National Agriculture & Food Research Organization
dc.date.accessioned2023-12-10T12:31:43Z
dc.date.accessioned2025-10-08T08:22:33Z
dc.date.available2025-10-08T08:22:33Z
dc.date.issued01-12-2023
dc.identifier.urihttp://digilib.fisipol.ugm.ac.id/repo/handle/15717717/35647
dc.description.abstractAbstract Root system architecture plays a crucial role in nutrient and water absorption during rice production. Genetic improvement of the rice root system requires elucidating its genetic control. Genome-wide association studies (GWASs) have identified genomic regions responsible for rice root phenotypes. However, candidate gene prioritization around the peak region often suffers from low statistical power and resolution. Transcriptomics enables other statistical mappings, such as transcriptome-wide association study (TWAS) and expression GWAS (eGWAS), which improve candidate gene identification by leveraging the natural variation of the expression profiles. To explore the genes responsible for root phenotypes, we conducted GWAS, TWAS, and eGWAS for 12 root phenotypes in 57 rice accessions using 427,751 single nucleotide polymorphisms (SNPs) and the expression profiles of 16,901 genes expressed in the roots. The GWAS identified three significant peaks, of which the most significant peak responsible for seven root phenotypes (crown root length, crown root surface area, number of crown root tips, lateral root length, lateral root surface area, lateral root volume, and number of lateral root tips) was detected at 6,199,732 bp on chromosome 8. In the most significant GWAS peak region, OsENT1 was prioritized as the most plausible candidate gene because its expression profile was strongly negatively correlated with the seven root phenotypes. In addition to OsENT1, OsEXPA31, OsSPL14, OsDEP1, and OsDEC1 were identified as candidate genes responsible for root phenotypes using TWAS. Furthermore, a cis-eGWAS peak SNP was detected for OsDjA6, which showed the eighth strongest association with lateral root volume in the TWAS. The cis-eGWAS peak SNP for OsDjA6 was in strong linkage disequilibrium (LD) with a GWAS peak SNP on the same chromosome for lateral root volume and in perfect LD with another SNP variant in a putative cis-element at the 518 bp upstream of the gene. These candidate genes provide new insights into the molecular breeding of root system architecture.
dc.language.isoEN
dc.publisherSpringerOpen
dc.subject.lccPlant culture
dc.titleGenome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice
dc.typeArticle
dc.description.keywordsRoot
dc.description.keywordsCandidate gene search
dc.description.keywordsGenetic variation
dc.description.keywordsAssociation mapping
dc.description.keywordsGenome-wide association study
dc.description.keywordsTranscriptome-wide association study
dc.description.pages1-17
dc.description.doi10.1186/s12284-023-00672-x
dc.title.journalRice
dc.identifier.e-issn1939-8433
dc.identifier.oai6b68fb57a04f4c929332d6690298d1ac
dc.journal.infoVolume 16, Issue 1


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