Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice
Abstract 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 phen...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2023-12-01
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| Series: | Rice |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12284-023-00672-x |
| _version_ | 1797397752198463488 |
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| author | Shujun Wei Ryokei Tanaka Taiji Kawakatsu Shota Teramoto Nobuhiro Tanaka Matthew Shenton Yusaku Uga Shiori Yabe |
| author_facet | Shujun Wei Ryokei Tanaka Taiji Kawakatsu Shota Teramoto Nobuhiro Tanaka Matthew Shenton Yusaku Uga Shiori Yabe |
| author_sort | Shujun Wei |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-09T01:15:38Z |
| format | Article |
| id | doaj.art-6b68fb57a04f4c929332d6690298d1ac |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-03-09T01:15:38Z |
| publishDate | 2023-12-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-6b68fb57a04f4c929332d6690298d1ac2023-12-10T12:31:43ZengSpringerOpenRice1939-84251939-84332023-12-0116111710.1186/s12284-023-00672-xGenome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated RiceShujun Wei0Ryokei Tanaka1Taiji Kawakatsu2Shota Teramoto3Nobuhiro Tanaka4Matthew Shenton5Yusaku Uga6Shiori Yabe7Institute of Crop Sciences, National Agriculture & Food Research OrganizationInstitute of Crop Sciences, National Agriculture & Food Research OrganizationInstitute of Agrobiological Sciences, National Agriculture & Food Research OrganizationInstitute of Crop Sciences, National Agriculture & Food Research OrganizationInstitute of Crop Sciences, National Agriculture & Food Research OrganizationInstitute of Crop Sciences, National Agriculture & Food Research OrganizationInstitute of Crop Sciences, National Agriculture & Food Research OrganizationInstitute of Crop Sciences, National Agriculture & Food Research OrganizationAbstract 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.https://doi.org/10.1186/s12284-023-00672-xRootCandidate gene searchGenetic variationAssociation mappingGenome-wide association studyTranscriptome-wide association study |
| spellingShingle | Shujun Wei Ryokei Tanaka Taiji Kawakatsu Shota Teramoto Nobuhiro Tanaka Matthew Shenton Yusaku Uga Shiori Yabe Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice Rice Root Candidate gene search Genetic variation Association mapping Genome-wide association study Transcriptome-wide association study |
| title | Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice |
| title_full | Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice |
| title_fullStr | Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice |
| title_full_unstemmed | Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice |
| title_short | Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice |
| title_sort | genome and transcriptome wide association studies to discover candidate genes for diverse root phenotypes in cultivated rice |
| topic | Root Candidate gene search Genetic variation Association mapping Genome-wide association study Transcriptome-wide association study |
| url | https://doi.org/10.1186/s12284-023-00672-x |
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