Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice
Direct seeding is considered an efficient cultivation technology that reduces water use and labor costs. Mesocotyl length is one of the significant traits in cultivation; long mesocotyl is beneficial for the rate and uniformity of seedling emergence. In this study, we used a core collection of 137 r...
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MDPI AG
2021-12-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/11/12/2527 |
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| author | Seong-Gyu Jang So-Yeon Park San Mar Lar Hongjia Zhang Ah-Rim Lee Fang-Yuan Cao Jeonghwan Seo Tae-Ho Ham Joohyun Lee Soon-Wook Kwon |
| author_facet | Seong-Gyu Jang So-Yeon Park San Mar Lar Hongjia Zhang Ah-Rim Lee Fang-Yuan Cao Jeonghwan Seo Tae-Ho Ham Joohyun Lee Soon-Wook Kwon |
| author_sort | Seong-Gyu Jang |
| collection | DOAJ |
| description | Direct seeding is considered an efficient cultivation technology that reduces water use and labor costs. Mesocotyl length is one of the significant traits in cultivation; long mesocotyl is beneficial for the rate and uniformity of seedling emergence. In this study, we used a core collection of 137 rice accessions to identify quantitative trait loci (QTL) for mesocotyl elongation. A genome-wide association study (GWAS), combined with a principal component analysis (PCA) and a kinship matrix analysis, was conducted for the genotype analysis of 2 million, high-quality single nucleotide polymorphisms (SNPs). Through this GWAS analysis, 11 lead SNPs were confirmed to be associated with mesocotyl length, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Based on the gene expression database and haplotype analysis, five candidate genes (<i>Os01g0269800</i>, <i>Os01g0731100</i>, <i>Os08g0136700</i>, <i>Os08g0137800,</i> and <i>Os08g0137900</i>) were detected to be significantly associated with phenotypic variation. Five candidate gene expressions are reported to be associated with various plant hormone responses. Interestingly, two biotic stress response genes and two copper-containing redox proteins were detected as the candidate genes. The results of this study provide associated SNPs in candidate genes for mesocotyl length and strategies for developing direct seeding in breeding programs. |
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| language | English |
| last_indexed | 2024-03-10T04:41:01Z |
| publishDate | 2021-12-01 |
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| series | Agronomy |
| spelling | doaj.art-e5be5bafce2748fbb32e2b8a97e3699d2023-11-23T03:23:17ZengMDPI AGAgronomy2073-43952021-12-011112252710.3390/agronomy11122527Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in RiceSeong-Gyu Jang0So-Yeon Park1San Mar Lar2Hongjia Zhang3Ah-Rim Lee4Fang-Yuan Cao5Jeonghwan Seo6Tae-Ho Ham7Joohyun Lee8Soon-Wook Kwon9Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, KoreaDepartment of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, KoreaDepartment of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, KoreaDepartment of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, KoreaDepartment of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, KoreaDepartment of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, KoreaDepartment of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, KoreaDepartment of Crop Science, Konkuk University, Seoul 05029, KoreaDepartment of Crop Science, Konkuk University, Seoul 05029, KoreaDepartment of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang 50463, KoreaDirect seeding is considered an efficient cultivation technology that reduces water use and labor costs. Mesocotyl length is one of the significant traits in cultivation; long mesocotyl is beneficial for the rate and uniformity of seedling emergence. In this study, we used a core collection of 137 rice accessions to identify quantitative trait loci (QTL) for mesocotyl elongation. A genome-wide association study (GWAS), combined with a principal component analysis (PCA) and a kinship matrix analysis, was conducted for the genotype analysis of 2 million, high-quality single nucleotide polymorphisms (SNPs). Through this GWAS analysis, 11 lead SNPs were confirmed to be associated with mesocotyl length, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Based on the gene expression database and haplotype analysis, five candidate genes (<i>Os01g0269800</i>, <i>Os01g0731100</i>, <i>Os08g0136700</i>, <i>Os08g0137800,</i> and <i>Os08g0137900</i>) were detected to be significantly associated with phenotypic variation. Five candidate gene expressions are reported to be associated with various plant hormone responses. Interestingly, two biotic stress response genes and two copper-containing redox proteins were detected as the candidate genes. The results of this study provide associated SNPs in candidate genes for mesocotyl length and strategies for developing direct seeding in breeding programs.https://www.mdpi.com/2073-4395/11/12/2527genome-wide association study (GWAS)mesocotyl lengthhaplotyperice |
| spellingShingle | Seong-Gyu Jang So-Yeon Park San Mar Lar Hongjia Zhang Ah-Rim Lee Fang-Yuan Cao Jeonghwan Seo Tae-Ho Ham Joohyun Lee Soon-Wook Kwon Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice Agronomy genome-wide association study (GWAS) mesocotyl length haplotype rice |
| title | Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice |
| title_full | Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice |
| title_fullStr | Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice |
| title_full_unstemmed | Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice |
| title_short | Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice |
| title_sort | genome wide association study gwas of mesocotyl length for direct seeding in rice |
| topic | genome-wide association study (GWAS) mesocotyl length haplotype rice |
| url | https://www.mdpi.com/2073-4395/11/12/2527 |
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