Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice
In this study, we used 2.9 million single nucleotide polymorphisms (SNP) and 393,429 indels derived from whole genome sequences of 591 rice landraces to determine the genetic basis of cooked and raw grain length, width and shape using genome-wide association study (GWAS). We identified a unique fine...
| Autores principales: | , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2017
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| Acceso en línea: | https://hdl.handle.net/10568/164990 |
| _version_ | 1855517863248396288 |
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| author | Misra, Gopal Badoni, Saurabh Anacleto, Roslen Graner, Andreas Alexandrov, Nickolai Sreenivasulu, Nese |
| author_browse | Alexandrov, Nickolai Anacleto, Roslen Badoni, Saurabh Graner, Andreas Misra, Gopal Sreenivasulu, Nese |
| author_facet | Misra, Gopal Badoni, Saurabh Anacleto, Roslen Graner, Andreas Alexandrov, Nickolai Sreenivasulu, Nese |
| author_sort | Misra, Gopal |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | In this study, we used 2.9 million single nucleotide polymorphisms (SNP) and 393,429 indels derived from whole genome sequences of 591 rice landraces to determine the genetic basis of cooked and raw grain length, width and shape using genome-wide association study (GWAS). We identified a unique fine-mapped genetic region GWi7.1 significantly associated with cooked and raw grain width. Additionally, GWi7.2 that harbors GL7/GW7 a cloned gene for grain dimension was found. Novel regions in chromosomes 10 and 11 were also found to be associated with cooked grain shape and raw grain width, respectively. The indel-based GWAS identified fine-mapped genetic regions GL3.1 and GWi5.1 that matched synteny breakpoints between indica and japonica. GL3.1 was positioned a few kilobases away from GS3, a cloned gene for cooked and raw grain lengths in indica. GWi5.1 found to be significantly associated with cooked and raw grain width. It anchors upstream of cloned gene GW5, which varied between indica and japonica accessions. GWi11.1 is present inside the 3′-UTR of a functional gene in indica that corresponds to a syntenic break in chromosome 11 of japonica. Our results identified novel allelic structural variants and haplotypes confirmed using single locus and multilocus SNP and indel-based GWAS. |
| format | Journal Article |
| id | CGSpace164990 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1649902024-12-19T14:12:04Z Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice Misra, Gopal Badoni, Saurabh Anacleto, Roslen Graner, Andreas Alexandrov, Nickolai Sreenivasulu, Nese In this study, we used 2.9 million single nucleotide polymorphisms (SNP) and 393,429 indels derived from whole genome sequences of 591 rice landraces to determine the genetic basis of cooked and raw grain length, width and shape using genome-wide association study (GWAS). We identified a unique fine-mapped genetic region GWi7.1 significantly associated with cooked and raw grain width. Additionally, GWi7.2 that harbors GL7/GW7 a cloned gene for grain dimension was found. Novel regions in chromosomes 10 and 11 were also found to be associated with cooked grain shape and raw grain width, respectively. The indel-based GWAS identified fine-mapped genetic regions GL3.1 and GWi5.1 that matched synteny breakpoints between indica and japonica. GL3.1 was positioned a few kilobases away from GS3, a cloned gene for cooked and raw grain lengths in indica. GWi5.1 found to be significantly associated with cooked and raw grain width. It anchors upstream of cloned gene GW5, which varied between indica and japonica accessions. GWi11.1 is present inside the 3′-UTR of a functional gene in indica that corresponds to a syntenic break in chromosome 11 of japonica. Our results identified novel allelic structural variants and haplotypes confirmed using single locus and multilocus SNP and indel-based GWAS. 2017-09-29 2024-12-19T12:54:35Z 2024-12-19T12:54:35Z Journal Article https://hdl.handle.net/10568/164990 en Open Access Springer Misra, Gopal; Badoni, Saurabh; Anacleto, Roslen; Graner, Andreas; Alexandrov, Nickolai and Sreenivasulu, Nese. 2017. Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice. Sci Rep, Volume 7, no. 1 |
| spellingShingle | Misra, Gopal Badoni, Saurabh Anacleto, Roslen Graner, Andreas Alexandrov, Nickolai Sreenivasulu, Nese Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice |
| title | Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice |
| title_full | Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice |
| title_fullStr | Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice |
| title_full_unstemmed | Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice |
| title_short | Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice |
| title_sort | whole genome sequencing based association study to unravel genetic architecture of cooked grain width and length traits in rice |
| url | https://hdl.handle.net/10568/164990 |
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