Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness
Rice varieties whose quality is graded as excellent have a lower percent grain chalkiness (PGC) of two per cent and below with higher whole grain yields upon milling, leading to higher economic returns for farmers. We have conducted a genome‐wide association study (GWAS) using a combined population...
| Autores principales: | , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2021
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164385 |
| _version_ | 1855519107303079936 |
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| author | Misra, Gopal Badoni, Saurabh Parween, Sabiha Singh, Rakesh Kumar Leung, Hei Ladejobi, OluFunmilayo Mott, Richard Sreenivasulu, Nese |
| author_browse | Badoni, Saurabh Ladejobi, OluFunmilayo Leung, Hei Misra, Gopal Mott, Richard Parween, Sabiha Singh, Rakesh Kumar Sreenivasulu, Nese |
| author_facet | Misra, Gopal Badoni, Saurabh Parween, Sabiha Singh, Rakesh Kumar Leung, Hei Ladejobi, OluFunmilayo Mott, Richard Sreenivasulu, Nese |
| author_sort | Misra, Gopal |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Rice varieties whose quality is graded as excellent have a lower percent grain chalkiness (PGC) of two per cent and below with higher whole grain yields upon milling, leading to higher economic returns for farmers. We have conducted a genome‐wide association study (GWAS) using a combined population panel of indica and japonica rice varieties, and identified a total of 746 single nucleotide polymorphisms (SNPs) that were strongly associated with the chalk phenotype, covered 78 Quantitative Trait Loci (QTL) regions. Among them, 21 were high‐value QTLs, as they explained at least 10 % of the phenotypic variance for PGC. A combined epistasis and GWAS was applied to dissect the genetics of the complex chalkiness trait, and its regulatory cascades were validated using gene regulatory networks. Promising novel epistatic interactions were found between the loci of chromosomes 6 (PGC6.1) and 7 (PGC7.8) that contributed to lower PGC. Based on haplotype mining only a few modern rice varieties confounded with a lower chalkiness, and they possess several PGC QTLs. The importance of PGC6.1 was validated through multi‐parent advanced generation intercrosses and several low‐chalk lines possessing superior haplotypes were identified. The results of this investigation have deciphered the underlying genetic networks that can reduce PGC to 2%, and will thus support future breeding programs to improve the grain quality of elite genetic material with high‐yielding potentials. |
| format | Journal Article |
| id | CGSpace164385 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1643852024-12-22T05:44:47Z Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness Misra, Gopal Badoni, Saurabh Parween, Sabiha Singh, Rakesh Kumar Leung, Hei Ladejobi, OluFunmilayo Mott, Richard Sreenivasulu, Nese agronomy crop science biotechnology plant science Rice varieties whose quality is graded as excellent have a lower percent grain chalkiness (PGC) of two per cent and below with higher whole grain yields upon milling, leading to higher economic returns for farmers. We have conducted a genome‐wide association study (GWAS) using a combined population panel of indica and japonica rice varieties, and identified a total of 746 single nucleotide polymorphisms (SNPs) that were strongly associated with the chalk phenotype, covered 78 Quantitative Trait Loci (QTL) regions. Among them, 21 were high‐value QTLs, as they explained at least 10 % of the phenotypic variance for PGC. A combined epistasis and GWAS was applied to dissect the genetics of the complex chalkiness trait, and its regulatory cascades were validated using gene regulatory networks. Promising novel epistatic interactions were found between the loci of chromosomes 6 (PGC6.1) and 7 (PGC7.8) that contributed to lower PGC. Based on haplotype mining only a few modern rice varieties confounded with a lower chalkiness, and they possess several PGC QTLs. The importance of PGC6.1 was validated through multi‐parent advanced generation intercrosses and several low‐chalk lines possessing superior haplotypes were identified. The results of this investigation have deciphered the underlying genetic networks that can reduce PGC to 2%, and will thus support future breeding programs to improve the grain quality of elite genetic material with high‐yielding potentials. 2021-05 2024-12-19T12:53:50Z 2024-12-19T12:53:50Z Journal Article https://hdl.handle.net/10568/164385 en Open Access Wiley Misra, Gopal; Badoni, Saurabh; Parween, Sabiha; Singh, Rakesh Kumar; Leung, Hei; Ladejobi, OluFunmilayo; Mott, Richard and Sreenivasulu, Nese. 2021. Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness. Plant Biotechnology Journal, Volume 19 no. 5 p. 910-925 |
| spellingShingle | agronomy crop science biotechnology plant science Misra, Gopal Badoni, Saurabh Parween, Sabiha Singh, Rakesh Kumar Leung, Hei Ladejobi, OluFunmilayo Mott, Richard Sreenivasulu, Nese Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness |
| title | Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness |
| title_full | Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness |
| title_fullStr | Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness |
| title_full_unstemmed | Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness |
| title_short | Genome-wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness |
| title_sort | genome wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness |
| topic | agronomy crop science biotechnology plant science |
| url | https://hdl.handle.net/10568/164385 |
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