New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study
Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to...
| Autores principales: | , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2024
|
| Acceso en línea: | https://hdl.handle.net/10568/163835 |
| _version_ | 1855522266387841024 |
|---|---|
| author | Sachdeva, Supriya Singh, Rakesh Maurya, Avantika Singh, Vikas K. Singh, Uma Maheshwar Kumar, Arvind Singh, Gyanendra Pratap |
| author_browse | Kumar, Arvind Maurya, Avantika Sachdeva, Supriya Singh, Gyanendra Pratap Singh, Rakesh Singh, Uma Maheshwar Singh, Vikas K. |
| author_facet | Sachdeva, Supriya Singh, Rakesh Maurya, Avantika Singh, Vikas K. Singh, Uma Maheshwar Kumar, Arvind Singh, Gyanendra Pratap |
| author_sort | Sachdeva, Supriya |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield. Results Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield. Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties. |
| format | Journal Article |
| id | CGSpace163835 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1638352025-05-14T10:24:02Z New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study Sachdeva, Supriya Singh, Rakesh Maurya, Avantika Singh, Vikas K. Singh, Uma Maheshwar Kumar, Arvind Singh, Gyanendra Pratap Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield. Results Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield. Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties. 2024-02-20 2024-12-19T12:53:04Z 2024-12-19T12:53:04Z Journal Article https://hdl.handle.net/10568/163835 en Open Access Springer Sachdeva, Supriya; Singh, Rakesh; Maurya, Avantika; Singh, Vikas K; Singh, Uma Maheshwar; Kumar, Arvind and Singh, Gyanendra Pratap. 2024. New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study. BMC Plant Biol, Volume 24, no. 1 |
| spellingShingle | Sachdeva, Supriya Singh, Rakesh Maurya, Avantika Singh, Vikas K. Singh, Uma Maheshwar Kumar, Arvind Singh, Gyanendra Pratap New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study |
| title | New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study |
| title_full | New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study |
| title_fullStr | New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study |
| title_full_unstemmed | New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study |
| title_short | New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study |
| title_sort | new insights into qtns and potential candidate genes governing rice yield via a multi model genome wide association study |
| url | https://hdl.handle.net/10568/163835 |
| work_keys_str_mv | AT sachdevasupriya newinsightsintoqtnsandpotentialcandidategenesgoverningriceyieldviaamultimodelgenomewideassociationstudy AT singhrakesh newinsightsintoqtnsandpotentialcandidategenesgoverningriceyieldviaamultimodelgenomewideassociationstudy AT mauryaavantika newinsightsintoqtnsandpotentialcandidategenesgoverningriceyieldviaamultimodelgenomewideassociationstudy AT singhvikask newinsightsintoqtnsandpotentialcandidategenesgoverningriceyieldviaamultimodelgenomewideassociationstudy AT singhumamaheshwar newinsightsintoqtnsandpotentialcandidategenesgoverningriceyieldviaamultimodelgenomewideassociationstudy AT kumararvind newinsightsintoqtnsandpotentialcandidategenesgoverningriceyieldviaamultimodelgenomewideassociationstudy AT singhgyanendrapratap newinsightsintoqtnsandpotentialcandidategenesgoverningriceyieldviaamultimodelgenomewideassociationstudy |