Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice
Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2017-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2017.00807/full |
| _version_ | 1819031632933289984 |
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| author | Anurag V. Daware Rishi Srivastava Ashok K. Singh Swarup K. Parida Akhilesh K. Tyagi Akhilesh K. Tyagi |
| author_facet | Anurag V. Daware Rishi Srivastava Ashok K. Singh Swarup K. Parida Akhilesh K. Tyagi Akhilesh K. Tyagi |
| author_sort | Anurag V. Daware |
| collection | DOAJ |
| description | Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs. Therefore, combined use of QTL and association mapping strategies can provide advantages associated with both these methods. In the current study, we utilized meta-analysis approach to identify metaQTLs associated with grain size/weight in diverse Indian indica and aromatic rice accessions. Subsequently, attempt has been made to narrow-down identified grain size/weight metaQTLs through individual SNP- as well as haplotype-based regional association analysis. The study identified six different metaQTL regions, three of which were successfully revalidated, and substantially scaled-down along with GS3 QTL interval (positive control) by regional association analysis. Consequently, two potential candidate genes within two reduced metaQTLs were identified based on their differential expression profiles in different tissues/stages of rice accessions during seed development. The developed strategy has broader practical utility for rapid delineation of candidate genes and natural alleles underlying QTLs associated with complex agronomic traits in rice as well as major crop plants enriched with useful genetic and genomic information. |
| first_indexed | 2024-12-21T06:49:09Z |
| format | Article |
| id | doaj.art-080da4f2b0c2489d91de638775aaca0b |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T06:49:09Z |
| publishDate | 2017-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-080da4f2b0c2489d91de638775aaca0b2022-12-21T19:12:31ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2017-05-01810.3389/fpls.2017.00807260976Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in RiceAnurag V. Daware0Rishi Srivastava1Ashok K. Singh2Swarup K. Parida3Akhilesh K. Tyagi4Akhilesh K. Tyagi5National Institute of Plant Genome ResearchNew Delhi, IndiaNational Institute of Plant Genome ResearchNew Delhi, IndiaDivision of Genetics, Indian Agricultural Research InstituteNew Delhi, IndiaNational Institute of Plant Genome ResearchNew Delhi, IndiaNational Institute of Plant Genome ResearchNew Delhi, IndiaDepartment of Plant Molecular Biology, University of Delhi South CampusNew Delhi, IndiaMolecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs. Therefore, combined use of QTL and association mapping strategies can provide advantages associated with both these methods. In the current study, we utilized meta-analysis approach to identify metaQTLs associated with grain size/weight in diverse Indian indica and aromatic rice accessions. Subsequently, attempt has been made to narrow-down identified grain size/weight metaQTLs through individual SNP- as well as haplotype-based regional association analysis. The study identified six different metaQTL regions, three of which were successfully revalidated, and substantially scaled-down along with GS3 QTL interval (positive control) by regional association analysis. Consequently, two potential candidate genes within two reduced metaQTLs were identified based on their differential expression profiles in different tissues/stages of rice accessions during seed development. The developed strategy has broader practical utility for rapid delineation of candidate genes and natural alleles underlying QTLs associated with complex agronomic traits in rice as well as major crop plants enriched with useful genetic and genomic information.http://journal.frontiersin.org/article/10.3389/fpls.2017.00807/fullgrain sizegrain weightmetaQTLQTL mappingregional association mappingrice |
| spellingShingle | Anurag V. Daware Rishi Srivastava Ashok K. Singh Swarup K. Parida Akhilesh K. Tyagi Akhilesh K. Tyagi Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice Frontiers in Plant Science grain size grain weight metaQTL QTL mapping regional association mapping rice |
| title | Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice |
| title_full | Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice |
| title_fullStr | Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice |
| title_full_unstemmed | Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice |
| title_short | Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice |
| title_sort | regional association analysis of metaqtls delineates candidate grain size genes in rice |
| topic | grain size grain weight metaQTL QTL mapping regional association mapping rice |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2017.00807/full |
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