Malik, P and Huang, M and Neelam, K and Bhatia, D and Kaur, R and Yadav, B and Singh, J and Sneller, C and Singh, K (2022) Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions. Rice, 15. pp. 1-23. ISSN 1939-8433
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Abstract
Being one of the most important staple dietary constituents globally, genetic enhancement of cultivated rice for yield, agronomically important traits is of substantial importance. Even though the climatic factors and crop management practices impact complex traits like yield immensely, the contribution of variation by underlying genetic factors surpasses them all. Previous studies have highlighted the importance of utilizing exotic germplasm, landraces in enhancing the diversity of gene pool, leading to better selections and thus superior cultivars. Thus, to fully exploit the potential of progenitor of Asian cultivated rice for productivity related traits, genome wide association study (GWAS) for seven agronomically important traits was conducted on a panel of 346 O. rufipogon accessions using a set of 15,083 high-quality single nucleotide polymorphic markers. The phenotypic data analysis indicated large continuous variation for all the traits under study, with a significant negative correlation observed between grain parameters and agronomic parameters like plant height, culm thickness. The presence of 74.28% admixtures in the panel as revealed by investigating population structure indicated the panel to be very poorly genetically differentiated, with rapid LD decay. The genome-wide association analyses revealed a total of 47 strong MTAs with 19 SNPs located in/close to previously reported QTL/genic regions providing a positive analytic proof for our studies. The allelic differences of significant MTAs were found to be statistically significant at 34 genomic regions. A total of 51 O. rufipogon accessions harboured combination of superior alleles and thus serve as potential candidates for accelerating rice breeding programs. The present study identified 27 novel SNPs to be significantly associated with different traits. Allelic differences between cultivated and wild rice at significant MTAs determined superior alleles to be absent at 12 positions implying substantial scope of improvement by their targeted introgression into cultivars. Introgression of novel significant genomic regions into breeder’s pool would broaden the genetic base of cultivated rice, thus making the crop more resilient.
| Item Type: | Article |
|---|---|
| Divisions: | Genebank |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | Oryza rufipogon, Population structure, Productivity related traits, SNP tagging, Genome-wide association study, Minimum Bayes Factor, LD decay, Gene annotation |
| Subjects: | Others > Rice |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 12 Mar 2024 06:18 |
| Last Modified: | 12 Mar 2024 06:18 |
| URI: | http://oar.icrisat.org/id/eprint/12566 |
| Official URL: | https://link.springer.com/article/10.1186/s12284-0... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | The authors thankfully acknowledge the financial support provided by Bayer Beachell- Borlaug International Scholarship Program (BBISP), formerly known as Monsanto Beachell-Borlaug International Scholarship Program (MBBISP) for carrying out the research. The authors also thank Ohio Supercomputer Center (OSC) for providing computational resources. The authors are grateful to Late Dr. Darshan Singh Brar, Adjunct Professor, Punjab Agricultural University for his inputs and discussions. The authors also express their thanks to Dr. Parveen Chhuneja and Dr. Yogesh Vikal for their feedback. |
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