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Original article
Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel
Arvind Kumar
International Rice Research Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5488-9410
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at Rice.
Background
Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers.
Results
The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought.
Conclusion
These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
Keywords
Reproductive-stage drought, rice, genetic diversity, association mapping, quantitative trait loci
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CURRENT STATUS: Published
Version 2
Posted 23 Jun, 2020
Published
On 06 Aug, 2020
No community comments so far
Editorial decision: Accept
On 01 Jul, 2020
Review #1 received
Received 28 Jun, 2020
Reviewer #1 agreed
On 24 Jun, 2020
Editor assigned
On 22 Jun, 2020
Reviewers invited
Invitations sent on 22 Jun, 2020
Submission checks complete
On 21 Jun, 2020
Editor invited
On 21 Jun, 2020
No comments provided
Editorial decision: Minor revision
On 09 Jun, 2020
Review #2 received
Received 03 Jun, 2020
Review #1 received
Received 18 May, 2020
Reviewer #2 agreed
On 14 May, 2020
Reviewer #1 agreed
On 11 May, 2020
Reviewers invited
Invitations sent on 07 May, 2020
Editor assigned
On 03 May, 2020
First submitted
On 02 May, 2020
Submission checks complete
On 02 May, 2020
Editor invited
On 02 May, 2020
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This preprint is under consideration at Rice. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Original article
Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel
Arvind Kumar
International Rice Research Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0002-5488-9410
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 2
Posted 23 Jun, 2020
Published
On 06 Aug, 2020
No community comments so far
Editorial decision: Accept
On 01 Jul, 2020
Review #1 received
Received 28 Jun, 2020
Reviewer #1 agreed
On 24 Jun, 2020
Editor assigned
On 22 Jun, 2020
Reviewers invited
Invitations sent on 22 Jun, 2020
Submission checks complete
On 21 Jun, 2020
Editor invited
On 21 Jun, 2020
No comments provided
Editorial decision: Minor revision
On 09 Jun, 2020
Review #2 received
Received 03 Jun, 2020
Review #1 received
Received 18 May, 2020
Reviewer #2 agreed
On 14 May, 2020
Reviewer #1 agreed
On 11 May, 2020
Reviewers invited
Invitations sent on 07 May, 2020
Editor assigned
On 03 May, 2020
First submitted
On 02 May, 2020
Submission checks complete
On 02 May, 2020
Editor invited
On 02 May, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at Rice.
Background
Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers.
Results
The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought.
Conclusion
These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9