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Original article
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Background
Salinity is one of the main adverse environmental factors severely inhibiting rice growth and decreasing grain productivity. Developing rice varieties with salt tolerance (ST) is one of the most economical approaches to cope with salinity stress. However, the valuable resources for rice breeding towards ST remain to be identified. In this study, the salt tolerance of 220 rice accessions from RDP1, representing five subpopulations, were evaluated at both seedling and reproductive stages.
Results
An apparent inconsistency was found for ST between the two stages. Through a gene-based / tightly linked genome-wide association study, a total of 214 single nucleotide polymorphisms (SNPs) related to 251 genes, significantly associated with 16 ST-related indices, were detected at both stages. Eighty-two SNPs with low frequency favorable (LFF) alleles in the population were proposed to hold high breeding potential in improving rice ST. Fifty-four rice accessions collectively containing all these LFF alleles were identified as donors of these alleles. Through the integration of meta-QTL for ST and the response patterns of differential expression genes to salt stress, thirty-one candidate genes were suggested to be involved in the regulation of rice ST.
Conclusions
In total, the present study provides valuable information for further characterizing ST-related genes and for breeding ST varieties across whole developmental stages through marker-assisted selection (MAS).
Keywords
Oryza sativa L., Natural accessions, Salt tolerance, Developmental stages, Breeding utilization
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This is a preprint. It has not completed peer review.
Original article
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 13 Apr, 2021
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Plant Molecular Biology and Genetics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Salinity is one of the main adverse environmental factors severely inhibiting rice growth and decreasing grain productivity. Developing rice varieties with salt tolerance (ST) is one of the most economical approaches to cope with salinity stress. However, the valuable resources for rice breeding towards ST remain to be identified. In this study, the salt tolerance of 220 rice accessions from RDP1, representing five subpopulations, were evaluated at both seedling and reproductive stages.
Results
An apparent inconsistency was found for ST between the two stages. Through a gene-based / tightly linked genome-wide association study, a total of 214 single nucleotide polymorphisms (SNPs) related to 251 genes, significantly associated with 16 ST-related indices, were detected at both stages. Eighty-two SNPs with low frequency favorable (LFF) alleles in the population were proposed to hold high breeding potential in improving rice ST. Fifty-four rice accessions collectively containing all these LFF alleles were identified as donors of these alleles. Through the integration of meta-QTL for ST and the response patterns of differential expression genes to salt stress, thirty-one candidate genes were suggested to be involved in the regulation of rice ST.
Conclusions
In total, the present study provides valuable information for further characterizing ST-related genes and for breeding ST varieties across whole developmental stages through marker-assisted selection (MAS).
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
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