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Open AccessArticle

Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress

1
Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
2
Center of Excellence in Environment and Plant Physiology, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
3
Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
4
Nakohn Ratchasima Rice Research Center, Rice Department, Ministry of Agriculture and Cooperative, Nakohn Ratchasima 30110, Thailand
5
Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
6
Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
7
Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
Genes 2019, 10(8), 562; https://doi.org/10.3390/genes10080562
Received: 15 June 2019 / Revised: 23 July 2019 / Accepted: 23 July 2019 / Published: 25 July 2019
(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)
Unfavourable environmental conditions, including soil salinity, lead to decreased rice (Oryza sativa L.) productivity, especially at the reproductive stage. In this study, we examined 30 rice varieties, which revealed significant differences in the photosynthetic performance responses under salt stress conditions during the reproductive stage, which ultimately affected yield components after recovery. In rice with a correlation between net photosynthetic rate (PN) and intercellular CO2 concentration (Ci) under salt stress, PN was found to be negatively correlated with filled grain number after recovery. Applying stringent criteria, we identified 130,317 SNPs and 15,396 InDels between two “high-yield rice” varieties and two “low-yield rice” varieties with contrasting photosynthesis and grain yield characteristics. A total of 2089 genes containing high- and moderate-impact SNPs or InDels were evaluated by gene ontology (GO) enrichment analysis, resulting in over-represented terms in the apoptotic process and kinase activity. Among these genes, 262 were highly expressed in reproductive tissues, and most were annotated as receptor-like protein kinases. These findings highlight the importance of variations in signaling components in the genome and these loci can serve as potential genes in rice breeding to produce a variety with salt avoidance that leads to increased yield in saline soil. View Full-Text
Keywords: genome; Oryza sativa L.; photosynthesis; salinity; yield genome; Oryza sativa L.; photosynthesis; salinity; yield
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Lekklar, C.; Suriya-arunroj, D.; Pongpanich, M.; Comai, L.; Kositsup, B.; Chadchawan, S.; Buaboocha, T. Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress. Genes 2019, 10, 562.

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