Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 22, Issue 9, Pages -Publisher
MDPI
DOI: 10.3390/ijms22094445
Keywords
anaerobic germination; AG2; candidate genes; enriched haplotype GWAS; rice (Oryza sativa); transcriptomics
Funding
- German Federal Ministry of Economic Cooperation and Development (BMZ) [81157485]
- Texas A&M graduate research assistantship
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A novel approach combining haplotype genome-wide association study successfully narrowed down the AG2 gene region and identified 27 candidate genes potentially controlling AG2, including the Rc gene responsible for red pericarp development. Transcriptome analysis revealed differential regulation of sugar metabolism, cell wall modification, and chloroplast development to be implicated in AG tolerance mechanisms.
Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize AG2 (qAG7.1), a major centromere-spanning AG tolerance QTL, derived from the indica variety Ma-Zhan Red, have failed. Here, a novel approach of enriched haplotype genome-wide association study based on the Ma-Zhan Red haplotype in the AG2 region was successfully used to narrow down AG2 from more than 7 Mb to less than 0.7 Mb. The AG2 peak region contained 27 genes, including the Rc gene, responsible for red pericarp development in pigmented rice. Through comparative variant and transcriptome analysis between AG tolerant donors and susceptible accessions several candidate genes potentially controlling AG2 were identified, among them several regulatory genes. Genome-wide comparative transcriptome analysis suggested differential regulation of sugar metabolism, particularly trehalose metabolism, as well as differential regulation of cell wall modification and chloroplast development to be implicated in AG tolerance mechanisms.
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