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Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice
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Journal article
Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice
International Journal of Molecular Sciences, Vol.22(9), 4445
24/04/2021
PMID: 33923150
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Abstract
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
(
), 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
region was successfully used to narrow down
from more than 7 Mb to less than 0.7 Mb. The
peak region contained 27 genes, including the
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
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.
Details
- Title
- Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice
- Creators
- Hedia Tnani (Author) - Université Tunis El ManarDmytro Chebotarov (Author) - International Rice Research Institute (Phillipines)Ranjita Thapa (Author) - Cornell UniversityJohn Carlos I Ignacio (Author) - The Ohio State UniversityWalter K Israel (Author) - Southern Cross UniversityFergie A Quilloy (Author) - International Rice Research Institute (Phillipines)Shalabh Dixit (Author) - International Rice Research Institute (Phillipines)Endang M Septiningsih (Author) - Texas A&M UniversityTobias Kretzschmar (Author) - Southern Cross University
- Publication Details
- International Journal of Molecular Sciences, Vol.22(9), 4445
- Publisher
- MDPI AG; Switzerland
- Grant note
- 81157485 / German Federal Ministry of Economic Cooperation and Development (BMZ)
- Identifiers
- 991012932297402368
- Copyright
- Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
- Academic Unit
- Faculty of Science and Engineering; Science; Southern Cross Plant Science
- Language
- English
- Resource Type
- Journal article