Dataset Information

Deciphering Genetics Underlying Stable Anaerobic Germination in Rice: Phenotyping, QTL Identification, and Interaction Analysis.

ABSTRACT: Anaerobic germination (AG) is an important trait for direct-seeded rice (DSR) to be successful. Rice usually has low germination under anaerobic conditions, which leads to a poor crop stand in DSR when rain occurs after seeding. The ability of rice to germinate under water reduces the risk of poor crop stand. Further, this allows the use of water as a method of weed control. The identification of the genetic factors leading to high anaerobic germination is required to develop improved DSR varieties. In the present study, two BC1F2:3 mapping families involving a common parent with anaerobic germination potential, Kalarata, an indica landrace, and two recurrent parents, NSIC Rc222 and NSIC Rc238, were used. Phenotyping was done under two environmental conditions and genotyping was carried out through the KASP SNP genotyping platform. A total of 185 and 189 individuals genotyped with 170 and 179 polymorphic SNPs were used for QTL analysis for the two populations, Kalarata/NSIC Rc238 and Kalarata/NSIC Rc222, respectively. A total of five QTLs on chromosomes 3, 5, 6, 7, and 8 for survival (SUR) and four QTLs on chromosomes 1, 3 (two locations), and 7 for the trait seedling height (SH) across the populations and over the screening conditions were identified. Except for the QTLs on chromosomes 5 and 8, the parent with AG potential, Kalarata, contributed all the other QTLs. Among the five QTLs for SUR, the second-largest QTL (qSUR6-1) was novel for AG potential in rice, showing a stable expression in terms of genetic background and screening conditions explaining 11.96% to 16.01% of the phenotypic variation. The QTL for SH (qSH1-1) was also novel. Considering different genetic backgrounds and different screening conditions, the QTLs identified for the trait SUR explained phenotypic variation in the range of 57.60% to 73.09% while that for the trait SH ranged from 13.53% to 34.30%.

SUBMITTER: Ghosal S

PROVIDER: S-EPMC6629739 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Deciphering Genetics Underlying Stable Anaerobic Germination in Rice: Phenotyping, QTL Identification, and Interaction Analysis.

Ghosal Sharmistha S Casal Carlos C Quilloy Fergie Ann FA Septiningsih Endang M EM Mendioro Merlyn S MS Dixit Shalabh S

Rice (New York, N.Y.) 20190715 1

Anaerobic germination (AG) is an important trait for direct-seeded rice (DSR) to be successful. Rice usually has low germination under anaerobic conditions, which leads to a poor crop stand in DSR when rain occurs after seeding. The ability of rice to germinate under water reduces the risk of poor crop stand. Further, this allows the use of water as a method of weed control. The identification of the genetic factors leading to high anaerobic germination is required to develop improved DSR variet ...[more]

PMID: 31309351

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Project description:Rice seeds germinating in flooded soils encounter hypoxia or even anoxia leading to poor seed germination and crop establishment. Introgression of AG1 and AG2 QTLs associated with tolerance of flooding during germination, together with seed pre-treatment via hydro-priming or presoaking can enhance germination and seedling growth in anaerobic soils. This study assessed the performance of elite lines incorporating AG1, AG2 and their combination when directly seeded in flooded soils using dry seeds. The QTLs were in the background of two popular varieties PSB Rc82 and Ciherang-Sub1, evaluated along with the donors Kho Hlan On (AG1) and Ma-Zhan Red (AG2) and recipient parents PSB Rc82 and Ciherang-Sub1. In one set of experiments conducted in the greenhouse, seedling emergence, growth, and carbohydrate mobilization from seeds were assessed. Metabolites associated with reactive oxygen species (ROS) scavenging including malondialdehyde (MDA) as a measure of lipid peroxidation, ascorbate, total phenolic concentration (TPC), and activities of ROS scavenging enzymes were quantified in seeds germinating under control (saturated) and flooded (10 cm) soils. In another set of experiments conducted in a natural field with 3-5 cm flooding depths, control and pretreated seeds of Ciherang-Sub1 introgression lines and checks were used. Flooding reduced seedling emergence of all genotypes, though emergence of AG1 + AG2 introgression lines was greater than the other AG lines. Soluble sugars increased, while starch concentration decreased gradually under flooding especially in the tolerant checks and in AG1 + AG2 introgression lines. Less lipid peroxidation and higher α-amylase activity, higher ascorbate (RAsA) and TPC were observed in the tolerant checks and in the AG1 + AG2 introgression lines. Lipid peroxidation correlated negatively with ascorbate, TPC, and with ROS scavengers. Seed hydro-priming or pre-soaking increased emergence by 7-10% over that of dry seeds. Introgression of AG2 and AG1 + AG2 QTLs with seed pretreatment showed 101-153% higher emergence over dry seeds of intolerant genotypes in the field. Lines carrying AG1 + AG2 QTLs showed higher α-amylase activity, leading to rapid starch degradation and increase in soluble sugars, ascorbate, and TPC, together leading to higher germination and seedling growth in flooded soils. Seed hydro-priming or pre-soaking for 24 h also improved traits associated with flooding tolerance. Combining tolerance with seed management could therefore, improve crop establishment in flooded soils and encourage large-scale adoption of direct seeded rice system.

Project description:The rising cost of transplanting rice has made direct seeding an affordable alternative for rice establishment, particularly in Africa. However, direct seeding, while cost-effective, faces crop establishment challenges due to flooding. Uncontrolled water, driven by erratic rains in low-lying areas or uneven fields, limit germination. Rice possesses the unique ability of anaerobic germination, enabling it to sprout and emerge in oxygen-deprived conditions. Understanding rice's response to anaerobic stress during germination is crucial for resilience breeding. Africa, although relying on direct seeding, has made limited progress in addressing flooding during germination compared to Asia. Anaerobic stress tolerance ensures successful crop emergence even in oxygen-limited environments and can help suppress weeds, a significant challenge in direct-seeded rice cultivation. This study aims to contribute by screening for potential rice donors exhibiting anaerobic stress tolerance. We screened 200 rice genotypes at Sokoine University of Agriculture (SUA) in Morogoro, Tanzania, primarily focusing on landraces with untapped potential. Using an alpha lattice design, we conducted two anaerobic experiments in September and October 2022, adding 7 cm of standing water immediately after dry seeding for flooded and maintaining a 2 cm water level after germination in the control for duration of 21 days. We identified potential donors based on selection index computed from genomic estimated breeding values (GEBVs) using eight variables: germination at 14 DAS, germination at 21 DAS, seedling height at 14 DAS, seedling height at 21 DAS, shoot dry matter at 21 DAS, root dry matter at 21 DAS, culm diameter at 21 DAS, and root length at 21DAS. Ten genotypes emerged as the most promising, exhibiting at least 70% germination in floodwater at 21 DAS and greater selection indices. These genotypes were like: Afaa Mwanza 1/159, Rojomena 271/10, Kubwa Jinga, Wahiwahi, Magongo ya Wayungu, Mpaka wa Bibi, Mwangaza, Tarabinzona, IB126-Bug 2013A, and Kanamalia with respective percentages of 75, 74, 71, 86, 75, 80, 71, 80, 70, and 73. These findings contribute to global efforts to mitigate the impacts of flooding during germination. These donors, will be potential to enrich the gene pool for anaerobic germination, providing valuable resources for breeding for flooding tolerance.

Dataset Information

Deciphering Genetics Underlying Stable Anaerobic Germination in Rice: Phenotyping, QTL Identification, and Interaction Analysis.

Publications

Deciphering Genetics Underlying Stable Anaerobic Germination in Rice: Phenotyping, QTL Identification, and Interaction Analysis.

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