Identification of QTLs for tolerance to hypoxia during germination in rice

Kim, Suk‐Man; Reinke, Russell

doi:10.1007/s10681-018-2238-8

Cited by 24 publications

(23 citation statements)

References 28 publications

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“…Such unknown factor or regulatory mechanism could thus contribute to species-specific as well as to withinspecies adaptive variation of complex traits (Wray et al 2007). Kim and Reinke (2018), discovered three QTLs, associated with anaerobic germination tolerance. The percentage of variance ranges from 5.49 to 14.14 % and maximum anaerobic germination of tolerant germplasms is approximately 50 %.…”

Section: Discussionmentioning

confidence: 99%

Identification of novel hypoxia-responsive factors in deep-water rice conferring tolerance to flood during germination

Kumar¹,

Das²,

Sarmah³

2020

Biol. plant.

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Flood in rice fields at the time of seed sowing and early seedling establishment causes extensive crop loss due to the inability of the seeds to tolerate and overcome submergence. In the present study, rice genotypes from Assam, India tolerant to hypoxia during germination were identified through systematic screening of deep-water rice genotype collection from flood-prone ecosystem of Brahmaputra river valley. The difference in tolerance to hypoxia during germination within the species provides scope for identification of novel hypoxia-responsive factors involved in tolerance as mechanism of tolerance may not be conserved across tolerant germplasms. Tolerant genotypes were further subjected to physiological and molecular characterization. Growth rate kinetics in tolerant genotypes new Rangdhakekua bao (RKB) and cultivar Khao Hlan On (KHO) from International Rice Research Institute (IRRI) used as positive control exhibited stronger escape strategy under hypoxic condition compared to sensitive genotype IR-64 (negative control). Activities of α-amylase and pyruvate decarboxylase were significantly higher in RKB and KHO than in IR-64, while no significant difference was observed in the alcohol dehydrogenase activity. Reverse transcription quantitative PCR confirmed increased amounts of transcripts of sucrose nonfermenting 1 related protein kinase, myeloblastosis-related protein S1, rice amylase 3D, and trehalose phosphate phosphatase 7 genes, which are known to be involved in hypoxia signaling cascade. Besides, transcription factors (TFs) like ethylene responce factors 71 and 63, ethylene insensitive 3-like 1a and proteins like expansins A7 and A2, which are involved in cell elongation had also significantly higher amounts in RKB compared to IR-64. Additional factors that include TFs like ERF71 and ERF63 that shows perturbation at transcription even within tolerant genotypes might constitute the genotype-specific regulation, evolved as a part of its adaptive mechanism to survive under submerged conditions.

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Section: Discussionmentioning

confidence: 99%

Identification of novel hypoxia-responsive factors in deep-water rice conferring tolerance to flood during germination

Kumar¹,

Das²,

Sarmah³

2020

Biol. plant.

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“…Ten dry seeds from each line were sowed in 3.5 cm of fine soil and covered with 1 cm of commercial soil. The lines were evaluated under hypoxic conditions (Kim & Reinke, ) using a phytotron facility (25 ± 3°C, 70%–75% RH) and natural flooding conditions in a glass house (22–27°C, 50%–65% RH) (Septiningsih et al, ). To create the hypoxic condition in the water reservoir, nitrogen gas was bubbled until the dissolved oxygen (DO) content of the water became <4.0 ppm and the reservoir was sealed with transparent plastic to maintain the established DO condition.…”

Section: Methodsmentioning

confidence: 99%

“…A major QTL, qAG7 , for AG derived from an upland landrace from India, Nanhi, was detected with an LOD of 13.93 and explained 22.3% of the phenotypic variance. More recently, three QTLs associated with AG tolerance, qAG1a and qAG1b on chromosome 1 and qAG8 on chromosome 8, were identified in a population derived from a cross between Tai Nguyen and Anda using a 6K SNP chip and composite interval mapping (CIM) analysis (Kim & Reinke, ).…”

Section: Introductionmentioning

confidence: 99%

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Marker‐assisted breeding for improvement of anaerobic germination in japonica rice (Oryza sativa)

Kim

Jeong

et al. 2019

Plant Breeding

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Direct seeding is increasingly being practiced in rice cultivation areas because it saves labour and reduces cost of production and management. In this study, four japonica‐type breeding lines were developed from a cross of a japonica cultivar and an AG‐tolerant donor, KHO, using marker‐assisted selection. Validation of the target genes AG1 and AG2 in the selected lines was examined by PCR analysis and the background recovery rate by the recurrent parent was confirmed by genotyping using a 6K SNP chip. Compared to the recurrent, the survival rates of the selected lines were improved in a range from 33% to 115% in three conditions; in particular, the survival rate was increased in more than twice that of the recurrent parent under the hypoxic condition. The main agronomic trait, yield and quality‐related traits were similar to those of the recurrent parent. The use of these lines will contribute to the expansion of the cultivation area due to the proven economic benefits of direct seeding in Korea.

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“…To develop improved breeding materials for seedling establishment under flooded conditions in DSR, quantitative trait loci (QTLs) for the rate of seedling emergence under anaerobic conditions (i.e., anaerobic germination) have been determined (Angaji, Septiningsih, Mackill & Ismail, 2010;Baltazar et al, 2014Baltazar et al, , 2019Kim & Reinke, 2018;Septiningsih et al, 2013). Among these QTLs, a trehalose-6-phosphate phosphatase gene (OsTPP7) was identified as the gene responsible for qAG-9-2 a major quantitative trait locus (QTL) for anaerobic germination (Kretzschmar et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Detection and characterization of quantitative trait loci for coleoptile elongation under anaerobic conditions in rice

Nishimura

Sasaki

Yamaguchi

et al. 2020

Plant Production Science

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Low oxygen concentrations in flooded paddy fields cause poor seedling establishment in wet direct seeded rice. We aimed to identify novel genomic regions associated with coleoptile elongation under anaerobic conditions in order to improve seedling establishment. Chromosome segment substitution lines (CSSLs), substituted with Koshihikari (Japonica-type) in the IR 64 genetic background (Indica-type) were evaluated. These lines were imbibed with a hydroponic solution containing Oxyrase to create a stable anaerobic condition and coleoptile lengths were measured six days after incubation at 30°C. Among the CSSLs, only SL2111 had a significantly longer coleoptile (23.9 mm) than that of IR 64 (14.3 mm). From genotype and phenotype analyses, a novel QTL, referred to as qACE3.1, for coleoptile elongation under anaerobic conditions was detected on chromosome 3. To explore the molecular mechanism of qACE3.1, the expression levels of genes encoding enzymes involved in starch degradation and fermentation were assessed. In SL2111 coleoptiles, the expression levels of pyruvate decarboxylase were significantly higher than in IR 64 coleoptiles whereas those of alcohol dehydrogenase were lower. In contrast, no differences were observed in the expression levels of genes associated with starch degradation. These results imply that qACE3.1 may specifically affect fermentative metabolism. In addition, we evaluated the impact of qACE3.1 on seedling establishment under flooded conditions in a paddy field.

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Identification of QTLs for tolerance to hypoxia during germination in rice

Cited by 24 publications

References 28 publications

Identification of novel hypoxia-responsive factors in deep-water rice conferring tolerance to flood during germination

Identification of novel hypoxia-responsive factors in deep-water rice conferring tolerance to flood during germination

Marker‐assisted breeding for improvement of anaerobic germination in japonica rice (Oryza sativa)

Detection and characterization of quantitative trait loci for coleoptile elongation under anaerobic conditions in rice

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