Molecular Dissection of a Genomic Region Governing Root Traits Associated with Drought Tolerance Employing a Combinatorial Approach of QTL Mapping and RNA-seq in Rice

Patil, Santosh; Srividhya, A.; Veeraghattapu, Roja; Deborah, Dondapati Annekitty; Kadambari, Gopalakrishna; Nagireddy, Ranjitkumar; Siddiq, E. A.; Vemireddy, Lakshminarayana R.

doi:10.1007/s11105-017-1037-z

Cited by 6 publications

(4 citation statements)

References 18 publications

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“…This analysis identi ed 10 annotated genes that were potential candidate genes for heat stress tolerance during the owering stage in rice. Out of 10, six genes are related to drought tolerance in rice, namely LOC_Os08g06430, LOC_Os08g06500, LOC_Os08g06630, LOC_Os08g07060, LOC_Os08g07440 and LOC_Os08g07760 [38,39,[41][42][43]46]. It has been reported that gene expression might play the same role under different stress conditions.…”

Section: Discussionmentioning

confidence: 99%

“…To further analyze the candidate genes in the chromosome region containing qHTT8, we predicted 65 putative genes in the Nipponbare genome using the Rice Genome Annotation Project database (RGAP http://rice.plantbiology.msu.edu/) (Supplementary Table 3). Among these genes, 10 genes that are located within the mapped region have been reported to be involved in abiotic stress tolerance, such as high night temperature, drought, cold, salinity and saline-alkaline (Table 4) [38][39][40][41][42][43][44][45][46][47].…”

Section: Qtl Mappingmentioning

confidence: 99%

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QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice

Chen

Wang

Zhang

et al. 2020

Preprint

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Abstract Background: High-temperature stress can cause serious abiotic damage that limits the yield and quality of rice. Heat tolerance during the flowering stage of rice is a key trait that can guarantee a high and stable yield under heat stress. Heat tolerance is a complex trait that is regulated by numerous quantitative trait loci (QTLs); of which, however, few underlying genes have been fine mapped and cloned.Results: In this study, the F2:3 population derived from a cross between Huanghuazhan (HHZ), a heat-tolerant indica cultivar, and 9311, a heat-sensitive indica rice variety, were used to map the QTLs for heat tolerance during the flowering stage of rice. The F2:3 lines were treated under 38 °C from 9:30 am to 3:30 pm continuously for 3 days in a phytotron, and spikelet fertility was assessed. A new major QTL, qHTT8, controlling heat tolerance was located on chromosome 8 using the bulked-segregant analysis (BSA)-seq method. The QTL qHTT8 was determined to be located in the 355500–4520000 bp region, with a size of 0.965 Mb. The candidate region of qHTT8 on chromosome 8 contained 65 predicted genes. Ten putative predicted genes were found to be associated with abiotic stress tolerance. In future studies, the backcross population will be constructed to fine map and validate the effect of qHTT8.Conclusion: The information obtained in this study is useful for the fine mapping and cloning of qHTT8 and breeding heat-tolerant varieties of rice using marker-assisted selection.

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Section: Discussionmentioning

confidence: 99%

Section: Qtl Mappingmentioning

confidence: 99%

QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice

Chen

Wang

Zhang

et al. 2020

Preprint

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“…In droughttolerant species, cell growth and cell wall biosynthesis genes are less affected under severe drought, while in drought-sensitive species they get repressed. Likewise, in droughttolerant species, carbohydrate metabolism genes were upregulated, while they were found to be downregulated in drought-sensitive genotypes under severe drought [70]. Autophagyassociated genes were found to be upregulated only in drought-sensitive species under drought stress [71].…”

Section: Drought Stressmentioning

confidence: 95%

Root System Architecture and Omics Approaches for Belowground Abiotic Stress Tolerance in Plants

2022

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Plant growth and productivity is negatively affected by several abiotic stresses. To overcome the antagonistic effect of a changing environment, plants have evolved several modifications at the physiological as well as molecular levels. Besides being a vital organ for a plant’s nutrient uptake, roots also plays a significant role in abiotic stress regulation. This review provides insight into changing Root System Architecture (RSA) under varying environmental stimuli using high-throughput omics technologies. Several next-generation and high-throughput omics technologies, such as phenomics, genomics, transcriptomics, proteomics, and metabolomics, will help in the analysis of the response of root architectural traits under climatic vagaries and their impact on crop yield. Various phenotypic technologies have been implied for the identification of diverse root traits in the field as well as laboratory conditions, such as root-box pinboards, rhizotrons, shovelomics, ground-penetrating radar, etc. These phenotypic analyses also help in identifying the genetic regulation of root-related traits in different crops. High-throughput genomic as well as transcriptome analysis has led researchers to unravel the role of the root system in response to these environmental cues, even at the single-cell level. Detailed analysis at the protein and metabolite levels can provide a better understanding of the response of roots under different abiotic stresses. These technologies will help in the improvement of crop productivity and development of resistant varieties.

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“…To further analyze the candidate genes in the chromosome region containing qHTT8, we predicted 65 putative genes in the Nipponbare genome using the RGAP database (Supplementary Table 3). Ten genes that were located within the mapped region have been reported to be involved in abiotic stress tolerance, such as high night temperature, drought, cold, salinity and saline-alkaline (Table 3 and Figure 2E) (Ma et al, 2009;Smita et al, 2010;Nguyen et al, 2014;Lee et al, 2015;Raineri et al, 2015;Saha et al, 2015;Huang et al, 2017;Patil et al, 2017;Li N. et al, 2018;Hoang et al, 2019;Yang et al, 2019).…”

Section: Candidate Genes Analysismentioning

confidence: 99%

QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice

et al. 2021

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High-temperature stress can cause serious abiotic damage that limits the yield and quality of rice. Heat tolerance (HT) during the flowering stage of rice is a key trait that can guarantee a high and stable yield under heat stress. HT is a complex trait that is regulated by multiple quantitative trait loci (QTLs); however, few underlying genes have been fine mapped and cloned. In this study, the F2:3 population derived from a cross between Huanghuazhan (HHZ), a heat-tolerant cultivar, and 9311, a heat-sensitive variety, was used to map HT QTLs during the flowering stage in rice. A new major QTL, qHTT8, controlling HT was identified on chromosome 8 using the bulked-segregant analysis (BSA)-seq method. The QTL qHTT8 was mapped into the 3,555,000–4,520,000 bp, which had a size of 0.965 Mb. The candidate region of qHTT8 on chromosome 8 contained 65 predicted genes, and 10 putative predicted genes were found to be associated with abiotic stress tolerance. Furthermore, qRT-PCR was performed to analyze the differential expression of these 10 genes between HHZ and 9311 under high temperature conditions. LOC_Os08g07010 and LOC_Os08g07440 were highly induced in HHZ compared with 9311 under heat stress. Orthologous genes of LOC_Os08g07010 and LOC_Os08g07440 in plants played a role in abiotic stress, suggesting that they may be the candidate genes of qHTT8. Generally, the results of this study will prove useful for future efforts to clone qHTT8 and breed heat-tolerant varieties of rice using marker-assisted selection.

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Molecular Dissection of a Genomic Region Governing Root Traits Associated with Drought Tolerance Employing a Combinatorial Approach of QTL Mapping and RNA-seq in Rice

Cited by 6 publications

References 18 publications

QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice

QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice

Root System Architecture and Omics Approaches for Belowground Abiotic Stress Tolerance in Plants

QTL Mapping and Identification of Candidate Genes for Heat Tolerance at the Flowering Stage in Rice

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