Genetic Differentiation Revealed by Selective Loci of Drought-Responding EST-SSRs between Upland and Lowland Rice in China

Xia, Hui; Zheng, Xiujun; Chen, Liang; Gao, Huan; Yang, Hua; Pan, Long; Rong, Jun; Lu, Bao‐Rong; Li, Jiajia; Luo, Lijun

doi:10.1371/journal.pone.0106352

Cited by 37 publications

(48 citation statements)

References 27 publications

(33 reference statements)

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“…2; Table S3). A similar percentage of outlier loci was reported by other authors (Nosil, Egan & Funk, 2008; Manel, Conord & Després, 2009; Nosil, Funk & Ortiz-Barrientos, 2009; Freeland et al, 2010; Xia et al, 2014). …”

Section: Discussionsupporting

confidence: 90%

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

Bilska

Szczecińska

2016

PeerJ

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BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20%) and ΦPT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

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Section: Discussionsupporting

confidence: 90%

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

Bilska

Szczecińska

2016

PeerJ

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“…Based on the findings of this study, we conclude that lower DNA methylation levels in stressed condition contribute to higher drought-resistance in upland rice. The differentially methylated epiloci found in this study should be good epigenetic markers to decipher the evolution of drought-resistance in rice, which could not fully explained by genetic differentiation (Xia et al, 2014). …”

Section: Discussionmentioning

confidence: 84%

Differentially Methylated Epiloci Generated from Numerous Genotypes of Contrasting Tolerances Are Associated with Osmotic-Tolerance in Rice Seedlings

et al. 2017

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DNA methylation plays an essential role in plant responses to environmental stress. Since drought develops into a rising problem in rice cultivation, investigations on genome-wide DNA methylation in responses to drought stress and in-depth explorations of its association with drought-tolerance are required. For this study, 68 rice accessions were used for an evaluation of their osmotic-tolerance related to 20% PEG6000 simulated physiological traits. The tolerant group revealed significantly higher levels of total antioxidant capacity and higher contents of H2O2 in both normal and osmotic-stressed treatments, as well as higher survival ratios. We furthermore investigated the DNA methylation status in normal, osmotic-stressed, and re-watering treatments via the methylation-sensitive amplification polymorphism (MSAP). The averaged similarity between two rice accessions from tolerant and susceptible groups was approximately 50%, similar with that between two accessions within the tolerant/susceptible group. However, the proportion of overall tolerance-associated epiloci was only 5.2% of total epiloci. The drought-tolerant accessions revealed lower DNA methylation levels in the stressed condition and more de-methylation events when they encountered osmotic stress, compared to the susceptible group. During the recovery process, the drought-tolerant accessions possessed more re-methylation events. Fourteen differentially methylated epiloci (DME) were, respectively, generated in normal, osmotic-stressed, and re-watering treatments. Approximately, 35.7% DME were determined as tolerance-associated epiloci. Additionally, rice accessions with lower methylation degrees on DME in the stressed conditions had a higher survival ratio compared to these with higher methylation degrees. This result is consistent with the lower DNA methylation levels of tolerant accessions observed in the stressed treatment. Methylation degrees on a differentially methylated epilocus may further influence gene regulation in the rice seedling in response to the osmotic stress. All these results indicate that DME generated from a number of genotypes could have higher probabilityies for association with stress-tolerance, rather than DME generated from two genotypes of contrasting tolerance. The DME found in this study are suspected to be good epigenetic markers for the application in drought-tolerant rice breeding. They could also be a valuable tool to study the epigenetic differentiation in the drought-tolerance between upland and lowland rice ecotypes.

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“…Use of insertion and deletions (INDELs) as well as SNPs to study the diversity between drought susceptible and tolerant rice indicates that QTLs related to photosynthesis are particularly important in drought stress tolerance in rice (Zhang et al, 2016). The use of SSRs to determine diversity of drought responding Expressed Sequence Tags (ESTs) between upland and lowland rice cultivars, has led to further establishment of the correlation between uplandlowland differentiation and drought resistance, suggesting upland rice cultivars to be more tolerant to drought (Xia et al, 2014). Recently, candidate gene based SSR (cgSSR) markers have identified in rice with respect to salt stress response.…”

Section: Prospects For Increasing Drought Tolerance In Ricementioning

confidence: 99%

Morphophysiological and molecular effects of drought stress in rice

et al. 2016

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Drought is a major abiotic stress that adversely affects the rice growth, mostly in the rainfed ecosystem that ultimately affects the biomass production and yield. Rice needs to adapt a series of physiological mechanisms with complicated regulatory network to fight and cope up with the unfavourable conditions due to drought stress. Morphological and physiological response in rice include inhibition of seed germination, slower growth rate, low root and shoot length, lower chlorophyll content, stomatal closure, lower rate of photosynthesis, yield reduction etc. Stress condition further results in development of response at the molecular level by the generation of reactive oxygen species (ROS) such as O2*-, H2O2, 1O2, OH* etc. which incites oxidative stress in the plants. Oxidative stress is overcome by the inherent capacity of plants to produce antioxidant species which may be enzymatic or non-enzymatic in nature. If however antioxidant defence mechanism cannot overpower the ROS generated, they cause oxidative damage to the plant tissues such as lipid peroxidation, protein oxidation, DNA damage, etc. resulting in cell death. Unlike other stresses, drought affects the physiology and biochemistry of the rice which adversely affects in the morphology and consequently delimits the yield of the plant. Therefore, understanding the morphological, biochemical and molecular mechanisms involved in rice against drought is utmost necessary for rice breeders to improve the rice for drought tolerant/resistance varieties for future green revolution. In this review, an attempt has been made to highlight the complex regulatory network involved in rice against drought with special emphasis on morphological, physiological and molecular mechanisms and to discuss the prospective and challenges for future plant breeders.

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Genetic Differentiation Revealed by Selective Loci of Drought-Responding EST-SSRs between Upland and Lowland Rice in China

Cited by 37 publications

References 27 publications

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

Differentially Methylated Epiloci Generated from Numerous Genotypes of Contrasting Tolerances Are Associated with Osmotic-Tolerance in Rice Seedlings

Morphophysiological and molecular effects of drought stress in rice

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