Description of phenotype, grain quality, molecular fingerprinting, and biodiversity using DNA barcoding of some elite rice genotypes

Omar, Ahmad A.; Zayed, E. M.; Oraby, Hesham F.; Elnaggar, Nehal; Elashtokhy, M.; Basuoni, Mostafa M.; Osman, Ali; Shamseldin, Sahar A.M.; Attia, Kotb A.; Mohamed, Azza H.

doi:10.1016/j.sajb.2023.01.045

Cited by 4 publications

(5 citation statements)

References 20 publications

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“…In other abiotic stress responsiveness of rice, some other molecular markers like SSR, ISSR, SNP were used in the rice landrace population (Ganie et al, 2016(Ganie et al, , 2014Karmakar et al, 2012;Meena et al, 2023;Roychowdhury et al, 2013). SCoT markerbased analysis is better than other frequently used molecular markers since primer creation does not need genomic sequence information (Omar et al, 2023) (Omar et al 2023). SCoT markers also have larger polymorphism rates than SSRs, making them better at distinguishing closely related genotypes.…”

Section: Discussionmentioning

confidence: 99%

“…SCoT marker-based analysis presents distinct advantages over other widely used molecular markers like SSR and SNP in rice as it does not require prior knowledge of genomic sequences for primer design, making them particularly valuable for non-model species or less studied rice varieties (Omar et al, 2023). Furthermore, SCoT markers offer higher polymorphism rates compared to SSRs, enabling more accurate discrimination between closely related genotypes, and enhancing the resolution in genetic diversity studies.…”

Section: Introductionmentioning

confidence: 99%

“…SCoT markers are a type of molecular marker used in crop genetic analysis and are based on the polymorphism on short ATG start codon region of genes, making them valuable tools for studying genetic diversity, population structure, and phylogenetic relationships among different rice varieties with stress tolerance properties (Collard and Mackill, 2009). SCoT marker-based analysis presents distinct advantages over other widely used molecular markers like SSR and SNP in rice as it does not require prior knowledge of genomic sequences for primer design, making them particularly valuable for non-model species or less studied rice varieties (Omar et al, 2023). Furthermore, SCoT markers offer higher polymorphism rates compared to SSRs, enabling more accurate discrimination between closely related genotypes, and enhancing the resolution in genetic diversity studies.…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativaL.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO₂levels

Mollier,

Roychowdhury,

Tzudir

et al. 2023

Preprint

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Rice (Oryza sativa L.) has a tremendous domestication history and is presently used as a major cereal all over the world. In Asia, India is considered as one of the centers of origin of indica rice and has several native landraces, especially in North-Eastern India (NEI), which have the potential to cope with the negative impact of present-day climate change. The current investigation aimed to evaluate the NEI rice landraces potential under high temperatures and elevated CO2 levels in comparison with a check variety for phenological, morphological, physiological and yield-associated parameters and molecularly validated with marker-assisted genotyping. The initial experiment was carried out with 75 rice landraces to evaluate their high heat tolerance ability. Seven better-performing landraces along with the check variety (N22) were further evaluated for aforesaid traits across two years (2019 and 2020) under control (or T1) and two stress treatments (i) mild stress or T2 [CO2 550 ppm + 4o C more than ambient temperature] and (ii) severe stress or T3 [CO2 750 ppm + 6o C more than ambient temperature] using bioreactors. In the molecular analysis, the eight selected genotypes were evaluated through 25 Start Codon Targeted (SCoT) markers. The results revealed that the mild stress (T2) had a positive impact on various morpho-physiological parameters like plant height, number of leaves, leaf area and yield parameters like spikelets panicle-1 (S/P), thousand-grain weight (TGW) and grain yield (GY). This effect could be attributed to the genotypes' ability to maintain a higher photosynthetic rate and possess better tolerance ability to moderately high temperatures. However, under high-temperature conditions in T3, all genotypes exhibited a significant decrease in the studied parameters including GY. It was found that pollen traits were significantly and positively correlated to spikelet fertility% at maturity, which was further significantly associated with GY under applied stress conditions. The physiological traits including shoot biomass were evident to have a significant positive effect on yield-associated parameters like S/P, harvest index (HI), TGW and GY. Overall, two landraces Kohima special and Lisem were found to be better responsive compared to other landraces as well as the check variety N22 under stress conditions. SCoT genotyping amplified a total of 77 alleles out of which 55 were polymorphic with the PIC value ranging from 0.22 to 0.67. The investigation suggests the presence of genetic variation among the tested rice lines and further supports evidence of the closely relatedness of Kohima special and Lisem. These two are two better-performing rice landraces from North-East India based on their improving morpho-physiological parameters and yield attributes in mild and severe high temperature and elevated CO2 stress environments. The shortlisted two rice landraces can be used as valuable pre-breeding materials for future rice breeding programs to improve the stress tolerance properties, particularly to high temperatures and elevated CO2 levels under ongoing changing climatic scenarios

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativaL.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO₂levels

Mollier,

Roychowdhury,

Tzudir

et al. 2023

Preprint

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“…In relation to the responsiveness of rice under other abiotic stresses, some other molecular markers, like SSR, ISSR, SNP, were used in the rice landrace population [13,14,34,36,52]. SCoT-marker-based analysis is better than other frequently used molecular markers since primer creation does not need genomic sequence information [23]. SCoT markers also have larger polymorphism rates than SSRs, making them better at distinguishing closely related genotypes.…”

Section: Scot Marker-assisted Genetic Analysis and Genotypic Selectionmentioning

confidence: 99%

“…SCoT markers are a type of molecular marker used in crop genetic analysis and are based on the polymorphism on short ATG start codon region of genes, making them valuable tools for studying genetic diversity, population structure, and phylogenetic relationships among different rice varieties with stress-tolerance properties [22]. SCoT-marker-based analysis presents distinct advantages over other widely used molecular markers, like SSR and SNP, in rice as it does not require prior knowledge of genomic sequences for primer design, making them particularly valuable for non-model species or less-studied rice varieties [23]. Furthermore, SCoT markers offer higher polymorphism rates compared to SSRs, enabling more accurate discrimination between closely related genotypes and enhancing the resolution in genetic diversity studies.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Morpho-Physiological and Yield-Associated Traits of Rice (Oryza sativa L.) Landraces Combined with Marker-Assisted Selection under High-Temperature Stress and Elevated Atmospheric CO2 Levels

Mollier,

Roychowdhury,

Tzudir

et al. 2023

Plants

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Rice (Oryza sativa L.) is an important cereal crop worldwide due to its long domestication history. North-Eastern India (NEI) is one of the origins of indica rice and contains various native landraces that can withstand climatic changes. The present study compared NEI rice landraces to a check variety for phenological, morpho-physiological, and yield-associated traits under high temperatures (HTs) and elevated CO2 (eCO2) levels using molecular markers. The first experiment tested 75 rice landraces for HT tolerance. Seven better-performing landraces and the check variety (N22) were evaluated for the above traits in bioreactors for two years (2019 and 2020) under control (T1) and two stress treatments [mild stress or T2 (eCO2 550 ppm + 4 °C more than ambient temperature) and severe stress or T3 (eCO2 750 ppm + 6 °C more than ambient temperature)]. The findings showed that moderate stress (T2) improved plant height (PH), leaf number (LN), leaf area (LA), spikelets panicle−1 (S/P), thousand-grain weight (TGW), harvest index (HI), and grain production. HT and eCO2 in T3 significantly decreased all genotypes’ metrics, including grain yield (GY). Pollen traits are strongly and positively associated with spikelet fertility at maturity and GY under stress conditions. Shoot biomass positively affected yield-associated traits including S/P, TGW, HI, and GY. This study recorded an average reduction of 8.09% GY across two seasons in response to the conditions simulated in T3. Overall, two landraces—Kohima special and Lisem—were found to be more responsive compared to other the landraces as well as N22 under stress conditions, with a higher yield and biomass increment. SCoT-marker-assisted genotyping amplified 77 alleles, 55 of which were polymorphic, with polymorphism information content (PIC) values from 0.22 to 0.67. The study reveals genetic variation among the rice lines and supports Kohima Special and Lisem’s close relationship. These two better-performing rice landraces are useful pre-breeding resources for future rice-breeding programs to increase stress tolerance, especially to HT and high eCO2 levels under changing climatic situations.

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Effectiveness of DNA barcoding, SCOT markers and phytochemical characterization in biodiversity assessment of some Zea mays hybrids

Rizk,

Zayed,

Amin

et al. 2024

South African Journal of Botany

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Description of phenotype, grain quality, molecular fingerprinting, and biodiversity using DNA barcoding of some elite rice genotypes

Cited by 4 publications

References 20 publications

Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativaL.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO₂levels

Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativaL.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO₂levels

Evaluation of Morpho-Physiological and Yield-Associated Traits of Rice (Oryza sativa L.) Landraces Combined with Marker-Assisted Selection under High-Temperature Stress and Elevated Atmospheric CO2 Levels

Effectiveness of DNA barcoding, SCOT markers and phytochemical characterization in biodiversity assessment of some Zea mays hybrids

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Description of phenotype, grain quality, molecular fingerprinting, and biodiversity using DNA barcoding of some elite rice genotypes

Cited by 4 publications

References 20 publications

Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativaL.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO2levels

Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativaL.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO2levels

Evaluation of Morpho-Physiological and Yield-Associated Traits of Rice (Oryza sativa L.) Landraces Combined with Marker-Assisted Selection under High-Temperature Stress and Elevated Atmospheric CO2 Levels

Effectiveness of DNA barcoding, SCOT markers and phytochemical characterization in biodiversity assessment of some Zea mays hybrids

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Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativaL.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO₂levels

Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativaL.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO₂levels