Genetic characterization of coarse and basmati rice (Oryza sativa L.) through microsatellite markers and morpho-agronomic traits

Luqman, Tahira; Qamar, Zia-ul; Tabasum, Aqsa; El-Kallawy, W.; Nazir, Talha; Attacha, Safira; Fiaz, Sajid; Nadeem, Muhammad Azhar; Hameed, Amjad; Maryum, Zahra; Itoh, Kazuyoshi; Attia, Kotb A.

doi:10.1007/s10722-023-01620-w

Cited by 3 publications

(4 citation statements)

References 21 publications

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“…reported PIC value 0.26 to 0.87 in quality rice from North-Eastern India by 48 SSR markers. Similarly, PIC values ranged from 0.36 (RM10) to 0.92 (RM6) in the analysis of molecular diversity between 37 course and Basmati rice genotypes of Pakistan with 35 SSR markers(Luqman et al 2023). All these previous studies corroborate our findings of occurrence of high PIC in the landrace materials.…”

supporting

confidence: 87%

“…Lapitan et al (2007) analyzed 164 SSR markers for genetic diversity assessment in 24 rice cultivars from Philippines and reported a total of 890 alleles with mean of 5.89 alleles per locus using 151 polymorphic SSRs. The low numbers of alleles (2.0 to 4.5 alleles/locus) were also detected by several researchers from Indian subcontinent (Hossain et al 2007;Talukdar et al 2017;Islam et al 2018b;Bhuvaneswari et al 2020;Luqman et al 2023;Pradhan et al 2023). Hossain et al (2007) detected 4.5 alleles per SSR locus in the analysis of 21 rice genotypes from Bangladesh using 30 microsatellite markers.…”

Section: Molecular Variability In Aromatic Rice Landracesmentioning

confidence: 62%

“…In addition, SSR often have flanking regions that are highly conserved in related species, which allows the use of same primer pairs in related genome (Cipriani et al 1999). Several researchers have molecularly characterized Basmati and non-Basmati aromatic rices using microsatellite markers (Nagaraju et al 2002;Jain et al 2004;Salgotra et al 2015;Kumbhar et al 2015;Talukdar et al 2017;Kumari et al 2018;Bhuvaneswari et al 2020;Behera et al 2023;Luqman et al 2023).…”

mentioning

confidence: 99%

“…Cluster II had 16 genotypes including Pusa Sugandh 4, Pusa Basmati1, Basmati 386, Vallabh Basmati 22, Nagina 22, Haryana Basmati, Basmati CSR3, Ranbir Basmati and 8 exotic collections.Cluster III consisted of 15 genotypes including Pusa Sugandh 5, Vallabh Basmati 24, Vallabh Basmati 21 and 12 exotic collections. Clustering based on morpho-agronomic traits showed clear separation between 37 coarse and Basmati rice genotypes into two groups(Luqman et al 2023) Roy et al (2023). used clustering analysis based on morphological traits to group 607 farmers' rice varieties into three major clusters.…”

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confidence: 99%

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Aromatic Rice (Oryza sativa L.) Landraces of Indo-Gangetic Plains of India Harbor Rich Genetic Diversity as Revealed by Phenotypic Traits and Microsatellite Markers

Bairwa

Yadav

Tiwari

et al. 2023

Preprint

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Rice (Oryza sativa L.) grains are vital for food security of half of the global population. India has rich diversity for aromatic rice landraces. In order to assess the genetic diversity and population structure in these specialty rices, we characterized 92 germplasm accessions of aromatic rice landraces of Indo-Gangetic Plain region including 10 popular landraces of other states of India using 23 phenotypic traits and 48 microsatellite markers. Landrace accessions displayed huge variability for plant height (PH), culm length (CL), flag-leaf length, auricle colour, leaf-blade pubescence and colour, panicle bearing tillers, panicle length (PL), peduncle length (PdL), panicle exsertion, grain length (GL), grain breadth (GB), hull colour and thousand grain weight (TGW). First five principal components contributed 81.24% phenotypic variation. High positive associations were found between PH and CL (r = 0.83), PdL and PL (0.66), GL and TGW (0.78), and GB and TGW (0.59). Molecular analysis with 48 genome-wide HvSSR markers revealed 11.0 alleles per locus, which evidently showed that a high level of DNA polymorphism exists between landrace accessions. The structure analysis revealed four subpopulations with numerous accessions sharing alleles with other groups. Gene diversity assay revealed high levels of gene diversity (HE = 0.83), Shannon's Information index (I = 1.99) and gene flow (Nm = 1.51) between accessions of aromatic rice landraces. Wright′s F-statistics revealed moderate genetic differentiation (FST = 0.14) among subpopulations and high degree of inbreeding (FIS=0.92) within subpopulations. This was also supported by high polymorphism information content (PIC = 0.806) and analysis of molecular variance (AMOVA), which revealed 79% variance among genotypes. The unique and rare alleles could be used for DNA fingerprinting and differentiation of genotypes. A high number of multiple alleles were observed in number of landrace accessions, which showed the presence of heterogeneity and heterozygotes in the landrace materials. The results of present study are useful for utilization of the landraces in genetic enhancement programmes specially designed for rice quality improvement and consumer's preference.

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supporting

confidence: 87%

Section: Molecular Variability In Aromatic Rice Landracesmentioning

confidence: 62%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Aromatic Rice (Oryza sativa L.) Landraces of Indo-Gangetic Plains of India Harbor Rich Genetic Diversity as Revealed by Phenotypic Traits and Microsatellite Markers

Bairwa

Yadav

Tiwari

et al. 2023

Preprint

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Genetic diversity of maize resources revealed by different molecular markers

Chňapek,

Balážová,

Špaleková

et al. 2024

Genet Resour Crop Evol

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Maize (Zea mays L.) is the third most important cereal crop in the world because of its nutritional value and industrial benefits. Molecular markers are used mainly by the breeders to study the genetic variability of genotypes and its application in the breeding process. Two types of molecular markers, 10 random amplified polymorphic DNA (RAPD) primers and 10 start codon target (SCoT) primers, were assayed to determine the genetic diversity of 25 Slovak maize lines and 25 maize cultivars. A high level of polymorphism was found with both RAPD and SCoT markers, which was confirmed by high average polymorphism information content (PIC) values using both techniques. The efficiency of individual marker techniques in the detection of genotype diversity can be compared by calculating the marker index (MI), detecting diversity index (DDI), discriminating power, resolving power (RP) and other indices. A higher MI (11.788), DDI (2.358) and RP (53.08) value was achieved by the SCoT technique compared to the RAPD method. Three joint dendrograms and PCoA plots constructed based on RAPD, SCoT and both methods combined confirmed the unambiguous separation of maize lines and cultivars from each other. The results obtained from the RAPD and SCoT analysis can be used for the selection of potentially suitable biological sources for further marker-assisted breeding.

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Development of Rice Mutants with Enhanced Resilience to Drought Stress and Their Evaluation by Lab Assay, Field, and Multivariate Analysis

Fatima,

Rashid,

Hameed

2024

Scientifica

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Drought is one of the foremost devastating abiotic stresses reported for rice crops. To improve the productivity of rice, diversity is being enlarged by induced mutation using a source of gamma rays. But this type of mutation rarely results in fruitful products because the chances of getting the desired mutant are very low. The present study aimed to evaluate the rice mutants against drought or osmotic stress. In this study, three experiments were conducted that comprised of seventy‐one mutants originating from different doses of gamma rays (Cs137) along with parent RICF‐160 and commercial variety (Kainat) were tested. In the first experiment, germination and seedling attributes were calculated under control and osmotic stress conditions created by using 16% (0.6 MPa) polyethylene glycol (PEG‐6000). Results revealed that all the mutants exhibited significant (p < 0.01) responses to PEG‐induced osmotic stress. Principal component biplot analysis (PCBA) revealed the first seventeen cumulative PCs with eigenvalues >1 contributed 88%. It was noted that the germination percentage (GP), germination rate (GR), coefficient velocity of germination (CVG), and seed vigor (SV) contributed maximum and positively in PC1. Results showed the highest germination percentage (GP) at 48 hrs in mutant NMSF‐11 (88.9%) followed by NMSf‐38 (73.3%). Similarly, the germination rate (GR) and coefficient velocity of germination (CVG) were measured highest in NMSF‐11 (9.7 and 118.1%), respectively. In stress conditions, the mutants NMSF‐35 and NMSF‐36 depicted the highest GP, GR, and CVG. The maximum seed vigor (SV), shoot length (SL), root length (RL), and fresh weight (FW) were observed in mutants NMSF‐50 and NMSF‐51 under both conditions, whereas the mutants NMSF‐59, NMSF‐60, NMSF‐64, and NMSF‐67 showed lower values for SV, SL, RL, and FW. In the second experiment, a field trial was conducted at the Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, in two control and stress sets. A bit different trend was observed among all mutants for agronomic parameters under both conditions. In the third experiment, biochemical profiling was done in Marker Assisted Breeding (MAB) Lab‐1, Plant Breeding and Genetics Division. A significant variation was seen in enzymatic antioxidants and chlorophyll content in both control and stress conditions. Under control conditions, the ascorbate peroxidase (APX) content was observed higher in mutant NMSF‐49 (106.07 Units/g. f. wt.). In comparison with the stress, the ascorbate peroxidase activity was higher in NMSF‐41 (82.34 Units/g. f. wt.). Catalase (CAT) activity was observed maximum in NMSF‐29 (17.54 Units/g. f. wt.) and NMSF‐40 (14.17 Units/g. f. wt.) under control and stress conditions, respectively. Peroxidase (POD) activity was observed maximum in NMSF‐51 (22.55 Units/g. f. wt. and 10.84 Units/g. f. wt.) under control and stress conditions, respectively. In conclusion, to fit in the changing climate conditions for resilient rice crop production, the promising mutant lines may be used to transfer the desirable drought‐tolerant/drought‐resistant genes in rice germplasm.

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Genetic characterization of coarse and basmati rice (Oryza sativa L.) through microsatellite markers and morpho-agronomic traits

Cited by 3 publications

References 21 publications

Aromatic Rice (Oryza sativa L.) Landraces of Indo-Gangetic Plains of India Harbor Rich Genetic Diversity as Revealed by Phenotypic Traits and Microsatellite Markers

Aromatic Rice (Oryza sativa L.) Landraces of Indo-Gangetic Plains of India Harbor Rich Genetic Diversity as Revealed by Phenotypic Traits and Microsatellite Markers

Genetic diversity of maize resources revealed by different molecular markers

Development of Rice Mutants with Enhanced Resilience to Drought Stress and Their Evaluation by Lab Assay, Field, and Multivariate Analysis

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