Genotypic diversity and abiotic stress response profiling of short-grain aromatic landraces of rice (Oryza sativa L. Indica)

Behera, Prafulla Kumar; Kumar, Vikash; Sharma, Shyam Sundar; Lenka, Sangram K.; Panda, Debabrata

doi:10.1016/j.cpb.2022.100269

Cited by 13 publications

(13 citation statements)

References 53 publications

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“…PCoA showed a cumulative genetic variation of 19.7%, 27.2%, and 32.5% among the populations with a mixed position of the populations. Conversely, Behera et al (2023) obtained two major and five sub-clusters concomitant with a very broad genetic base (K = 5) obtained with the STRUCTURE analysis. The results of previous studies on the molecular variance and structure analyses by ), Vanlalsanga et al (2019, P. S. Roy et al (2023), andPradhan et al (2023) broadly corroborate our finding of the presence of a high level of molecular variation in the germplasm of aromatic rice landraces.…”

Section: Genetic Differentiation and Gene Flow Of Populationsmentioning

confidence: 89%

Aromatic rice (Oryza sativa L.) landraces of Indo‐Gangetic Plains of India harbor rich genetic diversity

Bairwa,

Yadav,

Tiwari

et al. 2024

Crop Science

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Aromatic rice (Oryza sativa L.) germplasm conserved in global genebanks needs intensive characterization to assess genetic diversity and population structure for crop improvement. We analyzed a panel of 92 accessions of non‐Basmati aromatic rice landrace germplasm with 23 phenotypic traits and 48 microsatellite markers. The landrace accessions displayed a huge phenotypic diversity for traits, namely, culm length, flag‐leaf length, panicle‐bearing tillers (PBT), plant height, panicle length, peduncle length, panicle exsertion, grain length, grain width, hull color, and 1000‐grain weight (TGW). Phenotypic clustering revealed three major clusters and five principal components explained 81.24% of the variance. TGW was associated positively with grain length, grain width, peduncle length, and grain yield but negatively with culm length and PBT. A total of 528 microsatellite alleles were detected, with 11.0 alleles per locus, revealing the presence of high polymorphism. Genetically, four subpopulations were detected based on structure analysis. In the germplasm, high levels of gene flow (Nm = 1.51) and gene diversity (HE = 0.83) were found. Among the subpopulations, we discovered high levels of inbreeding (FIS = 0.92) and moderate genetic differentiation (FST = 0.14). High polymorphism information content (0.806) along with a high level of molecular variance among genotypes (79%) was detected. A large number of multiple alleles were detected in numerous landrace accessions, revealing the presence of heterogeneity and heterozygotes in the landrace germplasm. The results of the present study are vital for the utilization of landrace diversity in the genetic improvement programs designed for rice quality improvement and consumer preference.

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Section: Genetic Differentiation and Gene Flow Of Populationsmentioning

confidence: 89%

Aromatic rice (Oryza sativa L.) landraces of Indo‐Gangetic Plains of India harbor rich genetic diversity

Bairwa,

Yadav,

Tiwari

et al. 2024

Crop Science

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“…For further analysis, a national check rice variety Nagina22 (or N22) developed by the National Rice Research Institute (NRRI, Cuttack, India) was added. Many other studies used this heat-tolerant variety for a comparative study of heat stress response by other rice genotypes (Behera et al, 2023; Kilasi et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

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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“…The seedlings were grown under standard conditions and nurtured for a duration of 21 days. Subsequently, stress was imposed separately, adhering to the specified protocol for each stress ( Behera et al., 2023 ). One set of genotypes was maintained under nonstress conditions (control) until the end of the experiment ( Figure 1 ).…”

Section: Methodsmentioning

confidence: 99%

Enhancing stress resilience in rice (Oryza sativa L.) through profiling early-stage morpho-physiological and molecular responses to multiple abiotic stress tolerance

Kumar,

Pushpam,

Manonmani

et al. 2024

Front. Plant Sci.

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Under changing climatic conditions, crop plants are more adversely affected by a combination of various abiotic stresses than by a single abiotic stress. Therefore, it is essential to identify potential donors to multiple abiotic stresses for developing climate-resilient crop varieties. Hence, the present study was undertaken with 41 germplasm accessions comprising native landraces of Tamil Nadu, Prerelease lines and cultivars were screened independently for drought, salinity, and submergence at the seedling stage during Kharif and Rabi 2022–2023. Stress was imposed separately for these three abiotic stresses on 21-day-old seedlings and was maintained for 10 days. The studied genotypes showed a significant reduction in plant biomass (PB), Relative Growth Index (RGI), relative water content (RWC), leaf photosynthesis, chlorophyll fluorescence, and Chlorophyll Concentration Index (CCI) under drought followed by salinity and submergence. Stress-tolerant indices for drought, salinity, and submergence revealed significant variation for plant biomass. Furthermore, a set of 30 SSR markers linked to drought, salinity, and submergence QTLs has been used to characterize 41 rice germplasm accessions. Our analysis suggests a significantly high polymorphism, with 28 polymorphic markers having a 93.40% in 76 loci. The mean values of polymorphic information content (PIC), heterozygosity index (HI), marker index (MI), and resolving power (RP) were 0.369, 0.433, 1.140, and 2.877, respectively. Jaccard clustering grouped all the genotypes into two major and six subclusters. According to STRUCTURE analysis, all genotypes were grouped into two major clusters, which are concurrent with a very broad genetic base (K = 2). Statistically significant marker-trait associations for biomass were observed for five polymorphic markers, viz., RM211, RM212 (drought), RM10694 (salinity), RM219, and RM21 (submergence). Similarly, significant markers for relative shoot length were observed for RM551 (drought), RM10694 (salinity), and ART5 (submergence). Notably, the genotypes Mattaikar, Varigarudan samba, Arupatham samba, and APD19002 were identified as potential donors for multiple abiotic stress tolerance. Thus, identifying the genetic potential of germplasm could be useful for enhancing stress resilience in rice.

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Genotypic diversity and abiotic stress response profiling of short-grain aromatic landraces of rice (Oryza sativa L. Indica)

Cited by 13 publications

References 53 publications

Aromatic rice (Oryza sativa L.) landraces of Indo‐Gangetic Plains of India harbor rich genetic diversity

Aromatic rice (Oryza sativa L.) landraces of Indo‐Gangetic Plains of India harbor rich genetic diversity

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

Enhancing stress resilience in rice (Oryza sativa L.) through profiling early-stage morpho-physiological and molecular responses to multiple abiotic stress tolerance

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Genotypic diversity and abiotic stress response profiling of short-grain aromatic landraces of rice (Oryza sativa L. Indica)

Cited by 13 publications

References 53 publications

Aromatic rice (Oryza sativa L.) landraces of Indo‐Gangetic Plains of India harbor rich genetic diversity

Aromatic rice (Oryza sativa L.) landraces of Indo‐Gangetic Plains of India harbor rich genetic diversity

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

Enhancing stress resilience in rice (Oryza sativa L.) through profiling early-stage morpho-physiological and molecular responses to multiple abiotic stress tolerance

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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