Identification of SSR Markers for Salt-tolerance in Rice Variety CSR10 by Selective Genotyping

2008 ◽  
Vol 18 (1) ◽  
pp. 87-91 ◽  
Author(s):  
Poonam Rana ◽  
Sunita Jain ◽  
Sheetal Yadav ◽  
Navinder Saini ◽  
R. K. Jain
Keyword(s):  
Salt Tolerance ◽  
Ssr Markers ◽  
Rice Variety ◽  
Selective Genotyping

scholarly journals Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety “Pusa Basmati 1”

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Vivek Kumar Singh ◽  
Brahma Deo Singh ◽  
Amit Kumar ◽  
Sadhna Maurya ◽  
Subbaiyan Gopala Krishnan ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Rice Variety ◽  
Crop Improvement ◽  
Rice Cultivar ◽  
Seedling Stage ◽  
Basmati Rice ◽  
Recurrent Parent ◽  
Foreground Selection

Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol. A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478. Foreground selection was carried out using three Saltol-linked polymorphic SSR markers RM8094, RM493, and RM10793 and background selection by 62 genome-wide polymorphic SSR markers. In every backcross generation, foreground selection was restricted to the triple heterozygotes of foreground markers, which was followed by phenotypic and background selections. Twenty-four near isogenic lines (NILs), with recurrent parent genome recovery of 96.0–98.4%, were selected after two backcrosses followed by three selfing generations. NILs exhibited agronomic traits similar to those of PB1 and additional improvement in the seedling stage salt tolerance. They are being tested for per se performance under salt-affected locations for release as commercial varieties. These NILs appear promising for enhancing rice production in salinity-affected pockets of Basmati Geographical Indication (GI) areas of India.

Application of SSR Technique for the Identification of Markers Linked to Salinity Tolerance in Rice

2013 ◽  
Vol 19 (2) ◽  
pp. 57-65
Author(s):  
MH Kabir ◽  
MM Islam ◽  
SN Begum ◽  
AC Manidas
Keyword(s):  
Salt Tolerance ◽  
Ssr Markers ◽  
Salinity Tolerance ◽  
Seedling Stage ◽  
Phenotypic Screening ◽  
Salt Tolerant ◽  
Marker Assisted Breeding ◽  
Hydroponic System ◽  
Rice Landrace ◽  
Salt Susceptible

A cross was made between high yielding salt susceptible BINA variety (Binadhan-5) with salt tolerant rice landrace (Harkuch) to identify salt tolerant rice lines. Thirty six F3 rice lines of Binadhan-5 x Harkuch were tested for salinity tolerance at the seedling stage in hydroponic system using nutrient solution. In F3 population, six lines were found as salt tolerant and 10 lines were moderately tolerant based on phenotypic screening at the seedling stage. Twelve SSR markers were used for parental survey and among them three polymorphic SSR markers viz., OSR34, RM443 and RM169 were selected to evaluate 26 F3 rice lines for salt tolerance. With respect to marker OSR34, 15 lines were identified as salt tolerant, 9 lines were susceptible and 2 lines were heterozygous. While RM443 identified 3 tolerant, 14 susceptible and 9 heterozygous rice lines. Eight tolerant, 11 susceptible and 7 heterozygous lines were identified with the marker RM169. Thus the tested markers could be efficiently used for tagging salt tolerant genes in marker-assisted breeding programme.DOI: http://dx.doi.org/10.3329/pa.v19i2.16929 Progress. Agric. 19(2): 57 - 65, 2008

scholarly journals Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks

2021 ◽  
Vol 12 ◽  
Author(s):  
Pajaree Sonsungsan ◽  
Pheerawat Chantanakool ◽  
Apichat Suratanee ◽  
Teerapong Buaboocha ◽  
Luca Comai ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Time Course ◽  
Rice Variety ◽  
Enrichment Analysis ◽  
Normal Growth ◽  
Growth Conditions ◽  
Pathway Enrichment Analysis ◽  
Key Genes

Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of ‘Luang Pratahn’ rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.

scholarly journals Marker-assisted Backcrossing for Identification of Salt Tolerant Rice Lines

2013 ◽  
Vol 2 (2) ◽  
pp. 1-8 ◽  
Author(s):  
M Moniruzzaman ◽  
MS Islam ◽  
JA Rashid ◽  
SN Begum ◽  
MM Islam
Keyword(s):  
Genetic Diversity ◽  
Salt Tolerance ◽  
Ssr Markers ◽  
Marker Assisted Selection ◽  
Genetic Maps ◽  
Salt Tolerant ◽  
High Yielding Variety ◽  
Marker Assisted Backcrossing ◽  
Tolerant Genotype ◽  
New Cultivars

SSR or microsatellite markers are proved to be ideal for making genetic maps, assisting selection and studying genetic diversity in germplasm. SSR markers are playing important role to identify gene for salt tolerance that can be helpful for plant breeders to develop new cultivars. The experiment was conducted during the period from July 2009 to November 2010 in the experimental field and Biotechnology Laboratory of Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh to identify salt tolerant rice line of BC1F1 progenies of Binadhan-5 x FL-478 using SSR markers. Salt tolerant genotype, FL-478 was crossed with high yielding variety, Binadhan-5. Randomly selected 40 BC1F1 progenies along with their two parents (Binadhan-5, FL-478 and F1) were genotyped with microsatellite or SSR markers for identification of salt tolerant rice lines. Parental polymorphism survey was assayed by 10 SSR markers and three polymorphic SSR markers viz., RM 336, RM 510, and RM 585 were selected to evaluate BC1F1 rice lines for salt tolerance. In respect of Primer RM 336, 11 lines were found as salt tolerant and 25 lines were heterozygous and 3 lines were susceptible. Primer RM 510 identified two tolerant, 14 heterozygous and 22 susceptible lines. And primer RM 585 identified 4 lines as tolerant and 35 lines as susceptible. Thus, these markers could be efficiently used in tagging salt tolerant genes, in marker-assisted selection and quantitative trait loci (QTL) mapping. The selected BC1F1 could be used for developing BC2F1 and BC2F2 and mapping genes for salinity tolerance. DOI: http://dx.doi.org/10.3329/ijarit.v2i2.14008 Int. J. Agril. Res. Innov. & Tech. 2 (2): 1-8, December, 2012

scholarly journals Effect of Salt-Tolerant Bacterial Inoculations on Rice Seedlings Differing in Salt-Tolerance under Saline Soil Conditions

Agronomy ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1030 ◽  
Author(s):  
Rakiba Shultana ◽  
Ali Tan Kee Zuan ◽  
Mohd Rafii Yusop ◽  
Halimi Mohd Saud ◽  
Arolu Fatai Ayanda
Keyword(s):  
Salt Tolerance ◽  
Plant Growth ◽  
Water Content ◽  
Electrolyte Leakage ◽  
Relative Water Content ◽  
Rice Variety ◽  
Salt Tolerant ◽  
Relative Water ◽  
Plant Growth Promoting ◽  
Growth Promoting

Salt-tolerant plant growth-promoting rhizobacteria (PGPR) could be an alternative to alleviate salinity problems in rice plants grown in the coastal areas. This study was conducted to isolate and characterize salt-tolerant PGPR and observe their effects on the physiological and biochemical properties of rice plants grown under non-saline and saline glasshouse conditions. Three strains were selected based on their salt-tolerance and plant growth-promoting properties under in vitro saline conditions. These strains were identified as Bacillus tequilensis (UPMRB9), Bacillus aryabhattai (UPMRE6), and Providencia stuartii (UPMRG1) using a 16S rRNA technique. The selected strains were inoculated to three different rice varieties, namely BRRI dhan67 (salt-tolerant), Putra-1 (moderate salt-tolerant), and MR297 (salt-susceptible) under glasshouse conditions. Results showed that the MR297 rice variety inoculated with UPMRB9 produced the highest total chlorophyll content, with an increment of 28%, and lowest electrolyte leakage of 92%. The Putra-1 rice variety also showed a 156% total dry matter increase with the inoculation of this bacterial strain. The highest increase of relative water content and reduction of Na/K ratio were found upon inoculation of UPMRE6 and UPMRB9, respectively. The biggest significant effects of these bacterial inoculations were on relative water content, electrolyte leakage, and the Na/K ratio of the BRRI dhan67 rice variety under saline conditions, suggesting a synergistic effect on the mechanisms of plant salt-tolerance. This study has shown that the application of locally-isolated salt-tolerant PGPR strains could be an effective long-term and sustainable solution for rice cultivation in the coastal areas, which are affected by global climate change.

Analysis of genomic region spanning Saltol using SSR markers in rice genotypes showing differential seedlings stage salt tolerance

2015 ◽  
Vol 25 (3) ◽  
pp. 331-336 ◽  
Author(s):  
S. L. Krishnamurthy ◽  
S. K. Sharma ◽  
V. Kumar ◽  
S. Tiwari ◽  
N. K. Singh
Keyword(s):  
Salt Tolerance ◽  
Ssr Markers ◽  
Genomic Region ◽  
Rice Genotypes

scholarly journals Genetic Divergence and Heritability Study of Some NERICA Mutant Lines and Their Parents Using Microsatellites Marker and Morphological Traits in Rice

2019 ◽  
pp. 1-14
Author(s):  
Md. Ashraful Islam ◽  
Touhidur Rahman Anik ◽  
Saikat Chandra Dey ◽  
Mirza Mofazzal Islam
Keyword(s):  
Ssr Markers ◽  
Morphological Traits ◽  
Gene Diversity ◽  
Rice Variety ◽  
Climatic Conditions ◽  
Tiller Number ◽  
Genetic Advance ◽  
Panicle Number ◽  
The Mean ◽  
Mutant Lines

New Rice of Africa (NERICA) is drought tolerant and early maturing inter specific rice variety which was introduced in Bangladesh from Uganda in 2009. But the field record of NERICA was not very promising. In order to develop NERICA varieties suitable for agro-climatic conditions of Bangladesh different variations in yield contributing characters are required.In the experiment, physical mutagen treated (250, 300 and 350 Gy Gamma-rays) 18 NERICA mutant lines were selected from M4 to M5 generations along with 3 parents (NERICA-1, NERICA-4, NERICA-10) for morphological and molecular evaluation in orderto identify desired mutant linesusing 12 yield attributing characters and 3 simple sequence repeat (SSR) markers. We also estimated heritability, genetic advance and correlation among the studied morphological traits to identify besttraits based on which further selection could be made. Pearson’s correlation co-efficient of 12 morphological traits indicated that yield per plant had significant positive correlation with the number of tiller, number of effective tiller, panicle length, number of filled grainsper panicle and 1000 grain weight but negative correlation with Plant height and days to maturity. Broad sense heritability ( ) ranged from 71% to 99% while genetic advances in percent mean (GA%) varied from 10% to 60%. Yield per plant, unfilled grains per panicle, number of total tiller, number of effective tiller showed high heritability along with genetic advance as percent of the mean (GA%) value. A total of 24 alleles were detected by 3 SSR markers. The mean gene diversity and Polymorphism Information Content (PIC) values was 0.821 and 0.797, respectively.  Dendrogram constructed based on SSR markers clustered the genotypes into six distinct clusters. Combining molecular and morphological evaluation data eight mutant lines, N10/300/P-2-3-5, N10/300/P-2-3-5, N10/300/P-2-3-5-2, N1/300/P-2-3-5, N1/300/P-2-3-5, N1/250/P-7-6-4-1, N10/300/P-2(1)-4-1 and N1/250/P-7-3-7-1were selected as desired mutant lines having good yield attributing characters and could be recommended for further evaluation in rice breeding program.

scholarly journals Effect of salt stress on physiological response and leaf polyamine content in NERICA rice seedlings

2011 ◽  
Vol 57 (No. 12) ◽  
pp. 571-576 ◽  
Author(s):  
A. Yamamoto ◽  
H. Sawada ◽  
I.S. Shim ◽  
K. Usui ◽  
S. Fujihara
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Rice Variety ◽  
West African ◽  
Rice Seedlings ◽  
Rice Varieties ◽  
Stress Injury ◽  
African Rice ◽  
Polyamine Content ◽  
Vigorous Growth

NERICA is a new African rice variety, developed by the West African Rice Development Association (WARDA) in 1990s. NERICA rice shows both vigorous growth and tolerance of stressors such as drought and disease. The purpose of this study was to clarify the physiological and biochemical responses to salt stress of NERICA rice seedlings. The degree of growth inhibition caused by salt stress was small in NERICA rice varieties as compared with japonica Nipponbare. Na accumulation in leaf blades was high in salt-sensitive varieties. Accumulation of proline, a known compatible solute, was also induced by salt stress, especially in salt-sensitive varieties; it was thought that this accumulation was brought on salt-stress injury. The contents of polyamines, especially spermidine, were high in the pre-stressed leaf blades of NERICA rice seedlings. After the salt-stress treatment, the polyamine content of leaf blades differed with the degree of salt tolerance of the NERICA rice seedlings. These results suggested that the salt tolerance of NERICA rice seedlings might be associated not only with the regulation of Na absorption and translocation but also with their ability to maintain leaf polyamine levels under salt-stress conditions.  

Sign in / Sign up

Export Citation Format

Share Document