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 Morpho-Molecular Characterization and Screening of Rice (Oryza Sativa L.) Genotypes for Salinity Tolerance at Seedling Stage

2021 ◽  
Vol 18 (2) ◽  
pp. 1-15
Author(s):  
SAA Muti ◽  
MI Hoque ◽  
MM Islam ◽  
MA Siddique ◽  
MS Islam
Keyword(s):  
Salt Tolerance ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Seedling Stage ◽  
Group Method ◽  
Rice Varieties ◽  
Pair Group ◽  
Rice Genotypes ◽  
Near Future

Salinity is one of the major abiotic stresses which severely affect the production of crops across the world. Twenty rice genotypes of diverse origins were assessed to examine salt tolerance potentiality at seedling stage as well as to elucidate the genetic variation using SSR markers. Consequently, IRRI standard protocol was applied to screen out those varieties for tolerance at the glasshouse laboratory of Bangladesh Institute of Nuclear Agriculture, maintaining salt stress level at 6dS m-1, 8dS m-1, 10dS m-1 and 12 dS m-1. Data on morphological parameter were recorded as shoot length (cm), root length (cm) and total dry matter (TDM). For molecular characterization thirteen SSR markers were exploited to determine the genetic diversity and in this context, 53alleles were revealed while the mean number of alleles per locus was 4.The Polymorphism Information Content (PIC) value ranged from 0.37- 0.78 having an average of 0.58. The Un-weighted Pair Group Method with Arithmetic Mean (UPGMA) displayed three major clusters including some sub-clusters, where in Cluster 1, Binadhan- 8, Binadhan-10, Pokkali and FL478 were very close in their vicinity. Information obtained from this experiment, thus can be taken into account for stress breeding program and prospective genetic materials could be utilized for exploring the genetic architecture in favor of salt tolerance as well as for developing better salt tolerant rice varieties in near future. SAARC J. Agri., 18(2): 1-15 (2020)

scholarly journals Genetic diversity analysis of advanced rice lines for salt tolerance using SSR markers

2021 ◽  
Vol 7 (2) ◽  
pp. 214-221
Author(s):  
Tanoy Singha ◽  
Md Asif Mahamud ◽  
Shahin Imran ◽  
Newton Chandra Paul ◽  
Md Najmol Hoque ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Salt Tolerance ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Potential Role ◽  
Diversity Analysis ◽  
Marker Assisted Breeding ◽  
Genetic Diversity Analysis ◽  
Ssr Analysis ◽  
Rice Genotypes

Twenty-two rice lines were used to evaluate salt tolerance at the Laboratory of Biotechnology Division of Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh. Four SSR markers viz. AP3206f, RM1287, RM7075, and RM10793 were used to screen the germplasm for salt tolerance. SSR analysis revealed that the number of alleles per locus ranged from 3 to 5 with an average of 4.25 alleles per locus. Polymorphism Information Content (PIC) values ranged from 0.4762 (RM7075) to 0.7524 (AP3206f) with an average of 0.61 per locus. The highest genetic diversity (0.7810) was observed in loci AP3206f, and the lowest genetic diversity (0.5620) was observed in loci RM7075 with a mean diversity of 0.6663. The genotypes with genetic similarity clustered together in the dendrogram based on UPGMA method and we observed seven major clusters where cluster I contained most of the genotypes. Cluster I, II, III, IV, V, VI, and VII contained 6, 1, 2, 4, 4, 4 and 1 genotypes, respectively. These results revealed that marker AP3206f would be best in screening 22 rice genotypes followed by RM1287, RM7075, and RM10793 according to PIC values. These findings can have the potential role for further improvement of salinity tolerance rice genotypes through marker-assisted breeding. Asian J. Med. Biol. Res. 2021, 7 (2), 214-221

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 Genetic Diversity of Selected Rice Genotypes under Water Stress Conditions

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 27
Author(s):  
Mahmoud M. Gaballah ◽  
Azza M. Metwally ◽  
Milan Skalicky ◽  
Mohamed M. Hassan ◽  
Marian Brestic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Water Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Ssr Markers ◽  
Similarity Index ◽  
Stress Conditions ◽  
Yield Potential ◽  
Drought Tolerant ◽  
Rice Genotypes

Drought is the most challenging abiotic stress for rice production in the world. Thus, developing new rice genotype tolerance to water scarcity is one of the best strategies to achieve and maximize high yield potential with water savings. The study aims to characterize 16 rice genotypes for grain and agronomic parameters under normal and drought stress conditions, and genetic differentiation, by determining specific DNA markers related to drought tolerance using Simple Sequence Repeats (SSR) markers and grouping cultivars, establishing their genetic relationship for different traits. The experiment was conducted under irrigated (normal) and water stress conditions. Mean squares due to genotype × environment interactions were highly significant for major traits. For the number of panicles/plants, the genotypes Giza179, IET1444, Hybrid1, and Hybrid2 showed the maximum mean values. The required sterility percentage values were produced by genotypes IET1444, Giza178, Hybrid2, and Giza179, while, Sakha101, Giza179, Hybrid1, and Hybrid2 achieved the highest values of grain yield/plant. The genotypes Giza178, Giza179, Hybrid1, and Hybrid2, produced maximum values for water use efficiency. The effective number of alleles per locus ranged from 1.20 alleles to 3.0 alleles with an average of 1.28 alleles, and the He values for all SSR markers used varied from 0.94 to 1.00 with an average of 0.98. The polymorphic information content (PIC) values for the SSR were varied from 0.83 to 0.99, with an average of 0.95 along with a highly significant correlation between PIC values and the number of amplified alleles detected per locus. The highest similarity coefficient between Giza181 and Giza182 (Indica type) was observed and are susceptible to drought stress. High similarity percentage between the genotypes (japonica type; Sakha104 with Sakha102 and Sakha106 (0.45), Sakha101 with Sakha102 and Sakha106 (0.40), Sakha105 with Hybrid1 (0.40), Hybrid1 with Giza178 (0.40) and GZ1368-S-5-4 with Giza181 (0.40)) was also observed, which are also susceptible to drought stress. All genotypes are grouped into two major clusters in the dendrogram at 66% similarity based on Jaccard’s similarity index. The first cluster (A) was divided into two minor groups A1 and A2, in which A1 had two groups A1-1 and A1-2, containing drought-tolerant genotypes like IET1444, GZ1386-S-5-4 and Hybrid1. On the other hand, the A1-2 cluster divided into A1-2-1 containing Hybrid2 genotype and A1-2-2 containing Giza179 and Giza178 at coefficient 0.91, showing moderate tolerance to drought stress. The genotypes GZ1368-S-5-4, IET1444, Giza 178, and Giza179, could be included as appropriate materials for developing a drought-tolerant variety breeding program. Genetic diversity to grow new rice cultivars that combine drought tolerance with high grain yields is essential to maintaining food security.

Carbon isotope discrimination and salt tolerance of rice genotypes

2004 ◽  
Vol 32 (3) ◽  
pp. 339-346 ◽  
Author(s):  
James A. Poss ◽  
Linghe Zeng ◽  
Catherine M. Grieve
Keyword(s):  
Salt Tolerance ◽  
Carbon Isotope ◽  
Carbon Isotope Discrimination ◽  
Isotope Discrimination ◽  
Rice Genotypes

scholarly journals Evaluation of Rice Germplasm under Salt Stress at the Seedling Stage through SSR Markers

2013 ◽  
Vol 3 (1) ◽  
pp. 52-59 ◽  
Author(s):  
M Al-Amin ◽  
MM Islam ◽  
SN Begum ◽  
MS Alam ◽  
M Moniruzzaman ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Salinity Tolerance ◽  
Dry Matter ◽  
Growth Parameters ◽  
Seedling Stage ◽  
Salt Tolerant ◽  
Marker Assisted Breeding ◽  
Hydroponic System ◽  
Rice Genotypes ◽  
Salt Susceptible

Twenty eight rice germplasms were used for identification of salt tolerant rice genotypes at the seedling stage at the experimental farm and Biotechnology laboratory of the Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh during February 2009 to October 2009. Phenotyping for salinity screening of the rice genotypes was done using salinized (EC level 12 dS m-1) nutrient solution in hydroponic system. Genotypes were evaluated for salinity tolerance on 1-9 scale based on seedling growth parameters following modified Standard Evaluation Scoring (SES) of IRRI. Phenotypically, on the basis of SES and % total dry matter (TDM) reduction of the genotypes viz. PBSAL-614, PBSAL-613, PBSAL-730, Horkuch, S-478/3 Pokkali and PBSAL (STL)-15 were found to be salt tolerant; on the other hand Iratom-24, S-653/32, S-612/32, S-604/32, S-633/32, Charnock (DA6), BINA Dhan-6 and S-608/32 were identified as salt susceptible. For genotyping, ten SSR markers were used for polymorphism, where 3 primers (RM127, RM443 and RM140) were selected for evaluation of salt tolerance. In respect of Primer RM127, 7 lines were found salt tolerant and 11 lines were moderately tolerant and 10 lines were susceptible. Nine tolerant, 9 moderately tolerant and 10 susceptible lines were found when the primer RM140 was used and primer RM443 identified 8 lines as tolerant, 9 lines as moderately tolerant and 11 lines as susceptible. Thus, the salt tolerant lines can be used in further evaluation for salinity tolerance and the SSR markers used in this study are proving valuable for identifying salt tolerant genes in marker assisted breeding. Int. J. Agril. Res. Innov. & Tech. 3 (1): 52-59, June, 2013 DOI: http://dx.doi.org/10.3329/ijarit.v3i1.16093

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

Assessment of the genetic diversity and population structure of rice genotypes using SSR markers

2019 ◽  
Vol 70 (1) ◽  
pp. 76-86 ◽  
Author(s):  
William Titus Suvi ◽  
Hussein Shimelis ◽  
Mark Laing ◽  
Isack Mathew ◽  
Admire Isaac Tichafa Shayanowako
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Rice Genotypes
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