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

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

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

International Journal of Agricultural Research Innovation and Technology ◽

10.3329/ijarit.v3i1.16093 ◽

2013 ◽

Vol 3 (1) ◽

pp. 52-59 ◽

Cited By ~ 2

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

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Genomic and transcriptomic analysis reveal molecular basis of salinity tolerance in a novel strong salt-tolerant rice landrace Changmaogu

Rice ◽

10.1186/s12284-019-0360-4 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 3

Author(s):

Bing-Rui Sun ◽

Chong-Yun Fu ◽

Zhi-Lan Fan ◽

Yu Chen ◽

Wen-Feng Chen ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Salinity Tolerance ◽

Molecular Basis ◽

Carotenoid Biosynthesis ◽

Seedling Stage ◽

Differentially Expressed ◽

Salt Tolerant ◽

Transcriptomic Sequencing ◽

Rice Landrace

Abstract Background Salt stress is an important factor that limits rice yield. We identified a novel, strongly salt tolerant rice landrace called Changmaogu (CMG) collected from a coastal beach of Zhanjiang, Guangdong Province, China. The salt tolerance of CMG was much better than that of the international recognized salt tolerant rice cultivar Pokkali in the germination and seedling stages. Results To understand the molecular basis of salt tolerance in CMG, we performed BSA-seq for two extreme bulks derived from the cross between CMG and a cultivar sensitive to salt, Zhefu802. Transcriptomic sequencing was conducted for CMG at the germination and young seedling stages. Six candidate regions for salt tolerance were mapped on Chromosome 1 by BSA-seq using the extreme populations. Based on the polymorphisms identified between both parents, we detected 32 genes containing nonsynonymous coding single nucleotide polymorphisms (SNPs) and frameshift mutations in the open reading frame (ORF) regions. With transcriptomic sequencing, we detected a large number of differentially expressed genes (DEGs) at the germination and seedling stages under salt stress. KEGG analysis indicated two of 69 DEGs shared at the germination and seedling stages were significantly enriched in the pathway of carotenoid biosynthesis. Of the 169 overlapping DEGs among three sample points at the seedling stage, 13 and six DEGs were clustered into the pathways of ABA signal transduction and carotenoid biosynthesis, respectively. Of the 32 genes carrying sequence variation, only OsPP2C8 (Os01g0656200) was differentially expressed in the young seedling stage under salt stress and also showed sequence polymorphism in the ORFs between CMG and Zhefu802. Conclusion OsPP2C8 was identified as the target candidate gene for salinity tolerance in the seedling stage. This provides an important genetic resource for the breeding of novel salt tolerant rice cultivars.

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Identification of introgressed rice lines of Binadhan-7×FL-378 under salt stress through SSR markers

Journal of the Bangladesh Agricultural University ◽

10.3329/jbau.v10i1.12039 ◽

2012 ◽

Vol 10 (1) ◽

pp. 49-54 ◽

Cited By ~ 1

Author(s):

M A Haque ◽

M A Mahmud ◽

M M Islam ◽

S N Begum

Keyword(s):

Salt Tolerance ◽

Ssr Markers ◽

Gene Diversity ◽

Salt Tolerant ◽

Bc1f1 Population ◽

Backcross Population ◽

Ssr Loci ◽

Salt Susceptible ◽

Pattern Of Variation ◽

Positive Correlations

Thirty two rice lines of BC1F1 population (Binadhan-7/FL 378) were used to identify introgressed rice lines for salt tolerance using SSR markers at the Plant Breeding and Biotechnology Divisions of Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh. Seeds of BC1F1 population of Binadhan-7/FL-378 were collected from backcross population of F1 (Binadhan-7/FL 378). Salt tolerant genotype, FL-378 was crossed with high yielding variety, Binadhan-7. Randomly selected 32 BC1F1 progenies along with their two parents (Binadhan-7, FL-378) were genotyped with microsatellite or SSR markers for identification of introgressed rice lines. Parental polymorphism survey was assayed by 8 SSR markers and three polymorphic SSR markers viz., RM296, RM585 and OSR30 were selected to evaluate BC1F1 rice lines for salt tolerance. Primer RM585 indicated 16 lines as introgressed and 16 lines as susceptible in comparison with salt tolerant parent FL-378 and salt susceptible parent Binadhan-7. Primer RM296 identified 13 introgressed, and 19 susceptible lines. Nine introgressed and 23 susceptible lines were identified when BC1F1 lines were evaluated with marker OSR30. Line BC1F1-30, BC1F1-40, BC1F1-2, BC1F1-16 and BC1F1-34 were identified as introgressed in comparison with parent FL-378 (salt tolerant) when RM585 and RM296 markers were used but line BC1F1-1 and BC1F1-3 were identified as introgressed incase of 3 primers (RM585, RM296 and OSR30). Again the lines BC1F1-5, BC1F1-24, BC1F1-26, BC1F1-27, BC1F1-29, BC1F11F1-37 and BC1F1(PIC) values ranged from 0.3290 to 0.3671 with an average of 0.3544. The overall gene diversity of SSR loci for the 32 BC1F1 rice lines along with two parents was 0.4614, ranging from 0.4152 to 0.4844. Positive correlations were found between the genetic diversity and the maximum number of repeats. Among the lines, all the loci were polymorphic and clearly distinct and the cluster analysis (NJ tree and UPGMA) showed nearly similar pattern of variation which could be used for improvement of salt tolerant rice lines of rice through SSR markers.DOI: http://dx.doi.org/10.3329/jbau.v10i1.12039J. Bangladesh Agril. Univ. 10(1): 4954, 2012

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Identification of introgressed rice lines of Binadhan-7×FL-378 under salt stress through SSR markers

Journal of the Bangladesh Agricultural University ◽

10.3329/jbau.v10i2.14680 ◽

2013 ◽

Vol 10 (2) ◽

pp. 185-190

Author(s):

MA Haque ◽

MA Mahmud ◽

MM Islam ◽

SN Begum

Keyword(s):

Salt Tolerance ◽

Ssr Markers ◽

Gene Diversity ◽

Salt Tolerant ◽

Bc1f1 Population ◽

Backcross Population ◽

Ssr Loci ◽

Salt Susceptible ◽

Pattern Of Variation ◽

Positive Correlations

Thirty two rice lines of BC1F1 population (Binadhan-7/FL 378) were used to identify introgressed rice lines for salt tolerance using SSR markers at the Plant Breeding and Biotechnology Divisions of Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh. Seeds of BC1F1 population of Binadhan-7/FL-378 were collected from backcross population of F1 (Binadhan-7/FL 378). Salt tolerant genotype, FL-378 was crossed with high yielding variety, Binadhan-7. Randomly selected 32 BC1F1 progenies along with their two parents (Binadhan-7, FL-378) were genotyped with microsatellite or SSR markers for identification of introgressed rice lines. Parental polymorphism survey was assayed by 8 SSR markers and three polymorphic SSR markers viz., RM296, RM585 and OSR30 were selected to evaluate BC1F1 rice lines for salt tolerance. Primer RM585 indicated 16 lines as introgressed and 16 lines as susceptible in comparison with salt tolerant parent FL-378 and salt susceptible parent Binadhan-7. Primer RM296 identified 13 introgressed, and 19 susceptible lines. Nine introgressed and 23 susceptible lines were identified when BC1F1 lines were evaluated with marker OSR30. Line BC1F1-30, BC1F1-40, BC1F1-2, BC1F1-16 and BC1F1-34 were identified as introgressed in comparison with parent FL-378 (salt tolerant) when RM585 and RM296 markers were used but line BC1F1-1 and BC1F1-3 were identified as introgressed incase of 3 primers (RM585, RM296 and OSR30). Again the lines BC1F1-5, BC1F1-24, BC1F1-26, BC1F1-27, BC1F1-29, BC1F1-31, BC1F1-37 and BC1F1-38 were found susceptible as compared with parent Binadhan-7 when marker RM585, RM296 and OSR30 were used. The polymorphism information content (PIC) values ranged from 0.3290 to 0.3671 with an average of 0.3544. The overall gene diversity of SSR loci for the 32 BC1F1 rice lines along with two parents was 0.4614, ranging from 0.4152 to 0.4844. Positive correlations were found between the genetic diversity and the maximum number of repeats. Among the lines, all the loci were polymorphic and clearly distinct and the cluster analysis (NJ tree and UPGMA) showed nearly similar pattern of variation which could be used for improvement of salt tolerant rice lines of rice through SSR markers. DOI: http://dx.doi.org/10.3329/jbau.v10i2.14680 J. Bangladesh Agril. Univ. 10(2): 185190, 2012

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Evaluation of salinity tolerance indices in North African barley accessions at reproductive stage

Czech Journal of Genetics and Plant Breeding ◽

10.17221/50/2017-cjgpb ◽

2019 ◽

Vol 55 (No. 2) ◽

pp. 61-69 ◽

Cited By ~ 3

Author(s):

Dorsaf Allel ◽

Anis BenAmar ◽

Mounawer Badri ◽

Chedly Abdelly

Keyword(s):

Salt Tolerance ◽

Grain Yield ◽

Salinity Tolerance ◽

Selection Criteria ◽

Reproductive Stage ◽

Shoot Biomass ◽

Salt Tolerant ◽

North African ◽

Grain Number ◽

Selection Indices

Soil salinity is one of the main factors limiting cereal productivity in worldwide agriculture. Exploitation of natural variation in local barley germplasm is an effective approach to overcome yield losses. Three gene pools of North African Hordeum vulgare L. grown in Tunisia, Algeria and Egypt were evaluated at the reproductive stage under control and saline conditions. Assessment of stress tolerance was monitored using morphological, yield-related traits and phenological parameters of reproductive organs showing significant genetic variation. High heritability and positive relationships were found suggesting that some traits associated with salt tolerance could be used as selection criteria. The phenotypic correlations revealed that vegetative traits including shoot biomass, tiller number and leaf number along with yield-related traits such as spike number, one spike dry weight, grain number/plant and grain number/spike were highly positively correlated with grain yield under saline conditions. Hence, these traits can be used as reliable selection criteria to improve barley grain yield. Keeping a higher shoot biomass and longer heading and maturity periods as well as privileged filling ability might contribute to higher grain production in barley and thus could be potential target traits in barley crop breeding toward improvement of salinity tolerance. Multiple selection indices revealed that salt tolerance trait index provided a better discrimination of barley landraces allowing selection of highly salt-tolerant and highly productive genotypes under severe salinity level. Effective evaluation of salt tolerance requires an integration of selection indices to successfully identify and characterize salt tolerant lines required for valuable exploitation in the management of salt-affected areas.

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Early Growth Stage Characterization and the Biochemical Responses for Salinity Stress in Tomato

Plants ◽

10.3390/plants10040712 ◽

2021 ◽

Vol 10 (4) ◽

pp. 712

Author(s):

Md Sarowar Alam ◽

Mark Tester ◽

Gabriele Fiene ◽

Magdi Ali Ahmed Mousa

Keyword(s):

Salt Tolerance ◽

Salinity Tolerance ◽

Salinity Treatment ◽

Salt Tolerant ◽

Improvement Program ◽

Biochemical Basis ◽

Elevated Salinity ◽

Tolerance Indices ◽

Promising Source ◽

Tomato Genotypes

Salinity is one of the most significant environmental stresses for sustainable crop production in major arable lands of the globe. Thus, we conducted experiments with 27 tomato genotypes to screen for salinity tolerance at seedling stage, which were treated with non-salinized (S1) control (18.2 mM NaCl) and salinized (S2) (200 mM NaCl) irrigation water. In all genotypes, the elevated salinity treatment contributed to a major depression in morphological and physiological characteristics; however, a smaller decrease was found in certain tolerant genotypes. Principal component analyses (PCA) and clustering with percentage reduction in growth parameters and different salt tolerance indices classified the tomato accessions into five key clusters. In particular, the tolerant genotypes were assembled into one cluster. The growth and tolerance indices PCA also showed the order of salt-tolerance of the studied genotypes, where Saniora was the most tolerant genotype and P.Guyu was the most susceptible genotype. To investigate the possible biochemical basis for salt stress tolerance, we further characterized six tomato genotypes with varying levels of salinity tolerance. A higher increase in proline content, and antioxidants activities were observed for the salt-tolerant genotypes in comparison to the susceptible genotypes. Salt-tolerant genotypes identified in this work herald a promising source in the tomato improvement program or for grafting as scions with improved salinity tolerance in tomato.

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Advances and Challenges in the Breeding of Salt-Tolerant Rice

International Journal of Molecular Sciences ◽

10.3390/ijms21218385 ◽

2020 ◽

Vol 21 (21) ◽

pp. 8385

Author(s):

Hua Qin ◽

Yuxiang Li ◽

Rongfeng Huang

Keyword(s):

Food Security ◽

Salt Tolerance ◽

Quantitative Trait ◽

Molecular Mechanisms ◽

Soil Salinization ◽

Ecological Environment ◽

Salt Tolerant ◽

Salt Stress Tolerance ◽

Rice Varieties ◽

Salt Susceptible

Soil salinization and a degraded ecological environment are challenging agricultural productivity and food security. Rice (Oryza sativa), the staple food of much of the world’s population, is categorized as a salt-susceptible crop. Improving the salt tolerance of rice would increase the potential of saline-alkali land and ensure food security. Salt tolerance is a complex quantitative trait. Biotechnological efforts to improve the salt tolerance of rice hinge on a detailed understanding of the molecular mechanisms underlying salt stress tolerance. In this review, we summarize progress in the breeding of salt-tolerant rice and in the mapping and cloning of genes and quantitative trait loci (QTLs) associated with salt tolerance in rice. Furthermore, we describe biotechnological tools that can be used to cultivate salt-tolerant rice, providing a reference for efforts aimed at rapidly and precisely cultivating salt-tolerance rice varieties.

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Physiological and Biochemical Responses to Salt Stress of Alfalfa Populations Selected for Salinity Tolerance and Grown in Symbiosis with Salt-Tolerant Rhizobium

Agronomy ◽

10.3390/agronomy10040569 ◽

2020 ◽

Vol 10 (4) ◽

pp. 569

Author(s):

Annick Bertrand ◽

Craig Gatzke ◽

Marie Bipfubusa ◽

Vicky Lévesque ◽

Francois P. Chalifour ◽

...

Keyword(s):

Amino Acids ◽

Salt Stress ◽

Salt Tolerance ◽

Water Content ◽

Salinity Tolerance ◽

Osmotic Adjustment ◽

Recurrent Selection ◽

Aromatic Amino Acids ◽

Nacl Stress ◽

Salt Tolerant

Alfalfa and its rhizobial symbiont are sensitive to salinity. We compared the physiological responses of alfalfa populations inoculated with a salt-tolerant rhizobium strain, exposed to five NaCl concentrations (0, 20, 40, 80, or 160 mM NaCl). Two initial cultivars, Halo (H-TS0) and Bridgeview (B-TS0), and two populations obtained after three cycles of recurrent selection for salt tolerance (H-TS3 and B-TS3) were compared. Biomass, relative water content, carbohydrates, and amino acids concentrations in leaves and nodules were measured. The higher yield of TS3-populations than initial cultivars under salt stress showed the effectiveness of our selection method to improve salinity tolerance. Higher relative root water content in TS3 populations suggests that root osmotic adjustment is one of the mechanisms of salt tolerance. Higher concentrations of sucrose, pinitol, and amino acid in leaves and nodules under salt stress contributed to the osmotic adjustment in alfalfa. Cultivars differed in their response to recurrent selection: under a 160 mM NaCl-stress, aromatic amino acids and branched-chain amino acids (BCAAs) increased in nodules of B-ST3 as compared with B-TS0, while these accumulations were not observed in H-TS3. BCAAs are known to control bacteroid development and their accumulation under severe stress could have contributed to the high nodulation of B-TS3.

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Marker-assisted Backcrossing for Identification of Salt Tolerant Rice Lines

International Journal of Agricultural Research Innovation and Technology ◽

10.3329/ijarit.v2i2.14008 ◽

2013 ◽

Vol 2 (2) ◽

pp. 1-8 ◽

Cited By ~ 4

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

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