scholarly journals Genetic diversity assessment of Rice (Oryza sativa L.) germplasm using ssr markers

2015 ◽  
Vol 1 (1) ◽  
pp. 37-46 ◽  
Author(s):  
Ahasanul Hoque ◽  
Shamsun Nahar Begum ◽  
Lutful Hassan
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Growth Duration ◽  
Breeding Programs ◽  
Diversity Assessment ◽  
Days To Heading ◽  
Early Maturing ◽  
Rice Genotypes ◽  
Selection Of

Diversity at molecular level among thirty rice genotypes, selected based on earliness and morphometric diversity was evaluated through five SSR markers associated with days to heading. Three primers viz., RM147, RM167 and RM215 showed polymorphism for growth duration related traits. A total of 17 alleles were detected among the 30 rice genotypes with an average of 5.66 alleles per locus. Polymorphism Information Content (PIC) ranged from 0.356 to 0.798 with an average of 0.543. A dendrogram based on total microsatellite polymorphism grouped 30 genotypes into four major clusters at 0.39 similarity coefficient differentiating early maturing genotypes from others. This information about the genetic diversity will be very useful for proper identification and selection of appropriate parents for future breeding programs, including gene mapping. The results also showed that microsatellite markers associated to genes or QTLs controlling growth duration properties are suitable tools for marker assisted selection (MAS) to select rice lines with short growth duration. DOI: http://dx.doi.org/10.3329/ralf.v1i1.22354 Res. Agric., Livest. Fish.1(1): 37-46, Dec 2014

scholarly journals Diversity analysis of some selected rice genotypes through SSR- based molecular markers

2016 ◽  
Vol 12 (2) ◽  
pp. 307-311 ◽  
Author(s):  
MH Shahriar ◽  
AHK Robin ◽  
SN Begum ◽  
A Hoque
Keyword(s):  
Genetic Diversity ◽  
Marker Assisted Selection ◽  
Oryza Sativa L ◽  
Diversity Analysis ◽  
Growth Duration ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Early Maturing ◽  
Rice Genotypes

An experiment was carried out to assess the genetic diversity of advanced rice (Oryza sativa L.) breeding lines using three SSR markers viz., RM147, RM167 and RM215. Thirty T- aman advanced breeding lines at F9 generation along with 4 check varieties were assessed. All three primers showed polymorphism. A total of 29 alleles were detected among the rice genotypes with an average of 9.67 alleles per locus. Polymorphism information content (PIC) ranged from 0.47 to 0.88 with an average of 0.71. A dendrogram was constructed based on total microsatellite polymorphism and 34 genotypes were grouped into four major clusters at 0.36 similarity co-efficient differentiating the early maturing genotypes from the late maturing types. The information about the genetic diversity might be utilized in future breeding programs for developing rice varieties with much shorter growth duration. The results also suggested that microsatellite markers which are linked to genes or QTLs responsible for growth duration properties are suitable tools for marker assisted selection (MAS) to select the rice genotypes of shorter growth duration.J. Bangladesh Agril. Univ. 12(2): 307-311, December 2014

scholarly journals Assessment of diversity by using morphological, biochemical and molecular approaches of selected basmati rice (Oryza sativa L.) varieties

2016 ◽  
Vol 8 (1) ◽  
pp. 69-76 ◽  
Author(s):  
A. Mishra ◽  
Pradeep Kumar ◽  
R. S. Sengar ◽  
P. Kumar ◽  
R. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Molecular Analysis ◽  
Oryza Sativa L ◽  
Quality Parameters ◽  
Basmati Rice ◽  
Molecular Approaches ◽  
Gel Consistency ◽  
Rice Genotypes ◽  
Selection Of

The study investigates the genetic diversity among the Basmati rice genotypes. Selected nine Basmati rice genotypes were studied for twelve morphological traits, biochemical parameters and for molecular analysis with 11 SSR markers. Pusa Sugandha 5 and Basmati 370, showed strong aroma while other varieties showed medium aroma. Alkali spreading value were intermediate in Basmati 386, Vallabh Basmati 22 and Vallabh Basmati 24 while other varieties showed high values. Pusa Basmati 1 and Basmati 386 showed soft category of gel consistency while in rest varieties it was under medium category. Amylose percentage in grains were ranged from 18.02% (Taraori basmati) to 22.0% (Basmati370). Molecular analysis with 11 SSR markers showed 125 allels with an average number of allels 11.36 per locus. All the markers showed specific type of banding pattern along with 82 polymorphic allels in different genotypes. This study focuses on application of statistical methods and techniques in analysis of genetic diversity of the agronomic data, biochemical aspects related to quality parameters and at the molecular level using SSR markers for clustering procedure making dendrogram that helps the more accurate selection of the superior basmati genotypes for the further studies of the breeders and researchers.

scholarly journals Genetic diversity analysis of rice (Oryza sativa L.) landraces through RAPD markers

2014 ◽  
Vol 4 (1) ◽  
pp. 77-87
Author(s):  
MS Alam ◽  
SN Begum ◽  
R Gupta ◽  
SN Islam
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Oryza Sativa L ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Matrix ◽  
Arbitrary Primers ◽  
Breeding Programs ◽  
Rice Landraces ◽  
Rice Genotypes ◽  
Selection Of

The molecular marker is a useful tool for assessing genetic variations and resolving cultivar identities. Information on genetic diversity and relationships among rice landraces from Bangladesh is currently very limited. Thirty-five rice genotypes including 33 landraces and 01 HYV of Bangladesh and 1 Indian landrace of particular interest to breeding programs were evaluated by means of random amplified polymorphic DNA (RAPD) technique. For molecular characterization, RAPD markers viz., OPC 03, OPC 04 and OPA 01 gave reproducible and distinct polymorphic amplified products. A total of 20 RAPD bands were scored of which 15 polymorphic amplification products were obtained by using these arbitrary primers. The size of amplified fragments were ranged from 550 to 1775 bp. Based on analysis performed on a similarity matrix using UPGMA, 35 genotypes were grouped into 2 main clusters. Landrace Sylhet balam and Mota aman was totally different from other genotypes. The information will facilitate selection of genotypes to serve as parents for effective rice breeding programs in Bangladesh. DOI: http://dx.doi.org/10.3329/ijarit.v4i1.21099 Int. J. Agril. Res. Innov. & Tech. 4 (1): 77-87, June, 2014

Assessment of molecular divergence using microsatellite markers linked to drought-yield QTLs of rice (Oryza sativa L.)

2020 ◽  
Vol 57 (2) ◽  
pp. 94-99
Author(s):  
ND Rathan ◽  
SK Singh ◽  
RK Singh ◽  
PR Vennela
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Polymorphic Marker ◽  
Polymorphic Markers ◽  
Rainfed Conditions ◽  
Transgressive Segregants ◽  
Rice Genotypes ◽  
Contemporary Study ◽  
Selection Of

The drought stress is the major limitation for the production and yield stability in the rice (Oryza sativa L.) growing areas particularly under rainfed conditions. The assessment of genetic diversity among the rice genotypes using molecular markers linked to drought-yield QTLs will help in the selection of divergent parents to produce superior recombinants and transgressive segregants to develop high yielding cultivars for drought conditions. So the current study was conducted to estimate the genetic diversity among the set of twenty four advanced drought tolerent rice genotypes and commercial checks using SSR markers linked to major drought-yield QTLs. A total of 31 alleles were detected by 13 polymorphic markers across 24 rice genotypes with a mean of 1.94 alleles per polymorphic marker. Among the polymorphic markers, 11 markers formed 2 alleles each, 2 markers have produced 3 alleles each. The PIC value observed in the contemporary study ranged from 0.239 to 0.499 with an average PIC value of 0.346. The dendrogram displayed a total five clusters on the basis of dissimilarity coefficient values, the cluster II had maximum ten genotypes followed by cluster IB-a with five genotypes and clusters IA-a, IA-b, IB-b with three genotypes each. IR 82475-110-2-2-1-2 and IR92937-178-2-2 (R-155) were found to be the most divergent genotypes.

scholarly journals GENETIC DIVERSITY OF BALAM AND JESSO-BALAM RICE (Oryza sativa L.) GERMPLASM OF BANGLADESH REVEALED BY SSR MARKERS

2016 ◽  
Vol 27 (2) ◽  
pp. 17-24
Author(s):  
M. S. Ahmed ◽  
M. Khalequzzaman ◽  
M. K. Bashar ◽  
A. K. M. Shamsuddin
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Gene Diversity ◽  
Clustering Method ◽  
Land Races ◽  
Rice Genotypes

A total of 72 rice genotypes including Balam (40), Jesso-Balam (27) rice land races and popular varieties (5) from Bangladesh were characterized using 45 SSR markers for studying genetic diversity and identification of duplicate germplasm. Altogether 430 alleles were detected which varied from 4 to 18 per locus with an average of 9.6. The highest number of alleles (18) was found in the locus RM302. The highest gene diversity (0.91) was found in RM337 and RM224, while the lowest (0.52) was found in RM237. The PIC values ranged from 0.90 to 0.46 with an average of 0.78. The highest PIC value was observed in loci RM337 and RM224 followed by 0.89 in RM55, RM258, RM21 and RM206, respectively. The gene diversity and PIC values revealed that RM337, RM224, RM55, RM258, RM21 and RM206 were the best markers to identify and distinguish the genotypes. Besides, the UPGMA clustering method generated seven clusters, where no duplicate genotype was found. It also showed that Balam and Jesso-Balam groups of germplasm were constellated into separate clusters. The Nei’s genetic distance ranged from 0.3556 to 1.0. Conserved, characterization and utilization of the unique and distinct variability of all the similar or duplicate named land races of Balam and Jesso-Balam rice is suggested.

scholarly journals Estimation of Genetic Diversity in Rice (Oryza sativa L.) CMS Lines for High out Crossing Potential and Quality Traits

2020 ◽  
pp. 108-115
Author(s):  
Kasanaboina Krishna ◽  
Y. Chandra Mohan ◽  
V. Gouri Shankar ◽  
Ch. V. Durga Rani ◽  
L. Krishna
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa L ◽  
Kernel Length ◽  
Cluster Distance ◽  
Gel Consistency ◽  
Rice Genotypes ◽  
Total Divergence ◽  
High Degree ◽  
Hybridization Programme ◽  
Selection Of

In the present study genetic diversity among 40 rice genotypes was evaluated using Mahalanobis D2 statistic based on morphological markers. Based on cluster analysis, the germplasms were grouped into 4 clusters of which Cluster I comprising of 23 genotypes was the largest group followed by the cluster II comprising of 15 genotypes, the clusters III and IV were represented by single genotype indicating high degree of heterogeneity among the genotypes. Maximum intra cluster distance observed in cluster II is (146.8) followed by cluster I (112.9) indicating the existence of variability among the genotypes within these clusters. The highest inter-cluster distance was observed between cluster IV and III (606.5), While the lowest was noticed between cluster II and III (222.9), describing that the genotypes included in these clusters were closely related. The kernel length, kernel length after cooking, kernel breadth, gel consistency, days to 50% flowering and plant height together contributed 90.1% towards total divergence. Therefore, these characters should be given importance during hybridization and selection of segregating populations. The genotypes falling in different clusters with the high mean for grain yield and other component characters can be utilized for the hybridization programme to obtain elite segregants.

scholarly journals DNA Fingerprinting and Genetic Diversity Assessment of GM Cotton Genotypes for Protection of Plant Breeder Rights

2021 ◽  
Vol 25 (04) ◽  
pp. 768-776
Author(s):  
Shakra Jamil
Keyword(s):  
Genetic Diversity ◽  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Polyacrylamide Gel Electrophoresis ◽  
Core Set ◽  
Diversity Assessment ◽  
Cotton Genotypes ◽  
Diversity Studies ◽  
Selection Of

DNA fingerprinting is rapid, easy, and efficient method for discrimination, identification and characterization of various genotypes for protection of plant breeder’s rights (PBRs). Present study was designed for DNA fingerprinting and genetic diversity assessment of 25 GM cotton genotypes (possessing Cry1Ac gene) using 297 SSR markers through conventional PCR and Polyacrylamide gel electrophoresis. Out of 297 SSR markers, 25 markers were not amplified, 28 were monomorphic and 244 were polymorphic. A total of 1537 alleles were amplified among which 1294 (84.18%) were polymorphic. PIC value in our study ranged from 0.08 to 0.93 with an average of 0.73. Unique allelic pattern was observed for nineteen genotypes whereas six genotypes were identified using two-step identification methods. The UPGMA dendrogram divided the genotypes into two distinct clusters. Cluster I was comprised of 20 genotypes whereas cluster II was comprised of four genotypes. MNH-1020 did not obey any clustering and remained separated. The results of the structure analysis were complementary to cluster analysis and the population was divided into two subgroups. Our results evidenced narrow genetic base of the cotton genotypes cultivated in Punjab Pakistan due to use of common parents in the pedigree/parentage. Further, we proposed a core set of markers for future DNA fingerprinting and genetic diversity studies. The information generated in this study will be helpful in variety registration and subsequent protection under PBRs. Further our findings will be useful in selection of SSR markers for future studies which are focused on DNA fingerprinting and genetic diversity assessment. © 2021 Friends Science Publishers

scholarly journals Genetic Diversity and Screening of Rice (Oryza sativa L.) Genotypes for Drought Tolerance at Reproductive Phase

2018 ◽  
Vol 21 (1) ◽  
pp. 27-34
Author(s):  
MS Pervin ◽  
T Halder ◽  
M Khalequzzaman ◽  
MA Kader ◽  
TL Aditya ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Drought Stress ◽  
Oryza Sativa L ◽  
Genetic Distances ◽  
Grain Weight ◽  
Yield Reduction ◽  
Growth Duration ◽  
Reproductive Phase ◽  
Panicle Number ◽  
Rice Genotypes

Drought is a major abiotic constraint for growing rain-fed rice in Bangladesh. A total of 175 rice genotypes were evaluated using field-managed screening protocol to identify reproductive phase drought tolerant genotypes at Bangladesh Rice Research Institute, Gazipur, Bangladesh. Twelve morpho-physiological characters viz, growth duration, plant height, tiller number per plant, panicle number per plant, panicle length, filled grain number per plant, sterility percentage, filled grain weight per plant, 1000 grain weight (TGW), straw weight per plant, harvest index (HI) and percent yield reduction were recorded. Multivariate analysis was carried out by using software Genstat 5.5 to measure genetic divergence among the rice genotypes. In total 175 genotypes were constellated into ten clusters in which the cluster I exhibited maximum genetic distances from cluster V and the lowest genetic distance was between cluster II and X. Inter-cluster distances were higher than the intra-cluster distances suggesting wider genetic diversity among the genotypes of different clusters and homogeneity among the genotypes within the cluster. Among the 12 studied characters percent yield reduction contributed maximum towards total divergence in the genotypes, which revealed that these parameters contributed more to grain yield under drought stress. The genotypes of cluster I namely Canthi bakla (BRRI Genebank Acc. No. 7279), Nizersail (BRRI Genebank Acc. No. 7281), Hashim (BRRI Genebank Acc. No. 7283), Uricheora (BRRI Genebank Acc. No. 7311), Goura Kajol (BRRI Genebank Acc. No. 7312), Chini Sail (BRRI Genebank Acc. No. 7343), Tall Biruin (BRRI Genebank Acc. No. 7355), Sakkar Khora (BRRI Genebank Acc. No. 7506) and Boaincha Biruim (BRRI Genebank Acc. No. 7573) performed better under drought stress, which could be used in the crossing programme as donor parent for the development of varietyBangladesh Rice j. 2017, 21(1): 27-34

scholarly journals Genetic Diversity of Boro Rice (Oryza sativa L.) Landraces in Bangladesh

2016 ◽  
Vol 29 (2) ◽  
pp. 33-40 ◽  
Author(s):  
N. Akter ◽  
M. Z. Islam ◽  
M. A. Siddique ◽  
T. Chakrabarty ◽  
M. Khalequzzaman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Flag Leaf ◽  
Growth Duration ◽  
Cluster Distance ◽  
Transgressive Segregants ◽  
Rice Genotypes ◽  
1000 Grain Weight ◽  
Boro Rice

Genetic diversity of 45 traditional Bangladeshi boro rice genotypes was studied through Mahalanobis D2 statistics and was grouped into six clusters. The inter-cluster distances were higher than intra-cluster distances indicating wider genetic diversity among the genotypes of different clusters. The intra-cluster distances were lower in all the cases reflecting homogeneity of the genotypes within the cluster. The cluster V contained the highest number of genotypes (14) and the cluster I and VI contained the lowest (4) number. The highest intra-cluster distance was noticed for the cluster VI and the lowest for cluster V. The highest inter-cluster distance was observed between cluster I and VI followed by cluster II and VI, cluster I and V and the lowest between cluster II and IV. The genotypes from cluster VI could be selected as parents for hybridization for producing transgressive segregants. The highest cluster means for yield, grains per panicle and grain length-breath ratio were obtained from cluster I; whereas higher yield, grain breath, 1000 grain weight, flag leaf area, shortest growth duration were obtained from cluster V. Therefore, more emphasis should be given on cluster I, cluster V and cluster VI for selecting genotypes as parents to produce new recombinants with desired traits.

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