scholarly journals DNA Fingerprinting and Genetic Diversity in Aus Rice (Oryza sativa L.) Landraces of Bangladesh

2018 ◽  
Vol 21 (1) ◽  
pp. 59-65
Author(s):  
MA Siddique ◽  
M Khalequzzaman ◽  
K Fatema ◽  
MZ Islam ◽  
MHK Baktiar ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Rice Landraces ◽  
Genetic Groups ◽  
Improvement Programme ◽  
Genetic Coefficient

The allelic diversity and relationships among 48 Aus rice landraces were determined through DNA fingerprinting using microsatellite (SSR) markers. A total of 14 SSR markers for different chromosomes were used to characterize and differentiate the studied rice genotypes. The number of alleles per locus varied from three alleles (RM118) to 18 alleles (RM44) with an average of 9.88. The polymorphic information content (PIC) varied widely among the loci and ranged from 0.3725 (RM107) to 0.9146 (RM519) with an average of 0.7248. The genetic distance-based results found in the UPGMA clustering system revealed six genetic groups with a similarity coefficient of 0.35. Chakila and Shitki saitta had closest distance in the SSR based genetic distance might have same genetic background. Based on genetic coefficient, the diverse landraces Kasalot, Balam, Pankhiraj, Dular, Hashikalmi, Galong, Panbira, Marichbati, Pidi and Surjomoni could be selected as potential parents for varietal improvement programme. The findings of this study should be useful for varietal identification and could be useful for plant breeders in selecting suitable genetically diverse parents for the crossing programmeBangladesh Rice j. 2017, 21(1): 59-65

scholarly journals DNA fingerprinting and genetic diversities in some Bangladeshi aus rice (Oryza sativa L.) genotypes

2017 ◽  
Vol 15 (1) ◽  
pp. 123-137 ◽  
Author(s):  
MM Islam ◽  
HA Begum ◽  
MS Ali ◽  
M Kamruzzaman ◽  
S Hoque ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Allelic Diversity ◽  
Breeding Programs ◽  
Chord Distance ◽  
Genetic Dissimilarity

The allelic diversity and relationship among 120 Aus rice landraces were determined through DNA fingerprinting using microsatellite (SSR) markers. A total of 85 SSR markers were used to characterize and discriminate all tested Aus rice genotypes, 45 of which were polymorphic for different chromosome numbers. The number of alleles per locus varied from 6 alleles (RM484 and RM541) to 30 alleles (RM519) with an average of 13 alleles per locus. The polymorphic information content (PIC) values varied ranged from 0.5211 (RM536) to 0.9369 (RM519) with an average 0.8217. The highest PIC value (0.9369) was obtained for RM519 followed by RM286 (0.9357). The genetic distance-based results seen in the unrooted neighbor-joining tree clustering revealed nine genetic groups. Being grouped into distant clusters and with highest genetic distance, eleven genotypes viz., Atithi dhan, Kadar chap, Pankiraj, Japanese-7, Jamri saity, Logi jota, Joba, Lada moni, Manik Mondal-2, Boilum and Brmulka-2 could be selected as potential parents for crop improvement for their distinctive characters. Panchash and Parija had closest distance in the SSR based CS-Chord distance (0.000) might have same genetic background. The highest genetic dissimilarity (1.000) was found among the nineteen Aus genotypes combinations followed by the second highest (0.9778) among 94 Aus rice combinations. Whereas lowest genetic dissimilarity was found between Kala and Kalo Hizli (0.1778) followed by Holat and Holae (0.2667). This information will be useful in the selection of diverse parents, background selection during backcross breeding programs and assist in broadening germplasm-based rice breeding programs in the near future.SAARC J. Agri., 15(1): 123-137 (2017)

scholarly journals Optimal use of SSR markers for varietal identification of upland cotton

2015 ◽  
Vol 50 (7) ◽  
pp. 571-581 ◽  
Author(s):  
Guilherme da Silva Pereira ◽  
Ana Luíza Ramos Cazé ◽  
Michelle Garcia da Silva ◽  
Vanessa Cavalcante Almeida ◽  
Fernanda Oliveira da Cunha Magalhães ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Discrimination Power ◽  
Arithmetic Average ◽  
Pair Group ◽  
Varietal Identification ◽  
The World ◽  
The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

scholarly journals Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

2012 ◽  
Vol 37 (3) ◽  
pp. 389-398 ◽  
Author(s):  
S Islam ◽  
MS Haque ◽  
RM Emon ◽  
MM Islam ◽  
SN Begum
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Triticum Aestivum L ◽  
Allele Number ◽  
Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

scholarly journals GENETIC DIVERSITY OF UPLAND RICE LANDRACES FROM JAVA ISLAND AS REVEALED BY SSR MARKERS

2015 ◽  
Vol 16 (1) ◽  
pp. 1
Author(s):  
Sutoro Sutoro ◽  
Puji Lestari ◽  
Hakim Kurniawan
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Upland Rice ◽  
Diversity Index ◽  
Crop Improvement ◽  
Conservation Strategy ◽  
Genetic Diversity Index ◽  
Rice Landraces ◽  
Glutinous Rice

Java Island is one of origins of a large number of indigenous upland rice accessions, which may serve as valuable plant genetic resources for future crop improvement in Indonesia. However, these landraces especially non-glutinous and glutinous rice are rapidly being lost because of land-use, agricultural practices and other factors. A better understanding of genetic diversity of local upland rice is important for crop improvement program, crop management and conservation strategy. This study aimed to evaluate the genetic diversity of upland rice landraces originating from Java Island. A total of 82 upland rice accessions comprising of 55 non-glutinous rice and 27 glutinous type were genotyped using the 16 simple sequence repeat (SSR) markers. The result showed that a total of 74 alleles were found with major allele frequency found on RM431 (0.96). Most of the SSR markers (56.3%) showed high discriminating power as represented by polymorphic informa-tion content (PIC) value higher than 0.5. A moderate genetic diversity index was detected in all landraces, which was 0.55. Genetic diversity index of non-glutinous and glutinous rice were 0.54 and 0.53, respectively. Their genetic distance was about 0.057. The phylogenetic tree generated two main clusters that demonstrated discrimination among landraces according to the individual genetic properties rather than their geographical origins and grain types (non-glutinous and glutinous type). The levels of genetic diversity were varied across rice types and geographical origins. According to the regions, the closest genetic distance was found between upland rice landraces from Central Java and West Java (0.040). The information derived from this study is important, in combination with phenotypic data, to identify desired useful traits came from different origins of the gene pool to be used for breeding purposes.

scholarly journals SSR allelic diversity in relation to morphological traits and resistance to grain mould in sorghum

2010 ◽  
Vol 61 (3) ◽  
pp. 230 ◽  
Author(s):  
Rajan Sharma ◽  
S. P. Deshpande ◽  
S. Senthilvel ◽  
V. P. Rao ◽  
V. Rajaram ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Morphological Traits ◽  
Ssr Marker ◽  
Allelic Variation ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Average Score ◽  
Marker Loci

Allelic variation at 46 simple sequence repeat (SSR) marker loci well distributed across the sorghum genome was used to assess genetic diversity among 92 sorghum lines, 74 resistant and 18 susceptible to grain mould. Of the 46 SSR markers, 44 were polymorphic, with the number of alleles ranging from 2 to 20 with an average of 7.55 alleles per locus. Genetic diversity among the sorghum lines was high as indicated by polymorphic information content (PIC) and gene diversity values. PIC values of polymorphic SSR markers ranged from 0.16 to 0.90, with an average of 0.54. Gene diversity among the sorghum lines varied from 0.16 to 0.91, with an average score of 0.58 per SSR marker. AMOVA indicated that 12% of the total variation observed among the sorghum lines was accounted for between grain mould resistant and susceptible types. Diversity based on six morphological traits and grain mould scores indicated major roles of panicle type and glumes coverage, followed by grain colour, in clustering of the lines. Seven grain mould resistant/susceptible pairs with dissimilarity indices >0.50, but with similar flowering time, plant height, and panicle type/inflorescence within each pair, were selected for use in developing recombinant inbred line mapping populations to identify genomic regions (and quantitative trait loci) associated with sorghum grain mould resistance.

scholarly journals Characterization of Ugandan Sweetpotato Germplasm Using Fluorescent Labeled Simple Sequence Repeat Markers

HortScience ◽  
2010 ◽  
Vol 45 (2) ◽  
pp. 225-230 ◽  
Author(s):  
Benard Yada ◽  
Phinehas Tukamuhabwa ◽  
Bramwell Wanjala ◽  
Dong-Jin Kim ◽  
Robert A. Skilton ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Ipomoea Batatas ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Sequence Repeat ◽  
Simple Sequence

The genetic relationships among 192 superior, high–yielding, and disease-resistant sweetpotato [Ipomoea batatas (L.) Lam] accessions from the Ugandan germplasm collection were analyzed using 10 fluorescent labeled simple sequence repeat (SSR) markers. Relatedness among the genotypes was estimated using the Nei and Li genetic distance coefficient, cluster analysis and principle component analysis methods of NTSYS-pc software. The polymorphic information content of the SSR markers used in this study ranged from 0.23 to 0.76 for loci IB-S07 and IB-R12, respectively, with a mean value of 0.62. The number of polymorphic alleles detected per locus ranged from two to six with a mean of four, a confirmation of the effectiveness of microsatellite detection on an automated ABI 3730 sequencer. The mean pairwise genetic distance among the 192 genotypes was 0.57, an indication of moderately high genetic diversity. Cluster analysis divided the accessions into four major groups with no relationship to the district of origin. Two sets of duplicates were identified through SSR genotyping in this study. Up to 190 distinct accessions for use as potential parental genotypes in hybridization schemes for cultivar development in the region were identified.

scholarly journals Genetic Diversity Among Korean Rice Landraces (Oryza sativa L.) Based on Characters and SSR Markers

2015 ◽  
Vol 3 (3) ◽  
pp. 216-225
Author(s):  
Kyung Jun Lee ◽  
Jong-Ro Lee ◽  
Gi-An Lee ◽  
Ho Sun Lee ◽  
Soon Ik Kwon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Rice Landraces ◽  
Korean Rice

scholarly journals Microsatellite based DNA fingerprinting of 28 local rice (Oryza sativa L.) varieties of Bangladesh

1970 ◽  
Vol 8 (1) ◽  
pp. 7-17 ◽  
Author(s):  
MS Rahman ◽  
MKH Sohag ◽  
L Rahman
Keyword(s):  
Oryza Sativa ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Dna Fingerprinting ◽  
Oryza Sativa L ◽  
Pcr Amplification ◽  
Rice Varieties ◽  
High Level ◽  
Nei's Genetic Distance

A total of 28 local rice (Oryza sativa L.) varieties of Bangladesh were selected for DNA fingerprinting with seven microsatellite DNA markers. Upon PCR amplification the alleles were separated on Agarose gel using a sequencing gel electrophoresis system. The loci were polymorphic (P95) in all of the varieties. Variation was found in number of alleles, allele frequency, observed and expected heterozygosity. The primer, RM335 having motif (CTT)20 also yielded highest number of alleles (15) and highest PIC value (0.909). Genetic differentiation (Fst) values were found in the ranges 0.84 to 1.00 with an average of 0.92 and gene flow (Nm) values ranged from 0.047 to 0.00 with an average of 0.02. High level genetic differentiation and low level gene flow values in 28 rice (Oryza sativa L.) varieties which were indicated of diversity among the varieties as most of these varieties were of landraces. Over all Nei’s genetic distance value (D) ranged from nil to 2.56 among 378 varietals pairs resulting as a means of permutation combination of 28 rice varieties. The UPGMA dendrograme based on Nei's genetic distance placed the varieties into different clusters. All of the varieties were identified with at least one and/or combination of 7 primers. Keywords: Microsatellites; DNA fingerprinting; Oryza sativa; Bangladesh DOI: 10.3329/jbau.v8i1.6391J. Bangladesh Agril. Univ. 8(1): 7-17, 2010

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.

Sign in / Sign up

Export Citation Format

Share Document