scholarly journals Molecular Diversity Analysis in Boro Rice (Oryza sativa L.) Landraces using SSR Markers

2021 ◽  
pp. 36-48
Author(s):  
Farhana Afrin Vabna ◽  
Mohammad Zahidul Islam ◽  
Md. Ferdous Rezwan Khan Prince ◽  
Md. Ekramul Hoque
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Molecular Diversity ◽  
Genetic Relationships ◽  
Group Method ◽  
Diversity Analysis ◽  
Average Value ◽  
Rice Landraces ◽  
Boro Rice ◽  
Research Institute

Aims: The aim of the study was to determine the genetic diversity of twenty four Boro rice landraces using rice genome specific twelve well known SSR markers. Study Design: Genomic DNA extraction, PCR amplification, Polyacrylamide gel electrophoresis (PAGE) and data analysis-these steps were followed to perform the research work. Data was analysed with the help of following software; POWERMAKER version 3.25, AlphaEaseFC (Alpha Innotech Corporation) version 4.0. UPGMA dendrogram was constructed using MEGA 5.1 software. Place and Duration of Study: The study was conducted at the Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, Bangladesh during the period of November 2017 to March 2018. Methodology: Simple Sequence Repeat (SSR) markers were used to assay 24 landraces of Boro rice collected from the Gene Bank of Bangladesh Rice Research Institute (BRRI). Results: A total fifty four (54) alleles were detected, out of which forty five (45) polymorphic alleles were identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice landraces. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. Conclusion: The result revealed that SSR markers are very effective tools in the study of genetic diversity and genetic relationships and this result can be conveniently used for further molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.

scholarly journals Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

2021 ◽  
Author(s):  
Varun Hiremath ◽  
Kanwar Pal Singh ◽  
Neelu Jain ◽  
Kishan Swaroop ◽  
Pradeep Kumar Jain ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Genetic Relationships ◽  
Crop Improvement ◽  
Test Analysis ◽  
Average Value ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 802-810 ◽  
Author(s):  
Muwang Li ◽  
Li Shen ◽  
Anying Xu ◽  
Xuexia Miao ◽  
Chengxiang Hou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bombyx Mori ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Group Method ◽  
Sequence Repeat ◽  
Bombyx Mori L ◽  
Simple Sequence ◽  
Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 108-114 ◽  
Author(s):  
José Miguel Soriano ◽  
Carlos Romero ◽  
Santiago Vilanova ◽  
Gerardo Llácer ◽  
María Luisa Badenes
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Malus Domestica ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Mean Value ◽  
Eriobotrya Japonica ◽  
Fixation Index ◽  
Group Method ◽  
Malus Domestica Borkh

Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus × domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (–0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus × domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family.Key words: Eriobotrya japonica, SSR markers, microsatellites, genetic diversity.

scholarly journals Application of wheat SSR markers for detection of genetic diversity in triticale (x Triticosecale witt. )

Genetika ◽  
2015 ◽  
Vol 47 (3) ◽  
pp. 983-992
Author(s):  
Zelmíra Balázová ◽  
Andrej Trebichalský ◽  
Zdenka Gálová ◽  
Radomíra Hornyák-Gregáňová
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Ssr Marker ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Average Frequency ◽  
Polymorphic Markers ◽  
Average Value ◽  
Ssrs Markers

Present study aims to testify usefulness of particular wheat SSR markers for the detection of genetic diversity degree in the set of 59 triticale cultivars and new lines coming from different European countries and USA. For this purpose, a set of fifteen SSR markers were used. One SSR marker (Xwmc429) gave a uniform spectrum. The set of fourteen polymorphic markers provided 94 alleles with an average frequency of 6.71 alleles per locus. The number of alleles ranged between 2 (Xbarc 195) and 10 (Xbarc 137). Resulting from the number and frequency of alleles, diversity index (DI), polymorphic information content (PIC) and probabilities of identity (PI) were calculated. An average value of PIC for 14 markers was 0.640, the highest value was calculated for wheat SSR marker Xgwm 46 (0.809). Based on UPGMA algorithm, a dendrogram was constructed. It was able to separate 57 of 59 cultivars (96,6 %) from each other. American new-line NE-422T significantly separated from all cultivars and new lines. Only two french cultivars Bienvenu and Wilfried had not been separated from each other. A tested set of SSR markers allowed to better understand genetic relationships among European cultivars and American new lines. In general, a dendrogram along with results of calculated genetic indicators such as PIC, PI and DI point out at SSRs markers as high informative and usefull tool in genetic diversity research between close-related species.

Evaluation of Genetic Diversity of Local-Colored Rice Landraces Using SSR Markers

2018 ◽  
Vol 67 ◽  
pp. 24-34 ◽  
Author(s):  
Hoang Thi Hue ◽  
La Tuan Nghia ◽  
Hoang Tuyet Minh ◽  
La Hoang Anh ◽  
Le Thi Thu Trang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Relationships ◽  
Germplasm Conservation ◽  
Similarity Coefficients ◽  
Breeding Programs ◽  
Rice Landraces ◽  
Local Germplasm ◽  
Rice Improvement ◽  
Colored Rice

Analysis of genetic diversity of 90 Vietnamese local-colored rice accessions was evaluated by using 40 SSR markers. The numbers of polymorphic alleles ranged from 3 to 12 alleles per locus and average of 7.1 alleles per locus. The similarity coefficients of the rice landraces fluctuated from 0.76 to 0.93; at a genetic correlation level of 0.78. Ninety accessions of rice landraces were divided into five groups based on analysis of genetic relationships. The results have indicated that 11 markers included: M250, RM302, RM10926, RM208, RM227, RM17231, RM23251, RM5647, RM1376, RM339 and RM228 which gave the unique allele. These markers can be used effectively for genetic diversity of colored rice and provided a specific database and useful materials for landraces identification, local germplasm conservation for further colored rice improvement on rice quality via rice breeding programs in Vietnam.

Cross-species Amplification and Molecular Diversity Analysis in Greengram [Vigna radiata (L.) Wilczek] and Ricebean [Vigna umbellata Thunb.]

2020 ◽  
Author(s):  
D. Susmitha ◽  
P. Jayamani
Keyword(s):  
Ssr Markers ◽  
Molecular Diversity ◽  
Yellow Mosaic Virus ◽  
Diversity Analysis ◽  
Specific Level ◽  
Average Value ◽  
Pulse Crop ◽  
Ssr Primers ◽  
Specific Hybrid ◽  
A Minor

Background: Greengram is the fourth dominant pulse crop grown in India and is highly susceptible to bruchids and yellow mosaic virus. Ricebean belonging to the tertiary genepool of greengram shows resistance to this pest and disease. Ricebean being a minor pulse crop has limited SSR markers. Hence, the present study was conducted to test the cross-species amplification of SSR markers derived from related species which could be helpful in studying the molecular diversity available in each crop and for molecular confirmation of the inter- and intra-specific hybrid developed from the crosses.Methods: Molecular diversity analysis was carried out using 30 genotypes belonging to two species of Vigna (V. radiata and V. umbellata) based on 20 SSR primers derived from adzukibean, commonbean and greengram. Result: Cross species amplification was observed for all the SSR primers pairs used. The number of alleles detected varied from one (VJ 31122A) to four (CEDAAG 001 and MB 91) with an average of 2.55 alleles per primer. Allele size varied from 100 to 292 bp. The PIC value ranged from zero to 0.611 with an average value of 0.377. Dendrograms constructed based on UPGMA and Neighbour-Joining tree method, grouped the genotypes into five clusters and five groups, respectively. The V. umbellata genotypes were grouped in separate cluster from the V. radiata genotypes in both the methods. The obtained DNA polymorphism at intra- and inter-specific level will facilitate the application of molecular breeding approaches for greengram improvement. 

scholarly journals Genetic diversity in tomato (Solanum lycopersicum L.) genotypes revealed by simple sequence repeats (SSR) markers

2017 ◽  
Vol 9 (2) ◽  
pp. 966-973 ◽  
Author(s):  
Ashish Kaushal ◽  
Anita Singh ◽  
Anand Singh Jeena
Keyword(s):  
Genetic Diversity ◽  
Solanum Lycopersicum ◽  
Ssr Markers ◽  
Similarity Coefficient ◽  
Group Method ◽  
Distance Information ◽  
Average Value ◽  
Solanum Lycopersicum L ◽  
Pair Group ◽  
Jaccard’S Similarity Coefficient

Twenty five tomato (Solanum lycopersicum L.) genotypes were subjected to genetic diversity analysis using twenty SSR markers. Out of 20 markers used, 14 SSRs were polymorphic and a total numbers of 22 SSR alleles were generated by 14 SSR markers, out of which 19 were polymorphic and 3 were monomorphic, with an average of 1.57 alleles per locus. The range of amplified products was 100-400bp approximately. Jaccard’s similarity coefficient varied from 0.65 between germplasm EC519821 and CO-3 to a maximum of 1.0 between genotypes EC519769 and DARL-66, with an average value of 0.83. Cluster analysis based on Jaccard’s similarity coefficient using the unweighted pair-group method with arithmetic mean (UPGMA) revealed 2 distinct clusters, A and B, comprising 1 and 24 genotypes respectively and at 75 and 78 per cent similarity, respectively. The genotypes which showed similar morphological and genetic trends were grouped more or less together in both these cases were a few. Cluster A comprised most diverse germplasm (EC519821)belongs to pimpinellifolium wild species with similarity coefficient 0.65% and differentiated with other cultivated species.Cherry Tomato and Cherry-2 were trends in similar cluster similar with approximately 96% similarity.SSR markers were able in in differentiating the genotypes based on morphologically and genotypically.However, the grouping of 25 genotypes were independently of geographic distribution.The genetic distance information found in this study might be helpful to breeder for planning among these genotypes.

scholarly journals Development and characterization of STMS molecular markers and genetic diversity analysis of mungbean [Vigna radiata (L.) Wilczek]

2019 ◽  
Vol 79 (01) ◽  
Author(s):  
Sujan S. Bimal ◽  
S. P. Chavan ◽  
A. B. Gaikwad ◽  
K. V. Bhat
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Microsatellite Loci ◽  
Mung Bean ◽  
Genomic Library ◽  
Genetic Relationships ◽  
Genomic Research ◽  
Group Method ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis

Mung bean is an important crop in Asia because of its high protein content and other economic uses. However, because of the unavailability of polymorphic DNA markers, genomic research of mung bean is lacking. In this study, we developed and characterised simple sequence repeat (SSR) molecular markers by screening SSR-enriched partial genomic libraries with SSR probes and used them to analyse the genetic diversity of mung bean. Thus, we isolated, cloned, sequenced a genomic library that contained microsatellite loci from the mung bean variety ‘MCV-1’. The polymorphisms of microsatellite loci were evaluated using the unweighted pair group method of arithmetic means, and MDS cluster analysis showed genetic relationships in a panel of 96 mung bean core collection genotypes. Genetic diversity analysis results showed contrasted levels of variability within cultivated and wild accessions. A total of 98 alleles were detected using 19 polymorphic markers, with an average of 4.9 alleles per locus, whereas observed heterozygosity ranged from 0.1 to 0.5, with a mean of 0.42 per locus. The number of alleles and the high level of polymorphism make these new markers useful for gene tagging, diversity analyses and marker assisted selection in mung bean.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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