Analysis of genetic diversity in Elytrigia repens germplasm using intersimple sequence repeat (ISSR) markers

The genetic diversity among 30 accessions of Elytrigia repens (L.) Nevski was analyzed using 100 intersimple sequence repeat (ISSR) primers, 12 of which generated distinct amplification products. Out of the 132 repeatable bands detected, 100 bands were polymorphic. The percentage of polymorphic bands was 70.66%, with a mean of 8.33 percentage of polymorphic bands per primer. The ISSR-based genetic similarity coefficients among the 30 accessions ranged from 0.509 to 0.873, revealing high genetic diversity. The 30 E. repens accessions were divided into eight groups based on an unweighted pair-group method with arithmetic mean cluster analysis and a principal components analysis. We found that genetic distance is correlated with geographical distance among the 30 E. repens accessions studied (r = 0.812, p < 0.05) using Mantel’s test. Our results confirm the potential value of genetic diversity preservation for future breeding programs.

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Inter Simple Sequence Repeat (ISSR) markers to assess genetic diversity and relatedness within strawberry genotypes

Canadian Journal of Plant Science ◽

10.4141/cjps07088 ◽

2008 ◽

Vol 88 (2) ◽

pp. 313-322 ◽

Cited By ~ 22

Author(s):

S. C. Debnath ◽

S. Khanizadeh ◽

A. R. Jamieson ◽

C. Kempler

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Genetic Similarity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Group Method ◽

Sequence Repeat ◽

Breeding Lines ◽

Pair Group ◽

Simple Sequence

The goal of this study was to determine the level of genetic diversity and relatedness among 16 strawberry (Fragaria H ananassa Duch.) cultivars and 11 breeding lines developed in Canada, using Inter Simple Sequence Repeat (ISSR) markers. Seventeen primers generated 225 polymorphic ISSR-PCR bands. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) revealed a substantial degree of genetic similarity among the genotypes ranging from 63 to 77% that were in agreement with the principal coordinate (PCO) analysis. Geographical distribution for the place of breeding program explained only 1.4% of total variation as revealed by analysis of molecular variance (AMOVA). The ISSR markers detected a sufficient degree of polymorphism to differentiate among strawberry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in current strawberry breeding programs. Key words: Fragaria × ananassa, DNA fingerprinting, multivariate analysis, breeding, genetic similarity

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Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

Canadian Journal of Plant Science ◽

10.4141/p04-110 ◽

2006 ◽

Vol 86 (1) ◽

pp. 251-257 ◽

Cited By ~ 16

Author(s):

Zhao Weiguo ◽

Zhou Zhihua ◽

Miao Xuexia ◽

Wang Sibao ◽

Zhang Lin ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Genetic Relatedness ◽

Genetic Relationships ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Group Method ◽

Sequence Repeat ◽

Pair Group ◽

Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

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Genetic diversity and distance of Iranian goat breeds (Markhoz, Mahabadi and Lori) compared to the Beetal breed using inter-simple sequence repeat (ISSR) markers

Archives Animal Breeding ◽

10.5194/aab-59-477-2016 ◽

2016 ◽

Vol 59 (4) ◽

pp. 477-483 ◽

Cited By ~ 3

Author(s):

Leila Simaei-Soltani ◽

Alireza Abdolmohammadi ◽

Alireza Zebarjadi ◽

Saheb Foroutanifar

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Group Method ◽

Sequence Repeat ◽

Upgma Dendrogram ◽

Pair Group ◽

Genetic Diversity And Structure ◽

Simple Sequence

Abstract. The aim of this study was to investigate the genetic diversity and structure in three Iranian native goat breeds (Markhoz, Mahabadi and Lori) and the Beetal imported breed using inter-simple sequence repeat (ISSR) markers and also to investigate ISSR markers' potential in order to genetically separate single (S) and twin-birth (T) subpopulations. Blood samples were collected from 210 animals for this purpose. In total, 16 primers were used, and finally 5 primers were selected based on the number of clear bands and the level of polymorphisms. The result of this study showed that 76 of 86 observed fragments were polymorphic. Genetic diversity for each breed ranged from 0.23 in the Beetal breed to 0.26 in the Markhoz breed; this represents a relatively similar genetic diversity in these breeds. An unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on the Nei's standard genetic distance between the breeds studied showed that three Iranian goat breeds (Mahabadi, Lori and Markhoz) were clustered closer together, while the Beetal breed formed a separate cluster. In the constructed dendrogram of the subpopulations, the S and T subpopulations of each breed were clustered together. The constructed dendrogram of the Beetal breed and the S and T subpopulations of all breeds studied showed a separate cluster for the Beetal breed as an imported breed and another cluster for the S and T subpopulations as Iranian native breeds. The current study showed that the ISSR markers studied had no potential to genetically separate S and T subpopulations. On the other hand, these ISSR markers can be used for the clustering of distinct populations.

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Inter simple sequence repeat (ISSR) to assess genetic diversity within a collection of wild lingonberry (Vaccinium vitis-idaea L.) clones

Canadian Journal of Plant Science ◽

10.4141/p06-059 ◽

2007 ◽

Vol 87 (2) ◽

pp. 337-344 ◽

Cited By ~ 21

Author(s):

Samir C. Debnath

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Group Method ◽

Germplasm Management ◽

Sequence Repeat ◽

Pair Group ◽

Canadian Provinces ◽

Simple Sequence

Forty-three wild lingonberry [Vaccinium vitis-idaea ssp. minus (Lodd) Hult.] clones collected from four Canadian provinces were assessed for genetic variability by using inter simple sequence repeat (ISSR). Fifteen primers generated 356 polymorphic ISSR-PCR bands. A substantial degree of genetic diversity was found am ong the wild collections. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) separated the wild clones into four main clusters, and identified the two remaining clones as outliers. Furthermore, within four clusters, the genotypes tended to form sub-clusters that were in agreement with the principal coordinate (PCO) analysis. Geographical distribution explained 10% of total variation as revealed by analysis of molecular variance (AMOVA). The ISSR markers detected a sufficient degree of polymorphism to differentiate among lingonberry clones, making this technology valuable for germplasm management and the more efficient choice of parents in current lingonberry breeding programs. Key words: Vaccinium vitis-idaea, DNA fingerprinting, molecular marker

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Genetic diversity and interspecific relationships of some Allium species using inter simple sequence repeat markers

Bangladesh Journal of Plant Taxonomy ◽

10.3329/bjpt.v22i2.26029 ◽

2015 ◽

Vol 22 (2) ◽

pp. 67-75 ◽

Cited By ~ 4

Author(s):

Leila Samiei ◽

Mahnaz Kiani ◽

Homa Zarghami ◽

Farshid Memariani ◽

Mohammad Reza Joharchi

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Gene Diversity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Group Method ◽

Sequence Repeat ◽

Allium Species ◽

Interspecific Relationships ◽

Simple Sequence

In this study genetic diversity and interspecific relationships of 11 Allium L. species from Khorassan province of Iran including 32 accessions were investigated by inter simple sequence repeat (ISSR) markers. Nine ISSR primers produced a total of 80 polymorphic markers and revealed high polymorphism among the studied species. The average gene diversity, effective number of alleles and Shannons information index were 0.2, 1.28 and 0.3, respectively. Allium kuhsorkhense exhibited the greatest level of variation (He: 0.18), whereas A. stipitatum demonstrated the lowest level of variability (He: 0.05). UPGMA (Unweighted Pair Group Method with Arithmetic mean) analysis showed that Allium accessions have a similarity range of 0.60 to 0.95. Allium scapriscapum composed the most distant group in the dendrogram. The clustered groups of Allium species clearly reflect the recent taxonomic concept of the genus at the subgenus and section levels. The present study showed that the ISSR technique is an effective molecular approach for analyzing genetic diversity and relationship in Allium species.Bangladesh J. Plant Taxon. 22(2): 67-75, 2015 (December)

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Genetic diversity and relationships among Secale L. based on RAMP markers

Chinese Journal of Agricultural Biotechnology ◽

10.1079/cjb200419 ◽

2004 ◽

Vol 1 (2) ◽

pp. 73-78 ◽

Cited By ~ 3

Author(s):

Shang Hai-Ying ◽

Zheng You-Liang ◽

Wei Yu-Ming ◽

Wu Wei ◽

Yan Ze-Hong

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Pcr Amplification ◽

Group Method ◽

Transitional Region ◽

Arithmetic Average ◽

Pair Group ◽

Broad Leaf ◽

Polymorphic Bands ◽

High Level

AbstractGenetic diversity and relationships among 21 accessions of Secale L., including three species and 10 subspecies, were evaluated using RAMP markers. Forty-one out of 80 (50.5%) RAMP primers, which produced clear and polymorphic bands, were selected for PCR amplification of genomic DNA. A total of 446 bands were amplified from the 41 primers, and 428 of these bands (about 96%) were polymorphic. Three to 19 polymorphic bands could be amplified from each primer, with an average of 10.4 bands. The RAMP-based genetic similarity (GS) values among the 21 Secale accessions ranged from 0.266 to 0.658, with a mean of 0.449. A high level of genetic variation was found between or within the wild populations and the cultivars. Based on the GS matrix, a dendrogram was constructed using the unweighted pair group method with arithmetic average (UPGMA). All 21 accessions could be distinguished by RAMP markers. Clustering results showed that the genetic diversity of Secale based on RAMP markers was correlated with geographical distribution. Six rye cultivars, originating from Poland, Portugal, Mexico, Hungary, Armenia and Ukraine, were clustered into one group. The six countries are all located in the transitional region of broad-leaf forests between maritime and continental temperate zones, with narrow latitude span. In comparison, the other five cultivars from countries scattered over a region with large latitude span were distributed within different groups or subgroups. Genetic relationships based on RAMP markers had great deviation from the original taxonomy. Some subspecies of the same species were distributed within different groups, while some accessions of different species were closely clustered into one subgroup. These results suggest that RAMP markers could be an effective technique for detecting genetic diversity among Secale and give some useful information about its phylogenic relationships.

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Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers

Canadian Journal of Plant Science ◽

10.4141/cjps2013-062 ◽

2013 ◽

Vol 93 (6) ◽

pp. 1089-1096 ◽

Cited By ~ 13

Author(s):

Shiyong Chen ◽

Xinquan Zhang ◽

Xiao Ma ◽

Linkai Huang

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Tibet Plateau ◽

Group Method ◽

Similarity Coefficients ◽

Arithmetic Average ◽

Pair Group ◽

Elymus Nutans ◽

Qinghai Tibet Plateau ◽

Simple Sequence

Chen, S., Zhang, X., Ma, X. and Huang, L. 2013. Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers. Can. J. Plant Sci. 93: 1089–1096. Elymus nutans Griseb., an important alpine forage grass, is widely distributed in the Qinghai–Tibet Plateau. A total of 50 E. nutans accessions from the eastern Qinghai–Tibet Plateau were analyzed using simple sequence repeats (SSR) markers from wheat and Elymus species. Our results show that a total of 144 reliable bands were generated, of which 132 (91.38%) were found to be polymorphic. Nei-Li's genetic similarity coefficients ranged from 0.515 to 0.870 with an average of 0.719, which shows a high level of genetic diversity and a broad genetic base among accessions. There was a low correlation between genetic distance and geographical distance (r=0.121, P=0.088) in the region, which is consistent with the unweighted pair group method with arithmetic average cluster analysis of accessions. The mountain ridges and river valleys in the eastern Qinghai–Tibet region could serve as genetic barriers for pollinator movement and seed dispersal. The rule of the most genetic diversity at medium altitude of E. nutans in the Qinghai–Tibet Plateau was also validated in the study. The implications of these results for the conservation of E. nutans are discussed.

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Analysis of genetic diversity in Prunus sibirica L. in inner Mongolia using SCoT molecular markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01284-4 ◽

2022 ◽

Author(s):

Ha Buer ◽

Sa Rula ◽

Zi Yuan Wang ◽

Shu Fang ◽

Yu´e Bai

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Differentiation ◽

Inner Mongolia ◽

Start Codon ◽

Group Method ◽

Pair Group ◽

Protection And Utilization ◽

Minimum Number ◽

Polymorphic Bands

AbstractPopulation genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica L. populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 98.87% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT25 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of P. sibirica in Inner Mongolia. The analysis of molecular variance showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic cluster analysis, principal coordinate analysis and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of P. sibirica in Inner Mongolia can provide a reference for P. sibirica variety breeding and resource development.

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Evaluation of genetic diversity in geranium (Geraniaceae) using RAPD marker

Genetika ◽

10.2298/gensr2101363y ◽

2021 ◽

Vol 53 (1) ◽

pp. 363-378

Author(s):

Juan Yin ◽

Majid Khayatnezhad ◽

Abdul Shakoor

Keyword(s):

Genetic Diversity ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Morphological Characters ◽

Mantel Test ◽

Group Method ◽

Plant Resources ◽

High Genetic Diversity ◽

Pair Group ◽

Genetic Structure Of Populations

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Geranium genetic diversity. Therefore, we collected and analyzed thirteen species from nine provinces. Overall, one hundred and twenty-five plant specimens were collected. Our aims were 1) to assess genetic diversity among Geranium species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and multidimensional scaling divided Geranium species into two groups. G. sylvaticum depicted unbiased expected heterozygosity (UHe) in the range of 0.11. Shannon information was high (0.38) in G. columbinum. G. sylvaticum showed the lowest value, 0.14. The observed number of alleles (Na) ranged from 0.25 to 0.55 in G. persicum and G. tuberosum. The effective number of alleles (Ne) was in the range of 1.020-1.430 for G. tuberosum and G. collinum. Gene flow (Nm) was relatively low (0.33) in Geranium. The Mantel test showed correlation (r = 0.27, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Geranium species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Geranium species.

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Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers

Jurnal AgroBiogen ◽

10.21082/jbio.v7n1.2011.p47-55 ◽

2011 ◽

Vol 7 (1) ◽

pp. 47 ◽

Cited By ~ 4

Author(s):

Dani Satyawan ◽

I Made Tasma

Keyword(s):

Genetic Diversity ◽

Dna Markers ◽

Jatropha Curcas ◽

Group Method ◽

Diversity Analysis ◽

Similarity Coefficients ◽

Improvement Program ◽

Genetic Diversity Analysis ◽

Chain Reactions ◽

Pair Group

Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers. Dani Satyawan and I Made Tasma. Jatropha curcas nuts are rich in oil that is higly suitable for Hak Cipta © 2011, BB-Biogen the production of bio-diesel or to be used directly in modified diesel engines. The objective of this study was to assess the extent of genetic diversity among 50 J. curcas provenances and one accession of J. integerrima using RAPD markers. The fifty J. curcas provenances were collected from ecologically diverse regions of Indonesia, and planted in the Pakuwon Experimental Station (Sukabumi, West Java). Fourteen RAPD primers with 60-80% G+C content were used in this genetic diversity analysis and produced 64 bands with 95.7% polymorphism level. The Polymerase Chain Reactions used to generate the RAPD bands sometimes produced inconsistent and nonreproducible results, necessitating the duplication of each reaction to prevent scoring errors. Sixty one validated bands were subsequently used for genetic diversity analysis using Unweighted Pair Group Method Arithmetic (UPGMA) method and Dice coefficients. It was shown that the similarity coefficients among the provenances ranged from 0.2 to 0.98 with an average similarity of 0.75. Dendrogram analysis produced two major groups of provenances, with one outlier from South Lampung. There was no tendency for provenances originated from nearby regions to cluster together in each group, and several provenances showed more similarities with provenances originated from distant regions. This pattern lent credence to reports that Jatropha was introduced to Indonesia around four centuries ago and was mainly spread by humans. Based on the mean similarities among the accessions and their clustering pattern, the genetic diversity of the Jatropha collection appeared to be fairly low. Future additions of genetic materials from more diverse genetic background will be necessary to maintain the current progress of Jatropha improvement program.

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