Study of genetic diversity in wild raspberry (Rubus idaeus L.) germplasm collection using morphological characters and RAPD markers

Biologija ◽  
2008 ◽  
Vol 54 (2) ◽  
pp. 66-74 ◽  
Author(s):  
Jolanta Patamsytė ◽  
Donatas Žvingila ◽  
Juozas Labokas ◽  
Virgilijus Baliuckas ◽  
Laimutė Balčiūnienė ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Germplasm Collection ◽  
Morphological Characters ◽  
Rubus Idaeus

scholarly journals Detecting DNA polymorphism and genetic diversity in a wide pistachio germplasm by RAPD markers

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 783-798
Author(s):  
Xiaohui Qian ◽  
Shahram Mehri
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Morphological Characters ◽  
Mantel Test ◽  
Pistacia Vera ◽  
High Genetic Diversity ◽  
Horticultural Crops ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability

Assessing the genetic diversity in the population is the prerequisite to start and develop plant breeding projects. Pistacia vera is considered as a commercial species of Pistacia genus. In Iran, Pistachio export is in the second place in terms of non-oil exports and in the first place among horticultural crops. Therefore, we collected and analyzed 11 pistachio genotype (Pistacia vera), from two provinces of Iran regions. Our aims were 1) to assess genetic diversity among some of Irainian pistachio cultivars 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. Akbari cultivars depicted unbiased expected heterozygosity (UHe) in the range of 0.028. Shannon information was high (0.49) in Seifadini cultivars. Akbari cultivars howed the lowest value, 0.029. The observed number of alleles (Na) ranged from 0.261 to 2.700 in Shahpasand cultivars and Kalehghoochi cultivars. The effective number of alleles (Ne) was in the range of 1.021-1.800 for Akbari cultivars and Moosaabadi cultivars .Gene flow (Nm) was relatively low (0.38) in pistachio cultivars. The Mantel test showed correlation (r = 0.33, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the among some of Irainian pistachio cultivars 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 pistachio cultivars.

scholarly journals Genetic Diversity in Black Raspberry Detected by RAPD Markers

HortScience ◽  
2003 ◽  
Vol 38 (2) ◽  
pp. 269-272 ◽  
Author(s):  
C.A. Weber
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Fruit Production ◽  
Rubus Idaeus ◽  
Limiting Factor ◽  
Black Raspberry ◽  
Red Raspberry ◽  
Average Similarity ◽  
Improved Cultivars ◽  
Maximum Similarity

Lack of variation among black raspberry cultivars is thought to be a limiting factor in fruit production and in breeding improved cultivars. An assessment of the available diversity in black raspberry is needed to effectively develop improved cultivars. Such an assessment was done to estimate the genetic similarities for RAPD markers in 16 black raspberry genotypes and to determine the genetic diversity among these genotypes based on these markers. In addition, the ability to distinguish between the black raspberry genotypes, two red raspberry cultivars (Rubus idaeus L.), and a blackberry cultivar (Rubus hybrid) was determined. A similarity matrix from 379 RAPD markers was calculated, and a phylogenetic tree was constructed using the PHYLIP suite of phylogeny software, which revealed the relationship among the genotypes. An average of 81% similarity was calculated among 16 black raspberry genotypes with a maximum similarity of 98% and a minimum of 70%. The average similarity between black raspberry and red raspberry was 41% and was 26% between black raspberry and blackberry. Combined marker profiles from six RAPD primers could be used to distinguish between the 16 black raspberry genotypes. Red raspberry and blackberry could be distinguished from black raspberry by 27 and 29 of 30 RAPD primers tested, respectively. Genetic diversity was most prominent in genotypes from the extremes of the black raspberry indigenous range. Diversifying the germplasm pool for black raspberry cultivar improvement can be achieved through utilizing genotypes from the extremes of the black raspberry range and through interspecific hybridization.

scholarly journals Genetic diversity of tropical-adapted onion germplasm assessed by RAPD markers

2012 ◽  
Vol 30 (1) ◽  
pp. 112-118 ◽  
Author(s):  
Maria do Desterro M dos Santos ◽  
Carlos Francisco Ragassi ◽  
Maria Esther de N Fonseca ◽  
Anne Gizelle R Buzar ◽  
Valter R Oliveira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Germplasm Collection ◽  
Rio Grande ◽  
Breeding Programs ◽  
Tropical Regions ◽  
Low Genetic Diversity ◽  
Tropical Conditions ◽  
Average Similarity ◽  
Onion Germplasm

Onion is a crop of significant socioeconomic importance to Brazil. Onion germplasm with adaptation to tropical and sub-tropical conditions has played an important role in the development of this crop in the country. In this context, we studied the genetic diversity in a germplasm collection potentially useful for the development of cultivars for tropical and subtropical regions. The genetic variability of 21 accessions/cultivars that have been used as germplasm and/or were developed by onion breeding programs in Brazil was evaluated via RAPD markers. The following accessions were included in the study :'Red Creole', 'Roxa IPA-3', 'Valenciana 14', 'Beta Cristal', 'Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Alfa Tropical', 'Pêra IPA-4', 'Primavera', 'Belém IPA-9', 'Crioula Alto Vale', 'Conquista', 'Pira-Ouro', 'Vale-Ouro IPA-11', 'Franciscana IPA-10', 'Serrana', 'CNPH 6400', 'Petroline', and 'Baia Periforme'. From the 520 primers used in the initial screening only 38 displayed stable polymorphisms. They produced 624 amplicons, of which 522 (83.7%) were monomorphic and 102 (16.3%) were polymorphic. An average similarity coefficient of 0.72 was calculated among accessions based upon this subgroup of polymorphic amplicons. This allowed the discrimination of this germplasm collection into six groups with only one of them comprising more than one accession. The main group was formed by 16 accessions ('Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Conquista', 'Pira-Ouro', 'Serrana', 'Vale-Ouro IPA-11', 'Baia Periforme', 'Primavera', 'Franciscana IPA-10', 'Belém IPA-9', 'Crioula Alto Vale', 'Petroline', 'Pêra IPA-4' and 'Alfa Tropical'), for which the genetic origin (with few exceptions) can be traced back to the variety 'Baia Periforme'. The populations 'Red Creole', 'Roxa IPA-3', 'Beta Cristal', 'CNPH 6400', and 'Valenciana 14' comprised a set of five isolated groups, showing genetic divergence among them and in relation to main 'Baia Periforme' group. This germplasm displayed a relatively low genetic diversity, with the predominance of materials originated from the base population 'Baia Periforme'. There are, however, some accessions, which can add genetic diversity to this germplasm and they can be exploited by onion breeding programs aiming to develop cultivars for tropical regions of the world.

scholarly journals Molecular identification and genetic diversity in Hypericum L.: A high value medicinal plant using RAPD markers markers

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 393-405
Author(s):  
Dezhong Bi ◽  
Dan Chen ◽  
Majid Khayatnezhad ◽  
Zohreh Hashjin ◽  
Zifa Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Mantel Test ◽  
High Genetic Diversity ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability ◽  
Hypericum Species

Genus Hypericum (Guttiferae, Hypericoideae) is perennial, belonging to the Hypericaceae family, having 484 species in forms of trees, shrubs, and herbs, distributed in 36 taxonomic sections. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Hypericum genetic diversity. Therefore, we collected and analyzed six species from five provinces of Iran regions. Overall, seventy plant specimens were collected. Our aims were 1) to assess genetic diversity among Hypericum 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. H. dogonbadanicum depicted unbiased expected heterozygosity (UHe) in the range of 0.10. Shannon information was high (0.32) in H. perforaturm. H. dogonbadanicum showed the lowest value, 0.17. The observed number of alleles (Na) ranged from 0.22 to 0.53 in H. dogonbadanicum and H. elongaturn. Gene flow (Nm) was relatively low (0.87) in Hypericum. The Mantel test showed correlation (r = 0.45, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Hypericum 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 Hypericum species.

scholarly journals Genetic diversity of Lonicera L. (Caprifoliaceae) estimated by molecular markers and morphological characters

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 651-662
Author(s):  
Xin Ma ◽  
Huailiang Tian ◽  
Haiou Xia ◽  
Z Zeenat
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Mantel Test ◽  
High Genetic Diversity ◽  
Changing Environments ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability

Members of Lonicera are characterized by opposite, narrowly elliptic to obovate leaves, white, yellow, reddish, or purple-red corolla with capitate stigma and undulate calyx margin. In Flora Iranica, Wendelbo (1965) classified 19 species of the Lonicera into two subgenera (Chamaecerasus and Lonicera) and three sections, namely Isoxylosteum, Isika and Coeloxylosteum. The four studied species belong to subgenus Chamaecerasus and sections Isika and Coeloxylosteum. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Lonicera genetic diversity. Therefore, we collected and analyzed three species from 2 provinces regions. Overall, 45 plant specimens were collected. Our aims were 1) to assess genetic diversity among Lonicera 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. The Mantel test showed correlation (r=0.66, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Lonicera 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 Lonicera species.

scholarly journals Genetic diversity in sugar apple (Annona squamosa L.) by using RAPD markers

Revista CERES ◽  
2013 ◽  
Vol 60 (3) ◽  
pp. 428-431 ◽  
Author(s):  
João Filipi Rodrigues Guimarães ◽  
Silvia Nietsche ◽  
Márcia Regina Costa ◽  
Glaucia Bethania Rocha Moreira ◽  
Marlon Cristian Toledo Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Rapd Markers ◽  
Geographical Origin ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Annona Squamosa ◽  
Low Level ◽  
Molecular Grouping

Genetic diversity in a collection of 64 sugar apple accessions collected from different municipalities in northern Minas Gerais was assessed by RAPD analysis. Using 20 selected RAPD primers 167 fragments were generated, of which 48 were polymorphic (28.7%) producing an average of 2.4 polymorphic fragments per primer. Low percentage of polymorphism (< 29%) was observed by using the set of primers indicating low level of genetic variation among the 64 accessions evaluated. Genetic relationships were estimated using Jaccard's coefficient of similarity. Accessions from different municipalities clustered together indicating no correlation between molecular grouping and geographical origin. The dendrogram revealed five clusters. The first cluster grouped C19 and G29 accessions collected from the municipalities of Verdelândia and Monte Azul, respectively. The second cluster grouped G16 and B11 accessions collected from the municipalities of Monte Azul and Coração de Jesus, respectively. The remaining accessions were grouped in three clusters, with 8, 15 and 37 accessions, respectively. In summary, RAPD showed a low percentage of polymorphism in the germplasm collection.

scholarly journals Pawpaw [Asimina triloba (L.) Dunal] Germplasm Evaluation Using RAPD Markers

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 513D-513
Author(s):  
Hongwen Huang ◽  
Desmond R. Layne ◽  
Thomas L. Kubisiak
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Germplasm Collection ◽  
Germplasm Evaluation ◽  
Genetic Enhancement ◽  
Similar Species ◽  
Native Range ◽  
Woody Perennial ◽  
Asimina Triloba ◽  
Species Characteristics

Kentucky State Univ. (KSU) is the national clonal germplasm repository for Asimina species. Previous evaluation of the KSU pawpaw collection using 24 isozyme markers demonstrated that pawpaw has a relatively higher genetic diversity than that noted for other plant species with similar species characteristics (long-lived, woody, perennial, out-crossing, temperate, widespread, etc.). Current evaluation using RAPD markers will provide us with a more-accurate insight into pawpaw genetic diversity and population structure. In a preliminary experiment, one hundred 10-mer primers (OA1-20 through OE1-20, Operon Technologies Inc.) were screened against 32 commercial cultivars or advanced selections. A subset of 24 primers that amplify only the most-informative markers were used for germplasm evaluation. Sixty-eight RAPD markers were identified and used for determining genetic parameters. One-hundred-twenty pawpaw accessions were sampled from the KSU repository for RAPD analysis. These accessions represented nine widely distributed states within pawpaw's native range. RAPD data were subjected to various analyses using the NTSYS-PC computer program (ver. 1.8). Information generated from isozyme and RAPD markers will be used to formulate future germplasm collection strategies from wild populations within the native range. The implications of such information to the genetic enhancement of our repository and establishment of a core collection will be discussed.

scholarly journals Genetic relatedness of soybean genotypes based on agromorphological traits and RAPD markers

Genetika ◽  
2014 ◽  
Vol 46 (3) ◽  
pp. 839-854 ◽  
Author(s):  
Vesna Peric ◽  
Ana Nikolic ◽  
Vojka Babic ◽  
Aleksanda Sudaric ◽  
Mirjana Srebric ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quantitative Traits ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Diversity Index ◽  
Genetic Relationships ◽  
Morphological Characters ◽  
Morphological Description ◽  
Modern Agriculture ◽  
Soybean Genotypes

Modern agriculture, breeding procedures, as well as competition among breeding institutions contribute to further reduction of already narrowed diversity of soybean commercial varieties. The objective of the study was to characterize eighteen soybean cultivars from three different breeding programs for agro-morphological traits and to reveal genetic diversity using molecular markers. Morphological description was performed with 13 qualitative and 9 quantitative traits. The genetic relationships were estimated using 21 RAPD markers. PIC was calculated for RAPD data, while the diversity of qualitative traits was described by Shannon genetic diversity index. Cluster analysis based on qualitative morphological characters showed clear separation of genotypes on the basis of their plant growth type. PC analysis performed for quantitative traits divided genotypes according to their maturity group. Grouping pattern based on molecular marker data was in agreement with pedigree of cultivars. A great similarity was found, primarily between the varieties under the same institution, and then among all examined varieties. Comparison of three methods in the assessment of diversity indicated that morphological markers might provide useful information in breeding process and allow classification by pedigree to some extent, but RAPD markers were found to be superior in assessing differences among genetically very similar genotypes.

Spatially dependent genetic diversity within and between colonies of wild raspberry Rubus idaeus detected using RAPD markers

1997 ◽  
Vol 6 (11) ◽  
pp. 1001-1008 ◽  
Author(s):  
J. Graham ◽  
G. R. Squire ◽  
B. Marshall ◽  
R. E. Harrison
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Rubus Idaeus

scholarly journals Genetic Diversity of a Capsicum Germplasm Collection from Nepal as Determined by Randomly Amplified Polymorphic DNA Markers

2002 ◽  
Vol 127 (3) ◽  
pp. 318-324 ◽  
Author(s):  
J. Baral ◽  
P.W. Bosland
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Similarity Index ◽  
Germplasm Collection ◽  
Western Hemisphere ◽  
Randomly Amplified Polymorphic Dna ◽  
Index Value ◽  
Single Cluster

Domesticated chile (Capsicum annuum L. var. annuum) is a widely cultivated spice and vegetable crop. It originated in the Western Hemisphere, but spread rapidly throughout the globe after the voyage of Columbus. However, very little is known about the genetic diversity of chile in Asia and especially in Nepal. Thus, research was conducted to document morphological as well as molecular characterization of C. annuum var. annuum landraces collected from Nepal. Genetic diversity in C. annuum var. annuum landraces from Nepal was investigated using randomly amplified polymorphic DNA (RAPD) markers and compared with that of C. annuum var. annuum landraces from the center of diversity, Mexico. RAPD marker based cluster analysis of C. annuum var. annuum clearly separated each accession. All accessions of C. annuum var. annuum from Nepal grouped into a single cluster at a similarity index value of 0.80, whereas, accessions from Mexico grouped into eight different clusters at the same similarity level indicating greater genetic diversity in Mexican accessions. RAPD analysis indicated that the Nepalese chile population went through an additional evolutionary bottleneck or founder effect probably due to intercontinental migrations. Some Nepalese accessions had unique RAPD markers suggesting that additional sources of genetic variation are available in Nepalese germplasm.

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