scholarly journals PHENETIC ANALYSIS OF 28 SPECIES PANGASIID CATFISHES FROM ASIA

Zuriat ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Rudhy Gustiano ◽  
Laurent Pouyaud

A great variation in the external morphology of pangasiid catfishes and it is difficult to give a standard definition of their external appearance. The degree of similarity, known as phenetic analysis, is generally one of the criteria on which the recognition of taxa has been based. The objective of this phenetic analysis was to determine the degree of similarity. A measure of dissimilarity was computed from the coordinates of the first two axes of the Correspondence Analysis, using Euclidean distance. The distances were used to produce coefficients of similarity between each species pair. Distances are  non-negative and low values indicate similarity. Distance values for the matrix were then clustered with the unweighted pair-group method using the arithmetic average and summarized in a phenogram. The results showed that all species analysed for proposed genera aggregated. Analysis on 28 species supports that they should belong to four genera.

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.


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 ◽  
...  

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.


Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A Segovia-Lerma ◽  
R G Cantrell ◽  
J M Conway ◽  
I M Ray

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.


2020 ◽  
Vol 43 ◽  
pp. e53540
Author(s):  
Maria Fernanda de Souza Dias Maioli ◽  
Ronald José Barth Pinto ◽  
Tereza Aparecida da Silva ◽  
Diego Ary Rizzardi ◽  
Robson Akira Matsuzaki ◽  
...  

In this study, we aimed to estimate general and specific combining abilities (GCA and SCA, respectively) and to verify genetic divergence (Rogers distance, Unweighted Pair-Group Method Using Arithmetic Average - UPGMA) using microsatellite markers in maize inbred lines. Using a partial diallel scheme, a total of 19 inbred lines were crossed as (9 x 10), which were derived from the single hybrids SG6015 and P30F53, respectively. The 90 hybrids were evaluated in an incomplete randomized block design with common checks and three replications during the 2017-2018 growing season. Flowering time, average plant height, ear height insertion, average ear diameter, ear length, number of lodged and broken plants, mass of 100 grains and grain yield were measured. According to the analysis of variance, GCA, and SCA were significant (p < 0.05) in all the measured traits; inbred line B as well as 1 and 8, derived from the single hybrids SG6015 and P30F53, respectively, were selected due to their higher GCA values in grain yield to be used in crosses as testers, while the single cross hybrid (B x 1) was selected due to their higher SCA value in grain yield to be used in future breeding programs. The molecular marker analysis divided the inbred lines into two groups, where the highest dissimilarity (0.74) was observed between lines A and 9; however, these did not result in a high SCA value, therefore the hybrids obtained by such crossings were not selected for grain yield.


2004 ◽  
Vol 129 (5) ◽  
pp. 690-697 ◽  
Author(s):  
Pachanoor S. Devanand ◽  
Jianjun Chen ◽  
Richard J. Henny ◽  
Chih-Cheng T. Chao

Philodendrons (Philodendron Schott) are among the most popular tropical ornamental foliage plants used for interior decoration. However, limited information is available on the genetic relationships among popular Philodendron species and cultivars. This study analyzed genetic similarity of 43 cultivars across 15 species using amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. Forty-eight EcoR I + 2/Mse I + 3 primer set combinations were screened, from which six primer sets were selected and used in this investigation. Each selected primer set generated 96 to 130 scorable fragments. A total of 664 AFLP fragments were detected, of which 424 (64%) were polymorphic. All cultivars were clearly differentiated by their AFLP fingerprints, and the relationships were analyzed using the unweighted pair-group method of arithmetic average cluster analysis (UPGMA) and principal coordinated analysis (PCA). The 43 cultivars were divided into five clusters. Cluster I comprises eight cultivars with arborescent growth style. Cluster II has only one cultivar, `Goeldii'. There are 16 cultivars in cluster III, and most of them are self-heading interspecific hybrids originated from R.H. McColley's breeding program in Apopka, Fla. Cluster IV contains 13 cultivars that exhibit semi-vining growth style. Cluster V has five cultivars that are true vining in morphology, and they have lowest genetic similarity with philodendrons in other clusters. Cultivated philodendrons are generally genetically diverse except the self-heading hybrids in cluster III that were mainly developed using self-heading and semi-vining species as parents. Seven hybrid cultivars have Jaccard's similarity coefficients of 0.88 or higher, suggesting that future hybrid development needs to select parents with diverse genetic backgrounds.


2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.


2001 ◽  
Vol 91 (10) ◽  
pp. 973-980 ◽  
Author(s):  
K. H. Lamour ◽  
M. K. Hausbeck

Phytophthora capsici isolates were recovered from pepper and cucurbit hosts at seven locations in Michigan from 1998 to 2000. Isolates were characterized for compatibility type (CT), mefenoxam sensitivity (MS), and amplified fragment length polymorphism (AFLP) marker profiles. In total, 94 AFLP bands were resolved. Individual populations were highly variable. Within populations, 39 to 49% of the AFLP bands were polymorphic and estimated heterozygosities ranged from 0.16 to 0.19. Of the 646 isolates fingerprinted, 70% (454) had unique AFLP profiles. No clones were recovered between years or locations. Pairwise F statistics (ΦST) between populations from different locations ranged from 0.18 to 0.40. A tree based on unweighted pair-group method with arithmetic average cluster analysis indicates discrete clusters based on location. Isolates from the same location showed no clustering based on the year of sampling. Analysis of molecular variance partitioned variability among (40%) and within populations (60%). The overall estimated ΦST was 0.34 (SD = 0.03). A1/A2 CT ratios were ≈1:1, and MS frequencies were similar between years for the two locations sampled over time. These data suggest that P. capsici persists in discrete outcrossing populations and that gene flow among locations in Michigan is infrequent.


2004 ◽  
Vol 1 (2) ◽  
pp. 73-78 ◽  
Author(s):  
Shang Hai-Ying ◽  
Zheng You-Liang ◽  
Wei Yu-Ming ◽  
Wu Wei ◽  
Yan Ze-Hong

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.


2013 ◽  
Vol 93 (6) ◽  
pp. 1089-1096 ◽  
Author(s):  
Shiyong Chen ◽  
Xinquan Zhang ◽  
Xiao Ma ◽  
Linkai Huang

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.


2006 ◽  
Vol 131 (5) ◽  
pp. 622-631 ◽  
Author(s):  
E.J. Parks ◽  
J.W. Moyer ◽  
J.H. Lyerly

Fluorescent amplified fragment length polymorphism (F-AFLP) and microsatellites (SSRs) were used to evaluate new guinea impatiens (Impatiens hawkeri W. Bull) cultivars. Ninety-five quality-selected polymorphic fragments from 10 F-AFLP+3 primer combinations were used to evaluate 100 cultivars representing a variety of colors, forms, and breeding programs. Jaccard similarities and unweighted pair-group method of the arithmetic average (UPGMA) clustering formed a dendrogram with three cultivar groups, to a large extent clustering the cultivars by breeder with a high cophenetic correlation coefficient. A small insert genomic library was created and 442 kb of new guinea impatiens sequence was screened for repetitive motifs, resulting in 14 microsatellite markers. A subset of 46 cultivars representing five commercial breeding companies and 11 cultivar series was selected for microsatellite analysis. Seven loci were polymorphic, with two to six alleles per locus. Although both methods were equally effective in distinguishing the cultivars from one another, the topologies of the dendrograms for the two methods were different. The topology of the AFLP dendrogram reflected possible relationships based on cultivar series and breeding company, while the SSR dendrogram did not. The objectives of this research were to develop and validate both F-AFLP and SSR methodologies for new guinea impatiens, identify markers that can be reliably used for fingerprinting, and create a database for future cultivar comparisons.


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