Genetic Structure and Diversity among Species of Salacia: An Endangered Medicinal Herb of Western Ghats, India

Salacia is one of the medicinally valuable genus, distributed throughout tropical areas which include India, Sri Lanka, Southern China and other Southern Asian Countries. The genus Salacia is represented by 21 species in India, among them eight species are recorded from the state of Karnataka in the Southern part of India. Despite its pharmaceutical importance, very little information exists about the genetic diversity of Salacia at molecular level. Hence the present study was carried out to evaluate the genetic among six species of Salacia namely S. chinensis, S. malabarica, S. oblonga, S. macrosperma, S. reticulata and S. gambleana with the help of ISSR marker analysis. Dendrogram and genetic distance were generated adopting Unweighted Paired Group Method with Arithmetic mean (UPGMA) in the NTSYS-pc software. Basic genetic parameters were calculated by analysing the genetic data with Pop gene 1.32 and GenAlEx 6.2 software. The overall polymorphism across the ten primers screened revealed 26 % polymorphism. A 60% polymorphism was scored for the primer UBC 841, whereas, no polymorphism was observed for primer UBC 840 and ISSR 6. The average observed heterozygosity was more than expected heterozygosity. Observed heterozygosity (Ho) ranged from 0.15 (UBC 841) to 0.38 (ISSR 6) with an average of 0.25, whereas expected heterozygosity (He) ranged from 0.10 (UBC 843) to 0.35 (ISSR 6) with an average of 0.23 for Salacia species. The higher heterozygosity pointed towards increased genetic diversity amongst the species. ISSR marker analysis showed high level of inter and intra population genetic differentiation.

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GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

AGROFOR ◽

10.7251/agreng1603110k ◽

2016 ◽

Vol 1 (3) ◽

Author(s):

Veronika KUKUČKOVÁ ◽

Nina MORAVČÍKOVÁ ◽

Radovan KASARDA

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

The State ◽

Most Probable Number ◽

Pedigree Data ◽

Probable Number ◽

Expected Heterozygosity ◽

High Level ◽

The Bayesian Approach

The aim of this study was to assess genetic structure of Slovak Pinzgau populationbased on polymorphism at molecular markers using statistical methods. Femaleoffspring of 12 most frequently used bulls in Slovak Pinzgau breeding programmewere investigated. Pinzgau cattle were found to have a high level of diversity,supported by the number of alleles observed across loci (average 5.31, range 2-11)and by the high within-breed expected heterozygosity (average 0.66, range 0.64-0.73). The state of genetic diversity is satisfying and standard for local populations.Detection of 12 possible subpopulation structures provided us with detailedinformation of the genetic structure. The Bayesian approach was applied, detectingthree, as the most probable number of clusters. The similarity of eachsubpopulation using microsatellites was confirmed also by high-throughputmolecular data. The observed inbreeding (FROH=2.3%) was higher than thatexpected based on pedigree data (FPED=0.4%) due to the limited number ofavailable generations in pedigree data. One of the most important steps indevelopment of efficient autochthonous breed protection programs ischaracterization of genetic variability and assessment of the population structure.The chosen set of microsatellites confirmed the suitability in determination of thesubpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at moredetailed level was successfully performed using bovineSNP50 BeadChip.

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Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers

PeerJ ◽

10.7717/peerj.8038 ◽

2019 ◽

Vol 7 ◽

pp. e8038

Author(s):

Yanli Xiong ◽

Wenhui Liu ◽

Yi Xiong ◽

Qingqing Yu ◽

Xiao Ma ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Western China ◽

Tibet Plateau ◽

Group Method ◽

Breeding Strategies ◽

Population Genetic Differentiation ◽

Principal Coordinates ◽

Geographical Regions ◽

Genetic Diversity And Structure

Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread Elymus species. Elymus excelsus Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of E. excelsus germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of E. excelsus from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei’s genetic diversity (H) and Shannon’s diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of E. excelsus germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (Fst = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (He = 0.197) was greater than that of the GSC (He = 0.176) and XJC (He = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that E. excelsus accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable E. excelsus germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.

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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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Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

Plant Breeding and Seed Science ◽

10.1515/plass-2015-0024 ◽

2015 ◽

Vol 71 (1) ◽

pp. 81-95 ◽

Cited By ~ 7

Author(s):

Hoda Moradkhani ◽

Ali Ashraf Mehrabi ◽

Alireza Etminan ◽

Alireza Pour-Aboughadareh

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Genetic Relationships ◽

Issr Markers ◽

Issr Marker ◽

D Genome ◽

Ploidy Levels ◽

Marker Data ◽

Geographical Regions ◽

High Level

AbstractThe aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions ofAegilopsandTriticumspecies with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA) revealed that 81% (ISSR) and 84% (SSR) of variability was partitioned among individuals within populations. Comparing the genetic diversity ofAegilopsandTriticumaccessions, based on genetic parameters, shows that genetic variation ofAe. crassaandAe. tauschiispecies are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA) for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA), also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

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Genetic structure and diversity among individuals of Copaifera langsdorffii Desf. from Mato Grosso, Brazilian Amazon, using ISSR markers

Research Society and Development ◽

10.33448/rsd-v10i16.23025 ◽

2021 ◽

Vol 10 (16) ◽

pp. e187101623025

Author(s):

Daniele Paula Maltezo ◽

Julliane Dutra Medeiros ◽

Ana Aparecida Bandini Rossi

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Variability ◽

Polymorphic Information Content ◽

Issr Markers ◽

Group Method ◽

Mato Grosso ◽

Copaifera Langsdorffii ◽

Genetic Structure And Diversity ◽

Issr Primers

The Amazon is the largest tropical forest in the world and is home to around 20% of all the biodiversity on the planet, among the species present in the Amazon is Copaifera langsdorffii, exploited mainly for the extraction of oil-resin and wood, often in ways incorrect, which can cause the loss of genetic variability. The aim of this study was to evaluate the genetic structure and diversity among individuals of C. langsdorffii located in Mato Grosso, Brazil, using ISSR markers. We sampled leaves from 27 adult individuals of C. langsdorffii, whose total genomic DNA was extracted. A total of 12 ISSR primers were used for the molecular characterization of the individuals. A grouping analysis was performed using the unweighted pair group method, Bayesian analysis and characterized by the genetic diversity. The genetic diversity among and within the groups was demonstrated by the AMOVA. As a result, 106 fragments were amplified and 98.11% were polymorphic. The polymorphic information content of each primer ranged from 0.45 to 0.81. The dendrogram showed the formation of 4 distinct groups. The greatest genetic variability is found within the groups and not between them. The percentage of polymorphism, genetic dissimilarity values and genetic diversity indexes indicate that there is high genetic variability among Copaifera langsdorffii individuals, suggesting that ISSR primers were efficient in detecting polymorphism in this species and that the individuals have potential for compose programs aimed at the preservation of the species and the ability to integrate germplasm banks.

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Characterization and Identification of Pawpaw Cultivars and Advanced Selections by Simple Sequence Repeat Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.135.2.143 ◽

2010 ◽

Vol 135 (2) ◽

pp. 143-149 ◽

Cited By ~ 6

Author(s):

Kirk W. Pomper ◽

Jeremiah D. Lowe ◽

Li Lu ◽

Sheri B. Crabtree ◽

Shandeep Dutta ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Marker ◽

Genetic Erosion ◽

Null Alleles ◽

Group Method ◽

Genomic Libraries ◽

Pair Group ◽

Marker Loci ◽

High Level ◽

In The Beginning

Pawpaw [Asimina triloba (L.) Dunal.], a tree fruit native to eastern North America, is in the beginning stages of commercialization. Cultivars available in the early 20th century have been lost, and significant genetic erosion may have occurred. Polymorphic microsatellite marker loci were developed from enriched genomic libraries. Five marker loci were used to fingerprint 28 cultivars and 13 selections. For the 41 genotypes, 102 alleles were amplified and major allele frequency (0.16–0.94), number of genotypes (2–27), and allele size (144–343 bp) varied greatly by locus. Four loci were highly polymorphic, as indicated by values for expected heterozygosity (He), observed heterozygosity (Ho), and polymorphism information content, but only two alleles were detected at locus Pp-C104. A high level of genetic diversity was observed in the studied genotypes. The Ho (0.68) and He (0.70) were similar and indicated few null alleles. In the 41 genotypes, 39 unique fingerprints were observed. These new microsatellite marker loci will be useful for cultivar fingerprinting, management of collections, and investigation of genetic diversity in collections and wild populations. Grouping of genotypes in an unweighted pair group method with arithmetic mean dendrogram was generally consistent with their origins.

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Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers

Forests ◽

10.3390/f10030278 ◽

2019 ◽

Vol 10 (3) ◽

pp. 278 ◽

Cited By ~ 2

Author(s):

Hong-Ying Guo ◽

Ze-Liang Wang ◽

Zhen Huang ◽

Zhi Chen ◽

Han-Bo Yang ◽

...

Keyword(s):

Genetic Diversity ◽

Geographical Distribution ◽

Mantel Test ◽

Group Method ◽

Arithmetic Means ◽

Mountain Area ◽

Pair Group ◽

Hill Area ◽

Population Genetic Variation ◽

High Level

Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.

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Genetic Diversity in Populations of Phytophthora citricola Associated with Horticultural Crops in California

Plant Disease ◽

10.1094/pdis-91-12-1556 ◽

2007 ◽

Vol 91 (12) ◽

pp. 1556-1563 ◽

Cited By ~ 11

Author(s):

R. G. Bhat ◽

G. T. Browne

Keyword(s):

Genetic Diversity ◽

Fragment Length Polymorphism ◽

Group Method ◽

Aflp Data ◽

Analysis Of Molecular Variance ◽

Molecular Variance ◽

Horticultural Crops ◽

Pair Group ◽

Phytophthora Citricola ◽

High Level

California populations of the plant pathogen Phytophthora citricola were examined for amplified fragment length polymorphism (AFLP), pathogenicity on almond, and sensitivity to mefenoxam. The characterizations of AFLP variation and mefenoxam sensitivity were based on 86 isolates (44 from almond, 11 from avocado, 3 from strawberry, 18 from walnut, and 10 from six other hosts). Cluster analysis of the AFLP data using the unweighted pair group method indicated a high level of genetic diversity among the isolates, and four main clusters were identified—one dominated by isolates from almond, another including all isolates from avocado, and two including isolates from several hosts other than avocado. Analysis of molecular variance revealed that 38.4 and 24.9% of the AFLP variation were associated with host and geographical factors, respectively. Of 24 isolates, including those from almond, avocado, strawberry, and walnut, 22 were aggressive on almond shoots; there was no evidence of host specificity. All but 1 of the 86 isolates grew at different rates on V8 juice medium amended with mefenoxam at 1 ppm, indicating partial tolerance to the fungicide. Isolates of P. citricola from California populations are genetically diverse, and much of the variation is associated with host and geography. These populations are all potentially pathogenic on almond and tolerant to mefenoxam.

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Characterization and Genetic Diversity of Taif Chicken Ecotype Using Dense Microsatellites Panel

Bioscience Biotechnology Research Communications ◽

10.21786/bbrc/14.4.86 ◽

2021 ◽

Vol 14 (4) ◽

pp. 1962-1967

Author(s):

Ayman Sabry

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Inbreeding Coefficient ◽

Comprehensive Investigation ◽

Low Genetic Diversity ◽

Expected Heterozygosity ◽

Native Chicken ◽

High Level ◽

Weinberg Expectation ◽

Dense Panel

The current study is the first comprehensive investigation to address the native chicken ecotypes of the Taif region to unravel the genetic diversity using a dense panel of 40 microsatellites (SSR). Blood samples were collected from 25 hens randomly sampled from a village farm at Taif governorate. A total of 147 alleles were detected, with an average of 3.7 alleles per locus. The overall mean of polymorphic information content (PIC) was 0.43. The average observed heterozygosity (Hobs) of 0.28 was lower than the expected heterozygosity (Hexp) of 0.48. Out of 40l ocionly11 loci showed insignificant deviation from Hardy Weinberg expectation. The ecotypes showed low genetic diversity (HS = 0.65) and a high level of inbreeding (FIS= 0.75). The high FIS is indicative of the endangerment potentiality of this ecotype. Nine SSR showed an inbreeding coefficient of one. The significant estimate of the inbreeding coefficient of the present study calls for an immediate breeding plan to preserve such endangered ecotypes. Results of the present study will provide an initial guide to design further investigations for the development of sustainable genetic improvement and conservation programs for the Taif ecotype genetic resources.

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Genetic Diversity and Origin of Slovene Common Bean (Phaseolus vulgaris L.) Germplasm as Revealed by AFLP Markers and Phaseolin Analysis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.131.2.242 ◽

2006 ◽

Vol 131 (2) ◽

pp. 242-249 ◽

Cited By ~ 21

Author(s):

Jelka Šustar-Vozlič ◽

Marko Maras ◽

Branka Javornik ◽

Vladimir Meglič

Keyword(s):

Genetic Diversity ◽

Phaseolus Vulgaris ◽

Common Bean ◽

Seed Protein ◽

Fragment Length Polymorphism ◽

Aflp Markers ◽

Group Method ◽

Phaseolus Vulgaris L ◽

Pair Group ◽

High Level

There is a long tradition of common bean cultivation in Slovenia, which has resulted in the development of numerous landraces in addition to newly established cultivars. The genetic diversity of 100 accessions from the Genebank of the Agricultural Institute of Slovenia (AIS) were evaluated with amplified fragment length polymorphism (AFLP) markers and phaseolin seed protein. Twenty-seven standard accessions of known Mesoamerican and Andean origin, 10 wild Phaseolus vulgaris accessions and two related species, P. coccineus L. and P. lunatus L., were also included. Ten AFLP primer combinations produced 303 polymorphic bands, indicating a relatively high level of genetic diversity. Based on the marker data, unweighted pair group method with arithmethic mean (UPGMA) analysis and principal coordinate analysis (PCoA) all P. vulgaris accessions were separated into three well-defined groups. Two groups consisted of accessions of Mesoamerican and Andean origin, while the third was comprised of only four wild P. vulgaris accessions. A set of Slovene accessions formed a well-defined sub-group within the Andean cluster, showing their unique genetic structure. These data were supported by phaseolin analysis, which also revealed additional variants of “C” and “T” phaseolin types. The results are in agreement with previous findings concerning diversification of common bean germplasm introduced in Europe.

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