Genetic diversity studies of alfalfa germplasm (Medicago sativa L. subsp. sativa) of United States origin using microsatellite analysis

2017 ◽  
Author(s):  
Shuying Yin ◽  
Yanrong Wang ◽  
Zhibiao Nan
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Polymorphic Information Content ◽  
The United States ◽  
Microsatellite Analysis ◽  
Information Index ◽  
Diversity Studies ◽  
Two Populations

This study aimed to understand the genetic diversity and population structure of alfalfa germplasm from the United States. In this study, the population structure and genetic diversity of six alfalfa cultivars of United States origin were investigated by microsatellite analysis with 40 individuals per cultivar. A total of 312 discernible alleles were amplified from the whole genome with an average of 31.2 alleles per locus. The average values of polymorphic information content and Shannon’s information index were 0.928 and 0.133, respectively, showing high levels of genetic diversity. Two populations were identified by STRUCTURE software with principal coordinate analysis and neighbour-joining clustering. Analysis of molecular variance analysis (AMOVA) revealed that the majority of genetic variation was within cultivars (96.42%) rather than between cultivars (3.58%). In conclusion, analyses of genetic diversity and population structure may be useful for the genetic analysis and utilization of genetic variation in alfalfa breeding.

scholarly journals Population structure of Drosophila suzukii and signals of multiple invasions into the continental United States

2021 ◽  
Author(s):  
Kyle M Lewald ◽  
Antoine Abrieux ◽  
Derek A Wilson ◽  
Yoosook Lee ◽  
William R Conner ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Weather Conditions ◽  
The United States ◽  
Future Research ◽  
Drosophila Suzukii ◽  
Significant Damage ◽  
Wide Range ◽  
Multiple Invasions

Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. To improve on previous studies examining genetic structure of D. suzukii, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several representative sites in Europe, Brazil, and Asia, to identify hundreds of thousands of genetic markers for analysis. We analyzed these markers to detect population structure, to reconstruct migration events, and to estimate genetic diversity and differentiation within and among the continents. We observed strong population structure between West and East Coast populations in the U.S., but no evidence of any population structure North to South, suggesting there is no broad-scale adaptations occurring in response to the large differences in regional weather conditions. We also find evidence of repeated migration events from Asia into North America have provided increased levels of genetic diversity, which does not appear to be the case for Brazil or Europe. This large genomic dataset will spur future research into genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

scholarly journals Measurement of Genetic Diversity of Chinese Seashore Paspalum Resources through Morphological and Sequence-related Amplified Polymorphism Analysis

2019 ◽  
Vol 144 (6) ◽  
pp. 379-386
Author(s):  
Yan Liu ◽  
Hailin Guo ◽  
Yi Wang ◽  
Jingang Shi ◽  
Dandan Li ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Morphological Characteristics ◽  
The United States ◽  
Germplasm Resources ◽  
Seashore Paspalum ◽  
Chinese Germplasm

Seashore paspalum (Paspalum vaginatum) is a notable warm-season turfgrass. Certain germplasm resources are distributed in the southern regions of China. The objectives of this study were to investigate the genetic diversity and genetic variation of Chinese seashore paspalum resources. Morphological characteristics and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic relationships and genetic variation among 36 germplasm resources from China and six cultivars from the United States. The results showed significant variation for 13 morphological characteristics among 42 tested seashore paspalum accessions, and that the phenotypic cv was, in turn, turf height > turf density > internode length > inflorescence density > leaf width > reproductive branch height > spikelet width > leaf length > spikelet number > inflorescence length > internode diameter > inflorescence width > spikelet length. According to the morphological characteristics and cluster analysis, 42 seashore paspalum accessions were divided into six morphological types. In total, 374 clear bands were amplified using 30 SRAP primer combinations; among these bands, 321 were polymorphic with 85.83% polymorphism. SRAP marker cluster analysis showed that 42 seashore paspalum accessions were grouped into seven major groups, with a genetic similarity coefficient ranging from 0.4385 to 0.9893 and genetic distance values ranging from 0.0108 to 0.8244. The high level of genetic diversity occurred among Chinese germplasm, and the genetic distance was relatively high between Chinese germplasm and cultivars introduced from the United States. The patterns in morphological trait variations and genetic diversity will be useful for the further exploitation and use of Chinese seashore paspalum resources.

scholarly journals Contrasting Patterns of Genetic Diversity and Population Structure of Armillaria mellea sensu stricto in the Eastern and Western United States

2010 ◽  
Vol 100 (7) ◽  
pp. 708-718 ◽  
Author(s):  
Kendra Baumgartner ◽  
Renaud Travadon ◽  
Johann Bruhn ◽  
Sarah E. Bergemann
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Los Angeles ◽  
The United States ◽  
Sensu Stricto ◽  
Western United States ◽  
Eastern United States ◽  
Armillaria Mellea ◽  
Genetic Pools

Armillaria mellea infects hundreds of plant species in natural and managed ecosystems throughout the Northern hemisphere. Previously reported nuclear genetic divergence between eastern and western U.S. isolates is consistent with the disjunct range of A. mellea in North America, which is restricted mainly to both coasts of the United States. We investigated patterns of population structure and genetic diversity of the eastern (northern and southern Appalachians, Ozarks, and western Great Lakes) and western (Berkeley, Los Angeles, St. Helena, and San Jose, CA) regions of the United States. In total, 156 diploid isolates were genotyped using 12 microsatellite loci. Absence of genetic differentiation within either eastern subpopulations (θST = –0.002, P = 0.5 ) or western subpopulations (θST = 0.004, P = 0.3 ) suggests that spore dispersal within each region is sufficient to prevent geographic differentiation. In contrast to the western United States, our finding of more than one genetic cluster of isolates within the eastern United States (K = 3), revealed by Bayesian assignment of multilocus genotypes in STRUCTURE and confirmed by genetic multivariate analyses, suggests that eastern subpopulations are derived from multiple founder sources. The existence of amplifiable and nonamplifiable loci and contrasting patterns of genetic diversity between the two regions demonstrate that there are two geographically isolated, divergent genetic pools of A. mellea in the United States.

scholarly journals Genetic Diversity and Population Structure of Endangered Catfish Rita rita (Hamilton, 1822) Revealed by Heterologous DNA Microsatellite Markers

2021 ◽  
Vol 34 (2) ◽  
Author(s):  
MUHAMMAD FORHAD ALI ◽  
◽  
MD. RAFIQUL ISLAM SARDER ◽  
MOHAMMAD MATIUR RAHMAN ◽  
MD. FAZLUL AWAL MOLLAH ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Genetic Difference ◽  
Information Index ◽  
Hardy Weinberg Equilibrium ◽  
High Gene ◽  
High Level ◽  
Dna Microsatellite

Genetic information is essential for conservation and future aquaculture development of the endangered catfish Rita rita (Hamilton, 1822). Two hundred catfish, R. rita, 50 from four rivers, the Old Brahmaputra, Jamuna, Meghna and Kangsa were collected and analysed to evaluate the genetic diversity and population structure using five microsatellite primers (Cba06-KUL, Cba08-KUL, Cba09-KUL, Phy03-KUL and Phy07-KUL). Four of the five amplified loci were found polymorphic (P95) in all the populations and 46 alleles were recorded with 9 to 14 alleles per locus. Differences were observed in the total number of alleles ranging from 41 to 44, effective number of alleles from 29.96 to 37.46, observed heterozygosity from 0.57 to 0.76, Shannon’s information index from 2.09 to 2.30 and polymorphic information content from 0.84 to 0.88 among the four populations. Results exposed the highest levels of genetic diversity in the Meghna population while the lowest in the Kangsa population of R. rita. All the populations were significantly deviated (P < 0.001) from the Hardy-Weinberg equilibrium for all the loci. Nei’s genetic distance between populations ranged 0.007 to 0.017 with low overall genetic difference FST = 0.011 and high gene flow Nm = 24.333, indicating that R. rita populations were not subdivided. This study revealed a high level of gene diversity with deficiency in genetic heterogeneity in all the populations of R. rita, emphasising natural management, conservation and rehabilitation measures of this species.

scholarly journals Genetic Diversity and Population Structure of Fusicladium effusum on Pecan in the United States

Plant Disease ◽  
2014 ◽  
Vol 98 (7) ◽  
pp. 916-923 ◽  
Author(s):  
C. H. Bock ◽  
B. W. Wood ◽  
K. L. Stevenson ◽  
R. S. Arias
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Gene Diversity ◽  
The United States ◽  
Individual Tree ◽  
Pecan Scab ◽  
The Individual ◽  
Average Gene

Fusicladium effusum causes pecan scab, which is the most destructive disease of pecan orchards in the United States. Conidia of the pathogen are spread by rain splash and wind. The fungus is pathogenically diverse; yet there is no information on its genetic diversity or population genetics. Universally primed polymerase chain reaction (UP-PCR) was used to investigate the genetic diversity and population structure on a hierarchical sample of 194 isolates collected from 11 orchard locations from Florida to Texas, consisting of three to four isolates from each of five to six trees at each location. Genetic variation was high throughout the region, with all but nine of the multilocus haplotypes being unique. Nei's average gene diversity ranged from 0.083 for a population from Mississippi to 0.160 for a population from Kansas. An analysis of molecular variance of the hierarchically sampled populations found that the majority of the genetic variability (82.6%) occurred at the scale of the individual tree and only relatively small amounts among populations in trees from an orchard (5.0%) or within groups (i.e., orchard location populations) (12.5%). The results suggest little population differentiation in F. effusum in the southeastern United States, although φpt values of genetic distance for pairwise comparisons indicated some populations could be differentiated from others. There was evidence of linkage disequilibrium in certain populations, and the common occurrence of asexual reproduction in F. effusum could lead to measurable linkage disequilibrium under certain circumstances. However, the degree of genetic diversity and the scale over which diversity is distributed is evidence that F. effusum undergoes regular recombination despite no known sexual stage.

scholarly journals Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tika B. Adhikari ◽  
Norman Muzhinji ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Genetic Diversity ◽  
North Carolina ◽  
Population Structure ◽  
Genetic Variation ◽  
Dna Sequences ◽  
Random Mating ◽  
Population Expansion ◽  
The United States ◽  
Population Subdivision ◽  
The Impact

AbstractEarly blight (EB) caused by Alternaria linariae or Alternaria solani and leaf blight (LB) caused by A. alternata are economically important diseases of tomato and potato. Little is known about the genetic diversity and population structure of these pathogens in the United States. A total of 214 isolates of A. alternata (n = 61), A. linariae (n = 96), and A. solani (n = 57) were collected from tomato and potato in North Carolina and Wisconsin and grouped into populations based on geographic locations and tomato varieties. We exploited 220 single nucleotide polymorphisms derived from DNA sequences of 10 microsatellite loci to analyse the population genetic structure between species and between populations within species and infer the mode of reproduction. High genetic variation and genotypic diversity were observed in all the populations analysed. The null hypothesis of the clonality test based on the index of association $$\left( {\overline{r}_{d} } \right)$$ r ¯ d was rejected, and equal frequencies of mating types under random mating were detected in some studied populations of Alternaria spp., suggesting that recombination can play an important role in the evolution of these pathogens. Most genetic differences were found between species, and the results showed three distinct genetic clusters corresponding to the three Alternaria spp. We found no evidence for clustering of geographic location populations or tomato variety populations. Analyses of molecular variance revealed high (> 85%) genetic variation within individuals in a population, confirming a lack of population subdivision within species. Alternaria linariae populations harboured more multilocus genotypes (MLGs) than A. alternata and A. solani populations and shared the same MLG between populations within a species, which was suggestive of gene flow and population expansion. Although both A. linariae and A. solani can cause EB on tomatoes and potatoes, these two species are genetically differentiated. Our results provide new insights into the evolution and structure of Alternaria spp. and can lead to new directions in optimizing management strategies to mitigate the impact of these pathogens on tomato and potato production in North Carolina and Wisconsin.

scholarly journals Population Structure of the Blueberry Pathogen Monilinia vaccinii-corymbosi in the United States

2015 ◽  
Vol 105 (4) ◽  
pp. 533-541 ◽  
Author(s):  
Kathleen M. Burchhardt ◽  
Marc A. Cubeta
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
New York ◽  
Population Structure ◽  
Population Biology ◽  
Random Mating ◽  
The United States ◽  
Restricted Gene Flow ◽  
Southeast United States ◽  
Genetic Diversity And Structure

The fungus Monilinia vaccinii-corymbosi causes disease of blueberry (Vaccinium section Cyanococcus) shoots, flowers, and fruit. The objective of our research was to examine the population biology and genetics of M. vaccinii-corymbosi in the United States. A total of 480 samples of M. vaccinii-corymbosi were collected from 18 blueberry fields in 10 states; one field in Georgia, Massachusetts, Maine, Michigan, Mississippi, New Jersey, New York, Oregon, and Washington and nine fields in North Carolina. Analysis with 10 microsatellite markers revealed 247 unique multilocus haplotypes (MLHs), with 244 MLHs detected within 11 fields in the Northeast, Northwest, Midwest, and Southeast and three MLHs detected within seven fields in the Southeast United States. Genetic similarity and low genetic diversity of M. vaccinii-corymbosi isolates from the seven fields in the Southeast United States suggested the presence of an expansive, self-fertile population. Tests for linkage disequilibrium within 10 fields that contained ≥12 MLHs supported random mating in six fields and possible inbreeding and/or self-fertilization in four fields. Analysis of molecular variance, discriminate analysis of principal components, and Bayesian cluster analysis provided evidence for population structure and restricted gene flow among fields. This research represents the first comprehensive investigation of the genetic diversity and structure of field populations of M. vaccinii-corymbosi.

scholarly journals Genetic Diversity, Population Structure and Marker-Trait Association for 100-Seed Weight in International Safflower Panel Using SilicoDArT Marker Information

Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 652 ◽  
Author(s):  
Fawad Ali ◽  
Muhammad Azhar Nadeem ◽  
Muzaffer Barut ◽  
Ephrem Habyarimana ◽  
Hassan Javed Chaudhary ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Seed Weight ◽  
Mixed Linear Model ◽  
Oilseed Crop ◽  
Trait Association ◽  
Information Index ◽  
Expected Heterozygosity ◽  
Two Populations ◽  
100 Seed Weight

Safflower is an important oilseed crop mainly grown in the arid and semi-arid regions of the world. The aim of this study was to explore phenotypic and genetic diversity, population structure, and marker-trait association for 100-seed weight in 94 safflower accessions originating from 26 countries using silicoDArT markers. Analysis of variance revealed statistically significant genotypic effects (p < 0.01), while Turkey samples resulted in higher 100-seed weight compared to Pakistan samples. A Constellation plot divided the studied germplasm into two populations on the basis of their 100-seed weight. Various mean genetic diversity parameters including observed number of alleles (1.99), effective number of alleles (1.54), Shannon’s information index (0.48), expected heterozygosity (0.32), and unbiased expected heterozygosity (0.32) for the entire population exhibited sufficient genetic diversity using 12232 silicoDArT markers. Analysis of molecular variance (AMOVA) revealed that most of the variations (91%) in world safflower panel are due to differences within country groups. A model-based structure grouped the 94 safflower accessions into populations A, B, C and an admixture population upon membership coefficient. Neighbor joining analysis grouped the safflower accessions into two populations (A and B). Principal coordinate analysis (PCoA) also clustered the safflower accessions on the basis of geographical origin. Three accessions; Egypt-5, Egypt-2, and India-2 revealed the highest genetic distance and hence might be recommended as candidate parental lines for safflower breeding programs. The mixed linear model i.e., the Q + K model, demonstrated that two DArTseq markers (DArT-45483051 and DArT-15672391) had significant association (p < 0.01) for 100-seed weight. We envisage that identified DArTseq markers associated with 100-seed weight will be helpful to develop high-yielding cultivars of safflower through marker-assisted breeding in the near future.

scholarly journals Genetic Diversity and Population Structure of Didymella rabiei Affecting Chickpea in Ethiopia

2021 ◽  
Vol 7 (10) ◽  
pp. 820
Author(s):  
Gezahegne Getaneh ◽  
Tadele Tefera ◽  
Fikre Lemessa ◽  
Seid Ahmed ◽  
Tarekegn Fite ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Ascochyta Blight ◽  
Geographic Origin ◽  
Principal Component ◽  
Internal Transcribed Spacer Region ◽  
Pathogen Populations

Ascochyta blight, also known as chickpea blight, which is caused by the fungal pathogen, Didymella rabiei, is an important disease affecting chickpea (Cicer arietinum L.) in many countries. We studied the genetic diversity and population structure of 96 D. rabiei isolates collected from three geographic populations in Ethiopia using simple sequence repeat (SSR) markers. We confirmed the genetic identity of 89 of the D. rabiei isolates by sequencing their rRNA internal transcribed spacer region genes. The chickpea blight pathogen isolates were genetically diverse, with a total of 51 alleles identified across 6 polymorphic SSR loci, which varied from 3 to 18 (average 8.5) alleles per SSR marker. The observed heterozygosity and expected heterozygosity ranged from 0.01 to 0.92 and 0.19 to 0.86, respectively. The mean polymorphic information content value of the D. rabiei populations was 0.58, with a mean gene diversity of 0.61 among loci. Gene flow (Nm = number of migrants) for the three populations of D. rabiei isolates ranged from 1.51 to 24.10 (average 6.2) migrants/cluster. However, the genetic variation between the D. rabiei populations was small (8%), with most of the variation occurring within populations (92%). Principal component analysis to visualize genetic variation showed that the D. rabiei isolates obtained from most of the chickpea samples formed roughly three groups on a two-dimensional coordinate plane. Similarly, the clustering of individuals into populations based on multi-locus genotypes (using Clumpak) grouped isolates into three clusters but with individual isolate admixtures. Hence, no clear geographic origin-based structuring of populations could be identified. To our knowledge, this is the first report of D. rabiei diversity in Ethiopia. Virulence studies should be conducted to develop chickpea varieties that are resistant to more aggressive pathogen populations.

Academic Regionalism and the Study of Human Genetic Variation in a Transnational Context

2018 ◽  
Author(s):  
Shirley Sun
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Clinical Trials ◽  
Genetic Variation ◽  
South Korea ◽  
Asian Population ◽  
The United States ◽  
Population Variation ◽  
Human Genetic Variation

This chapter discusses academic regionalism and racialization of ethnicity in Asia. Geneticists from China, Japan, and South Korea were interviewed about Asianism and the racialization of ethnicity. Four major themes emerged from these interviews: that there is a need to recognize the genetic diversity of the Asian population in clinical trials in the United States, that ethnicity was used as a basis to start the population variation study, that the consortium identified genetic diversity through ethnicity as defined by local geneticists, and that a reaction to Eurocentrism underpins the pride of emerging Asian players in genome science. The overall conclusion resulting from the discussions with the geneticists is that ethnicity is a sociopolitical construct rather than biological.

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