To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations?

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

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Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽

10.7717/peerj.2936 ◽

2017 ◽

Vol 5 ◽

pp. e2936 ◽

Cited By ~ 13

Author(s):

Caroline E. Dubé ◽

Serge Planes ◽

Yuxiang Zhou ◽

Véronique Berteaux-Lecellier ◽

Emilie Boissin

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Microsatellite Loci ◽

Natural Populations ◽

454 Sequencing ◽

Genetic Distances ◽

Null Alleles ◽

Future Research ◽

Significant Linkage ◽

Pacific Species

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

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Genetic diversity and population structure in natural populations of Tunisian Azarole (Crataegus azarolus L. var. aronia L.) assessed by microsatellite markers

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2015.01.025 ◽

2015 ◽

Vol 59 ◽

pp. 264-270 ◽

Cited By ~ 6

Author(s):

Salma Khiari ◽

Mohamed Boussaid ◽

Chokri Messaoud

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Natural Populations

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Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers

Parasitology ◽

10.1017/s0031182002002020 ◽

2002 ◽

Vol 125 (7) ◽

pp. S51-S59 ◽

Cited By ~ 50

Author(s):

J. CURTIS ◽

R. E. SORENSEN ◽

D. J. MINCHELLA

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Molecular Markers ◽

Microsatellite Markers ◽

Natural Populations ◽

Mitochondrial Marker ◽

Tropical Regions ◽

Blood Flukes

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

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Genome-wide assessment of genetic diversity and population structure in Magnolia odoratissima based on SLAF-Seq

10.21203/rs.3.rs-747821/v1 ◽

2021 ◽

Author(s):

Tao Zhang ◽

Xue Li ◽

Shuilian He

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Natural Populations ◽

Environmental Parameters ◽

Candidate Snps ◽

Small Populations ◽

Nucleotide Polymorphisms ◽

High Genetic Diversity ◽

Genome Wide

Abstract Magnolia odoratissima is a highly threatened species with small populations and scattered distribution due to habitat fragmentation and human activity. The species is recognized as a Plant Species with Extremely Small Populations (PSESP) and is endemic to China. In the current study, the population structure and levels of genetic diversity of M. odoratissima in the five remaining natural populations and three cultivated populations were evaluated using single nucleotide polymorphisms (SNPs) derived from Specific-Locus Amplified Fragment Sequencing (SLAF-seq). A total of 180,650 SNP loci were found in seventy M. odoratissima individuals. The genome-wide Nei’s and Shannon’s nucleotide diversity indexes of the total M. odoratissima population were 0.3035 and 0.4695, respectively. The observed heterozygosity (Ho) and expected heterozygosity (He) were 0.1122 and 0.3011. Our results suggest that M. odoratissima has relatively high genetic diversity at the genomic level. FST and AMOVA indicated that high genetic differentiation existed among populations. A phylogenetic neighbor-joining tree, Bayesian model–based clustering and principal components analysis (PCA) all divided the studied M. odoratissima individuals into three distinct clusters. The Treemix analysis showed that there was low gene flow among the natural populations and a certain gene flow from the wild populations to the cultivated population (LS to KIB, and GN to JD). In addition, a total of 36 unique SNPs were detected as being significantly associated with environmental parameters (altitude, temperature and precipitation). These candidate SNPs were found to be involved in multiple pathways including several molecular functions and biological process, suggesting they may play key roles in environmental adaptation. Our results suggested that three distinct evolutionary significant units (ESUs) should be set up to conserve this critically endangered species.

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Do microsatellites reflect genome-wide genetic diversity in natural populations? A comment on Väliet al.(2008)

Molecular Ecology ◽

10.1111/j.1365-294x.2010.04522.x ◽

2010 ◽

Vol 19 (5) ◽

pp. 851-855 ◽

Cited By ~ 42

Author(s):

MARCUS LJUNGQVIST ◽

MIKAEL ÅKESSON ◽

BENGT HANSSON

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Genome Wide

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Genetic diversity of Tambaqui (Teleostei - Characidae) broodstocks from Northern region of Brazil using microsatellite markers

Semina Ciências Agrárias ◽

10.5433/1679-0359.2020v41n6supl2p3249 ◽

2020 ◽

Vol 41 (6supl2) ◽

pp. 3249-3258

Author(s):

Angela Maria Urrea-Rojas ◽

◽

Felipe Pinheiro de Souza ◽

Ed Christian Suzuki de Lima ◽

Andrei Lincoln Yamachita ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Native Species ◽

Natural Populations ◽

Low Frequency ◽

Northern Region ◽

Fish Farms ◽

Amazonian Fish ◽

Optimal Value ◽

Increase Productivity

The Amazonian fish Tambaqui (Colossoma macropomum) is the most common native species in Brazil. This species has the highest production rate in the Northern region, especially in the State of Rondônia. The genetic evaluation of Tambaqui is an extremely important to increase productivity in fish farms or improve the adaptability in restocking natural populations. The objective of this study was to evaluate the genetic diversity of three Tambaqui broodstocks in Rondônia, Brazil. Six microsatellite markers were used to analyze a total of 89 breeders collected from three fish farms located in Ji-Paraná (JP), Ouro Preto do Oeste (OP) and Presidente Médici (PM). A total of 37 alleles between 140 and 310 bp were found, including the presence of exclusive and low frequency alleles in the three broodstocks. The average values of observed heterozygosity ranged from 0.404 (PM) to 0.499 (JP). The FIS coefficient values were positive for the three broodstocks, demonstrating a deficit of heterozygotes. The Molecular Variance Analysis (AMOVA) showed greater variation within the stocks than between them. The genetic differentiation was moderate and significant between the stocks, with higher differentiation between JP x PM and lower between OP x PM. The Bayesian analysis designated an optimal value of K = 3 groupings. Although there is moderate genetic diversity between broodstocks, the high FIS indicates a possible decline of diversity in the next generations, and therefore, the incorporation of new breeders is suggested to increase the genetic diversity in the three stocks.

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Partial selfing eliminates inbreeding depression while maintaining genetic diversity

10.1101/210005 ◽

2017 ◽

Author(s):

Ivo M. Chelo ◽

Bruno Afonso ◽

Sara Carvalho ◽

Ioannis Theologidis ◽

Christine Goy ◽

...

Keyword(s):

Genetic Diversity ◽

Inbreeding Depression ◽

Experimental Evolution ◽

Natural Populations ◽

Ancestral Population ◽

Origin And Evolution ◽

C Elegans ◽

Genome Wide ◽

Adaptive Genetic Diversity

AbstractClassical theory on the origin and evolution of selfing and outcrossing relies on the role of inbreeding depression created by unlinked partially-deleterious recessive alleles to predict that individuals from natural populations predominantly self or outcross. Comparative data indicates, however, that maintenance of partial selfing and outcrossing at intermediate frequencies is common in nature. In part to explain the presence of mixed reproductive modes within populations, several hypotheses regarding the evolution of inbreeding depression have been put forward based on the complex interaction of linkage and identity disequilibrium among fitness loci, together with Hill-Robertson effects. We here ask what is the genetic basis of inbreeding depression so that populations with intermediate selfing rates can eliminate it while maintain potentially adaptive genetic diversity. For this, we use experimental evolution in the nematode C. elegans under partial selfing and compare it to the experimental evolution of populations evolved under exclusive selfing and predominant outcrossing. We find that the ancestral risk of extinction upon enforced inbreeding by selfing is maintained when populations evolve under predominant outcrossing, but reduced when populations evolve under partial or exclusive selfing. Analysis of genome-wide single-nucleotide polymorphism (SNP) during experimental evolution and after enforced inbreeding suggests that, under partial selfing, populations were purged of unlinked deleterious recessive alleles that segregate in the ancestral population, which in turn allowed the expression of unlinked overdominant fitness loci. Taken together, these observations indicate that populations evolving under partial selfing gain the short-term benefits of selfing, in purging deleterious recessive alleles, but also the long-term benefits of outcrossing, in maintaining genetic diversity that may important for future adaptation.

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