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

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

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1120596.576810 ◽

2008 ◽

Author(s):

Richard Frankham

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Natural Populations ◽

Genome Wide

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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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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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Genetic Diversity in Natural Populations of Abies chensiensis Based on Nuclear Simple Sequence Repeat Markers

CHINESE BULLETIN OF BOTANY ◽

10.3724/sp.j.1259.2012.00413 ◽

2013 ◽

Vol 47 (4) ◽

pp. 413-421

Author(s):

Li Weimin ◽

Li Sifeng ◽

Li Bin

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Natural Populations ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Abies Chensiensis ◽

Simple Sequence

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The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.042390 ◽

2017 ◽

Vol 7 (7) ◽

pp. 2391-2403 ◽

Cited By ~ 11

Author(s):

Amanda S Lobell ◽

Rachel R Kaspari ◽

Yazmin L Serrano Negron ◽

Susan T Harbison

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Natural Populations ◽

Direct Role ◽

Genome Wide ◽

A Genome ◽

Fitness Trait ◽

Sleep Parameters ◽

Activity Behavior ◽

Ovariole Number

Abstract Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila. However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1. Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.

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Genetic diversity and population structure of popcorn germplasm resources using genome-wide SNPs through genotyping-by-sequencing

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01137-0 ◽

2021 ◽

Author(s):

Diansi Yu ◽

Hui Wang ◽

Wei Gu ◽

Tao Qin ◽

Pingdong Sun ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genotyping By Sequencing ◽

Germplasm Resources ◽

Genome Wide

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On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Genetics Selection Evolution ◽

10.1186/s12711-021-00639-w ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Gabriele Senczuk ◽

Salvatore Mastrangelo ◽

Paolo Ajmone-Marsan ◽

Zsolt Becskei ◽

Paolo Colangelo ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Melting Pot ◽

Cattle Breeds ◽

Snp Data ◽

Early Migration ◽

Genome Wide ◽

European Colonization ◽

Approximate Bayesian ◽

European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

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