Mosaic microecological differential stress causes adaptive microsatellite divergence in wild barley, Hordeum spontaneum, at Neve Yaar, Israel

Genetic diversity at 38 microsatellite (short sequence repeats (SSRs)) loci was studied in a sample of 54 plants representing a natural population of wild barley, Hordeum spontaneum, at the Neve Yaar microsite in Israel. Wild barley at the microsite was organized in a mosaic pattern over an area of 3180 m2 in the open Tabor oak forest, which was subdivided into four microniches: (i) sunrock (11 genotypes), (ii) sunsoil (18 genotypes), (iii) shadesoil (11 genotypes), and (iv) shaderock (14 genotypes). Fifty-four genotypes were tested for ecologicalgenetic microniche correlates. Analysis of 36 loci showed that allele distributions at SSR loci were nonrandom but structured by ecological stresses (climatic and edaphic). Sixteen (45.7%) of 35 polymorphic loci varied significantly (p < 0.05) in allele frequencies among the microniches. Significant genetic divergence and diversity were found among the four subpopulations. The soil and shade subpopulations showed higher genetic diversities at SSR loci than the rock and sun subpopulations, and the lowest genetic diversity was observed in the sunrock subpopulation, in contrast with the previous allozyme and RAPD studies. On average, of 36 loci, 88.75% of the total genetic diversity exists within the four microniches, while 11.25% exists between the microniches. In a permutation test, GST was lower for 4999 out of 5000 randomized data sets (p < 0.001) when compared with real data (0.1125). The highest genetic distance was between shade-soil and sunrock (D = 0.222). Our results suggest that diversifying natural selection may act upon some regulatory regions, resulting in adaptive SSR divergence. Fixation of some loci (GMS61, GMS1, and EBMAC824) at a specific microniche seems to suggest directional selection. The pattern of other SSR loci suggests the operation of balancing selection. SSRs may be either direct targets of selection or markers of selected haplotypes (selective sweep).Key words: natural selection, genetic diversity, microsatellites, adaptation, Hordeum spontaneum, wild barley, microsite divergence.

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Assessment of genetic diversity among Jordanian wild barley (Hordeum spontaneum) genotypes revealed by SSR markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-015-0285-8 ◽

2015 ◽

Vol 63 (5) ◽

pp. 813-822 ◽

Cited By ~ 6

Author(s):

Y. Shakhatreh ◽

M. Baum ◽

N. Haddad ◽

M. Alrababah ◽

S. Ceccarelli

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Wild Barley ◽

Hordeum Spontaneum

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Genetic diversity and environmental associations of wild barley,Hordeum spontaneum, in Turkey

Genetica ◽

10.1007/bf02424444 ◽

1986 ◽

Vol 68 (3) ◽

pp. 203-213 ◽

Cited By ~ 35

Author(s):

E. Nevo ◽

D. Zohary ◽

A. Beiles ◽

D. Kaplan ◽

N. Storch

Keyword(s):

Genetic Diversity ◽

Wild Barley ◽

Hordeum Spontaneum

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Genetic Diversity and Environmental Future

Environmental Conservation ◽

10.1017/s0376892900005580 ◽

1978 ◽

Vol 5 (2) ◽

pp. 127-132 ◽

Cited By ~ 8

Author(s):

Gabor Vida

Keyword(s):

Genetic Diversity ◽

Natural Selection ◽

Human Population ◽

Natural Populations ◽

Wild Populations ◽

Modern Agriculture ◽

Total Genetic Diversity ◽

Enormous Amount ◽

Suitable Amount ◽

Historical Times

Increasing evidence indicates that a major portion of the enormous amount of polymorphism present in natural populations is maintained by natural selection. This polymorphism is necessary for adaptation. In the absence of a suitable amount of genetic diversity, a species will tend to die out in a changing environment.The genetic diversity of most species has been considerably reduced in historical times. Breeding for uniformity, and reduction in the number and size of wild populations, are largely responsible for this loss. Replacement of a natural forest ecosystem by modern agriculture reduces the genetic diversity by three orders of magnitude at the very least. A comparison of the estimated prehistoric and present amount of genetic diversity leads to the alarming conclusion that we may already have lost as much as 90% of the total genetic diversity of the biosphere. Further loss is expected because of the rapid growth of human population.

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Empirical threshold values for quantitative trait mapping.

Genetics ◽

10.1093/genetics/138.3.963 ◽

1994 ◽

Vol 138 (3) ◽

pp. 963-971 ◽

Cited By ~ 134

Author(s):

G A Churchill ◽

R W Doerge

Keyword(s):

Quantitative Trait ◽

Permutation Test ◽

Simulated Data ◽

Real Data ◽

Threshold Value ◽

Empirical Method ◽

Data Sets ◽

Threshold Values ◽

Quantitative Trait Mapping ◽

Qtl Effects

Abstract The detection of genes that control quantitative characters is a problem of great interest to the genetic mapping community. Methods for locating these quantitative trait loci (QTL) relative to maps of genetic markers are now widely used. This paper addresses an issue common to all QTL mapping methods, that of determining an appropriate threshold value for declaring significant QTL effects. An empirical method is described, based on the concept of a permutation test, for estimating threshold values that are tailored to the experimental data at hand. The method is demonstrated using two real data sets derived from F(2) and recombinant inbred plant populations. An example using simulated data from a backcross design illustrates the effect of marker density on threshold values.

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Simple Sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea macrophylla

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.132.3.341 ◽

2007 ◽

Vol 132 (3) ◽

pp. 341-351 ◽

Cited By ~ 12

Author(s):

Sandra M. Reed ◽

Timothy A. Rinehart

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Allelic Diversity ◽

Sequence Repeat ◽

Hydrangea Macrophylla ◽

Total Genetic Diversity ◽

Ssr Loci ◽

Diversity Studies ◽

Simple Sequence

Genetic diversity studies using 39 simple-sequence repeat (SSR) markers were carried out with 114 taxa of Hydrangea macrophylla (Thunb.) Ser., including 87 H. macrophylla ssp. macrophylla cultivars and 20 members of H. macrophylla ssp. serrata (Thunb.) Makino. The SSR loci were highly variable among the taxa, producing a mean of 8.26 alleles per locus. Overall allelic richness was relatively high at 5.12 alleles per locus. H. macrophylla ssp. serrata contained nearly twice the allelic diversity of H. macrophylla ssp. macrophylla. The majority of genetic diversity was found to reside within the subspecies, with only 12% of the total genetic diversity observed occurring between subspecies. Although the elevation of H. macrophylla ssp. serrata to species level has recently been recommended by several hydrangea authorities, these data support the subspecies designation. Four cultivars (Preziosa, Pink Beauty, Tokyo Delight, and Blue Deckle) appeared to be hybrids between the two subspecies. Genetic similarities were found among five remontant cultivars (Bailmer, Oak Hill, David Ramsey, Decatur Blue, and Penny Mac) and several nonremontant cultivars, including General Vicomtesse de Vibraye, Nikko Blue, All Summer Beauty, and La France. No close genetic relationship was found between the remontant cultivar Early Sensation and other remontant cultivars. Genetic similarities were found among variegated and double-flower cultivars. Within H. macrophylla ssp. macrophylla, cultivars with mophead inflorescences clustered separately from most lacecap cultivars. This indicates the cultivars with lacecap inflorescences that were among some of the earliest introductions to Europe were not widely used in the breeding of mophead forms. Some presumed synonyms were found to be valid (‘Preziosa’ and ‘Pink Beauty’, ‘Rosalba’ and ‘Benigaku’, ‘Geoffrey Chadbund’ and ‘Mowe’), whereas others were not (‘Harlequin’ and ‘Monrey’, ‘Nigra’ and ‘Mandschurica’). This study identified potentially unexploited sources of germplasm within H. macrophylla and relationships between existing cultivars of this popular shrub. This information should be of value when selecting parents for breeding programs.

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PERFect: PERmutation Filtering test for microbiome data

Biostatistics ◽

10.1093/biostatistics/kxy020 ◽

2018 ◽

Vol 20 (4) ◽

pp. 615-631 ◽

Cited By ~ 2

Author(s):

Ekaterina Smirnova ◽

Snehalata Huzurbazar ◽

Farhad Jafari

Keyword(s):

Permutation Test ◽

Real Data ◽

Data Sets ◽

Therapeutic Approaches ◽

Experiment Data ◽

Microbiome Research ◽

Inflammatory Bowel ◽

Microbiome Data ◽

Processing Steps

Summary The human microbiota composition is associated with a number of diseases including obesity, inflammatory bowel disease, and bacterial vaginosis. Thus, microbiome research has the potential to reshape clinical and therapeutic approaches. However, raw microbiome count data require careful pre-processing steps that take into account both the sparsity of counts and the large number of taxa that are being measured. Filtering is defined as removing taxa that are present in a small number of samples and have small counts in the samples where they are observed. Despite progress in the number and quality of filtering approaches, there is no consensus on filtering standards and quality assessment. This can adversely affect downstream analyses and reproducibility of results across platforms and software. We introduce PERFect, a novel permutation filtering approach designed to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. Methods are assessed on three “mock experiment” data sets, where the true taxa compositions are known, and are applied to two publicly available real microbiome data sets. The method correctly removes contaminant taxa in “mock” data sets, quantifies and visualizes the corresponding filtering loss, providing a uniform data-driven filtering criteria for real microbiome data sets. In real data analyses PERFect tends to remove more taxa than existing approaches; this likely happens because the method is based on an explicit loss function, uses statistically principled testing, and takes into account correlation between taxa. The PERFect software is freely available at https://github.com/katiasmirn/PERFect.

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GENETIC DIVERSITY AND ENVIRONMENTAL ASSOCIATIONS OF WILD BARLEY,HORDEUM SPONTANEUM, IN ISRAEL

Evolution ◽

10.1111/j.1558-5646.1979.tb04737.x ◽

1979 ◽

Vol 33 (3) ◽

pp. 815-833 ◽

Cited By ~ 1

Author(s):

Eviatar Nevo ◽

Daniel Zohary ◽

A. H. D. Brown ◽

Michael Haber

Keyword(s):

Genetic Diversity ◽

Wild Barley ◽

Hordeum Spontaneum

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Long-term balancing selection drives evolution of immunity genes in Capsella

10.1101/477612 ◽

2018 ◽

Cited By ~ 2

Author(s):

Daniel Koenig ◽

Jörg Hagmann ◽

Rachel Li ◽

Felix Bemm ◽

Tanja Slotte ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Natural Selection ◽

Balancing Selection ◽

Population Bottleneck ◽

Genomic Variability ◽

Immune Systems ◽

Immunity Genes ◽

Evolution Of Immunity

ABSTRACTGenetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. Our data point to long term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck.

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