Genetic relationships and population structure within taxa of the endemic Sideritis pusilla (Lamiaceae) assessed using RAPDs

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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Whole-genome SNP analysis elucidates the genetic population structure and diversity of Acrocomia species

10.1101/2020.10.08.331140 ◽

2020 ◽

Author(s):

Brenda G. Díaz ◽

Maria I. Zucchi ◽

Alessandro. Alves-Pereira ◽

Caléo P. de Almeida ◽

Aline C. L. Moraes ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Structure ◽

Genetic Relationships ◽

Geographical Area ◽

Taxonomic Classification ◽

Genomic Diversity ◽

Productive Capacity ◽

Snp Analysis ◽

Genetic Population

AbstractAcrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of seven species of Acrocomia including 117 samples of A. aculeata covering a wide geographical area of occurrence, using single nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS). The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

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Study of genetic differences among Slovak Tsigai populations using microsatellite markers

Czech Journal of Animal Science ◽

10.17221/1670-cjas ◽

2009 ◽

Vol 54 (No. 10) ◽

pp. 468-474 ◽

Cited By ~ 3

Author(s):

S. Kusza ◽

E. Gyarmathy ◽

J. Dubravska ◽

I. Nagy ◽

A. Jávor ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Microsatellite Markers ◽

Mating System ◽

Population Differentiation ◽

Genetic Relationships ◽

The Other ◽

Potential Risks ◽

Substantial Degree

In this study genetic diversity, population structure and genetic relationships of Tsigai populations in Slovakia were investigated using microsatellite markers. Altogether 195 animals from 12 populations were genotyped for 16 microsatellites. 212 alleles were detected on the loci. The number of identified alleles per locus ranged from 11 to 35. In the majority of the populations heterozygosity deficiency and potential risks of inbreeding could be determined. High values of <I>F</I><sub>ST</sub> (0.133) across all the loci revealed a substantial degree of population differentiation. The estimation of genetic distance value showed that the Slovak Vojin population was the most different from the other populations. The 12 examined populations were able to group into 4 clusters. With this result our aim is to help the Slovak sheep breeders to establish their own mating system, to avoid genetic loss and to prevent diversity of Tsigai breed in Slovakia.

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Domestication and Spread of Broomcorn Millet (Panicum miliaceum L.) Revealed by Phylogeography of Cultivated and Weedy Populations

Agronomy ◽

10.3390/agronomy9120835 ◽

2019 ◽

Vol 9 (12) ◽

pp. 835

Author(s):

Yue Xu ◽

Minxuan Liu ◽

Chunxiang Li ◽

Fengjie Sun ◽

Ping Lu ◽

...

Keyword(s):

Population Structure ◽

Northeast China ◽

Genetic Relationships ◽

Staple Food ◽

Panicum Miliaceum ◽

The Loess Plateau ◽

Structure Pattern ◽

Broomcorn Millet ◽

In The Wild ◽

Simple Sequence

Cultivated broomcorn millet (Panicum miliaceum L.), one of the most ancient crops, has long been an important staple food in the semiarid regions of Eurasia. Weedy broomcorn millet (Panicum ruderale (Kitag.) Chang comb. Nov.), the companion weed of cultivated broomcorn millet, is also widely distributed throughout Eurasia and can produce fertile offspring by crossing with cultivated broomcorn millet. The evolutionary and genetic relationships between weedy and cultivated broomcorn millets, and the explicit domestication areas and detailed spread routes of this cereal are still unclear. The genetic diversity and population structure of 200 accessions of weedy and cultivated broomcorn millets were explored to elucidate the genetic relationship between weedy and cultivated broomcorn millets, and to trace the explicit domestication areas and detailed spread routes of broomcorn millets by using 23 simple sequence repeats (SSR) markers. Our results show that the weedy populations in China may harbor the ancestral variations that gave rise to the domesticated broomcorn millet. The population structure pattern observed in the wild and domesticated broomcorn millets is consistent with the hypothesis that there may be at least two independent domestication areas in China for the cultivated broomcorn millet, the Loess Plateau and the Northeast China, with both following the westward spread routes. These two westward spread routes of cultivated broomcorn millet coincide exactly with the prehistoric Oasis Route and Steppe Route, respectively.

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Ancestry, population structure, and conservation genetics of Arctic grayling (Thymallus arcticus) in the upper Missouri River, USA

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f09-113 ◽

2009 ◽

Vol 66 (10) ◽

pp. 1758-1774 ◽

Cited By ~ 14

Author(s):

Douglas P. Peterson ◽

William R. Ardren

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

River Basin ◽

Genetic Relationships ◽

Missouri River ◽

Arctic Grayling ◽

Headwater Lakes ◽

Native Populations ◽

Thymallus Arcticus ◽

Two Populations

We genotyped Arctic grayling ( Thymallus arcticus ) at 10 microsatellite loci in 18 samples (n = 726) from Montana, Wyoming, and Saskatchewan to determine genetic relationships among native, captive, and naturalized populations in the upper Missouri River basin, to assess patterns in genetic diversity, and to infer recent demographic histories. Substantial genetic subdivision was observed among sample populations (global FST = 0.10). Canadian populations have been isolated from Missouri River populations long enough for mutation to cause genetic differences between regions (mean pairwise FST = 0.18, RST = 0.54). Within the Missouri River basin, most naturalized lacustrine populations traced their ancestry to Red Rock lakes. Two populations in headwater lakes within the Big Hole River watershed appear to be native. We found neither evidence for introgression of Canadian-origin grayling nor any effect of hatchery stocking in native populations. The native fluvial Big Hole River group was genetically distinct and most diverse (HE = 0.89), whereas native Madison River and Red Rock lakes populations exhibited lower genetic diversity (HE = 0.74 and 0.80, respectively) and evidence of recent bottlenecks. The existing Big Hole and Red Rock populations are at low abundance but do not appear to be at immediate risk of inbreeding depression (Ne = 207.7–228.2).

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Genetic relationships and population structure of the endangered Steamboat buckwheat,Eriogonum ovalifoliumvar.williamsiae(Polygonaceae)

American Journal of Botany ◽

10.2307/2657059 ◽

2001 ◽

Vol 88 (4) ◽

pp. 608-615 ◽

Cited By ~ 11

Author(s):

Jenny K. Archibald ◽

Paul G. Wolf ◽

V. J. Tepedino ◽

Janet Bair

Keyword(s):

Population Structure ◽

Genetic Relationships

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Pyricularia grisea Causing Gray Leaf Spot of Perennial Ryegrass Turf: Population Structure and Host Specificity

Plant Disease ◽

10.1094/pdis.2001.85.8.817 ◽

2001 ◽

Vol 85 (8) ◽

pp. 817-826 ◽

Cited By ~ 38

Author(s):

G. Viji ◽

B. Wu ◽

S. Kang ◽

W. Uddin ◽

D. R. Huff

Keyword(s):

United States ◽

Population Structure ◽

Winter Wheat ◽

Perennial Ryegrass ◽

Leaf Spot ◽

Genetic Relationships ◽

The United States ◽

Gray Leaf Spot ◽

Pyricularia Grisea ◽

Highly Virulent

Gray leaf spot is a serious disease of perennial ryegrass (Lolium perenne) turf in the United States. Isolates of Pyricularia grisea causing the disease in perennial ryegrass were characterized using molecular markers and pathogenicity assays on various gramineous hosts. Genetic relationships among perennial ryegrass isolates were determined using different types of trans-posons as probes. Phylogenetic analysis using Pot2 and MGR586 probes, analyzed with AMOVA (analysis of molecular variance), showed that these isolates from perennial ryegrass consist of three closely related lineages. All the isolates belonged to a single mating type, MAT1-2. Among 20 isolates from 16 host species other than perennial ryegrass, only the isolates from wheat (Triticum aestivum) and triticale (× Triticosecale), showed notable similarity to the perennial ryegrass isolates based on their Pot2 fingerprints. The copy number and fingerprints of Pot2 and MGR586 in isolates of P. grisea from perennial ryegrass indicate that they are genetically distinct from the isolates derived from rice (Oryza sativa) in the United States. The perennial ryegrass isolates also had the same sequence in the internal transcribed spacer (ITS) region of the genes encoding ribosomal RNA as that of the wheat and triticale isolates, and exhibited rice isolate sequence polymorphisms. In pathogenicity assays, all the isolates of P. grisea from Legacy II perennial ryegrass caused characteristic blast symptoms on Marilee soft white winter wheat, Bennett hard red winter wheat, Era soft white spring wheat, and Presto triticale, and they were highly virulent on these hosts. An isolate from wheat and one from triticale (from Brazil) were also highly virulent on perennial ryegrass and Rebel III tall fescue (Festuca arundinacea). None of the isolates from perennial ryegrass caused the disease on Lagrue rice, and vice versa. Understanding the population structure of P. grisea isolates infecting perennial ryegrass and their relatedness to isolates from other gramineous hosts may aid in identifying alternate hosts for this pathogen.

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