<b>Population structure and impact of recurrent selection on popcorn using EST-SSR markers

The success of any recurrent selection program depends on the genetic variability of the evaluated population, which is used to refer to the diversity of existing alleles at many genetic loci. Thus, the goal of the present study was to investigate the impact of recurrent selection across nine cycles of a UENF-14 popcorn population through the analysis of genetic diversity and structure using microsatellite markers (EST-SSRs). Genomic DNA was extracted from young leaves of 25 individuals from each cycle (C0, C1 C2, C3, C4, C5, C6, C7, and C8), totaling 225 samples from the UENF-14 population. Fifty EST-SSR markers were used for the analysis of genetic diversity across the recurrent selection cycles, 16 of which were polymorphic. Thirty-four alleles were detected, with an average of 2.13 alleles per locus. Throughout all the recurrent selection cycles, there was a reduction in heterozygosity and an increase in inbreeding. The population structure showed a sharing of alleles, inferring that some may be directly related to the main selection characteristics.

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Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

10.21203/rs.3.rs-673512/v1 ◽

2021 ◽

Author(s):

Varun Hiremath ◽

Kanwar Pal Singh ◽

Neelu Jain ◽

Kishan Swaroop ◽

Pradeep Kumar Jain ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Genetic Relationships ◽

Crop Improvement ◽

Test Analysis ◽

Average Value ◽

Population Structure Analysis ◽

Genetic Diversity And Structure

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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How diverse can rare species be on the margins of genera distribution?

AoB Plants ◽

10.1093/aobpla/plz037 ◽

2019 ◽

Vol 11 (4) ◽

Author(s):

Alice Backes ◽

Geraldo Mäder ◽

Caroline Turchetto ◽

Ana Lúcia Segatto ◽

Jeferson N Fregonezi ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Variability ◽

Habitat Loss ◽

Evolutionary History ◽

Founder Effects ◽

Geographical Isolation ◽

Genetic Diversity And Structure ◽

Genetic Patterns

Abstract Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.

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Genetic Diversity and Population Structure of Traditional Greek and Cypriot Melon Cultigens (Cucumis melo L.) Based on Simple Sequence Repeat Variability

HortScience ◽

10.21273/hortsci.44.7.1820 ◽

2009 ◽

Vol 44 (7) ◽

pp. 1820-1824 ◽

Cited By ~ 13

Author(s):

Emmanouil N. Tzitzikas ◽

Antonio J. Monforte ◽

Abdelhak Fatihi ◽

Zacharias Kypriotakis ◽

Tefkros A. Iacovides ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Ssr Markers ◽

Structure Analysis ◽

Simple Sequence Repeat ◽

Cucumis Melo ◽

Sequence Repeat ◽

Population Structure Analysis ◽

Simple Sequence

Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure among traditional Greek and Cypriot melon cultigens (Cucumis melo L.). All SSR markers were polymorphic with a total number of 81 alleles, whereas all cultigens could be distinguished with at least one SSR, except cultigens 43 and 41. Reference accessions showed larger genetic variability with an average of four alleles per locus and 0.65 gene of diversity compared with an average of 2.47 alleles per locus and 0.30 of gene diversity for the Greek/Cypriot cultigens. Observed heterozygosity was very low, indicating a lack of outcrossing, at least in recent times. Unrooted neighbor-joining tree analysis and population structure analysis clustered the cultigens and the reference genotypes into five groups. All cultigens could be distinguished; the Cypriot cultigens were more closely related to the inodorus ‘Piel de Sapo’, whereas the Greek cultigens were located in an intermediate position between the inodorus ‘Piel de Sapo’ and the cantalupensis ‘Védrantais’. The cultigen ‘Kokkini’ was the most divergent among the Greek and Cypriot cultigens. This association between geographic origin and genetic similarity among Greek and Cypriot cultigens indicates geographic isolation. Most of the cultivars from the same cultivar group (i.e., inodorus, cantalupensis) clustered together, but some exceptions were found, suggesting that former inodorus landraces would have been transformed to cantalupensis as a result of intercrossing and further selection by farmers. Results of population structure analysis support mixing between cantalupensis and inodorus. ‘Agiou Basileiou’, an inodorus cultigen, was assigned to the subpopulation IV/II of which II is a pure cantalupensis subpopulation. Greek and Cypriot melon cultigens were developed from a broader germplasm base than western Mediterranean cultivars and exhibited useful for melon breeding programs genetic variability.

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Genetic Diversity and Structure of Oryza rufipogon Griff. Populations in the Philippines

10.1101/2020.07.17.194829 ◽

2020 ◽

Author(s):

Sandy Jan E. Labarosa ◽

Neah Rosandra Sevilla ◽

Dindo Agustin A. Tabanao ◽

Nenita B. Baldo ◽

Helen L.V. Ebuña ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Conservation Status ◽

The Philippines ◽

Oryza Rufipogon ◽

Cultivated Rice ◽

Diversity Assessment ◽

Comparison Results ◽

Genetic Diversity And Structure

ABSTRACTOryza rufipogon Griff. or ‘Rufi’ is the wild progenitor of the cultivated rice, Oryza sativa L. In the Philippines, Rufi was previously known to be found only in Lake Apo, Bukidnon. However, a new population was identified in Lake Napalit in the same province. Based on previous morphological diversity assessment, both populations are unique for at least three characters, i.e., leaf, culm, and awn lengths. Environmental parameters such as rainfall and air temperature also differed between the two lakes. With these, an assessment of Rufi’s genetic diversity at the molecular level is beneficial to further ascertain its usefulness in rice breeding and gain insights on its conservation status. Thus, this study estimated the degree of genetic diversity and determined the population structure of 41 samples of natural Rufi populations in the Philippines using SSR markers. A total of 98 genome wide polymorphic SSR markers were selected to examine the genetic diversity and structure of Rufi populations, along with seven rice cultivars for comparison. Results showed that Philippine Rufi populations have lower genetic diversity compared to cultivated rice accessions and other Rufi populations in Southeast Asia and China. This low genetic diversity suggested that Rufi populations might be in a genetic bottleneck, perhaps due to observed unsustainable farming practices near their habitat and lack of awareness of their importance. A significant population structure and differentiation were determined using the STRUCTURE and phylogenetic analyses. Population differentiation might be due to geographic isolation which prevented gene flow between the two populations and the unique climatic conditions between the two lakes.

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Blue whale (Balaenoptera musculus musculus) genome: population structure and history in the North Atlantic

10.22541/au.161842590.09830459/v1 ◽

2021 ◽

Author(s):

Sushma Jossey ◽

Oliver Haddrath ◽

Livia Loureiro ◽

Burton Lim ◽

Jacqueline Miller ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

North Atlantic ◽

Conservation Strategies ◽

Balaenoptera Musculus ◽

Blue Whale ◽

Genetic Diversity And Structure ◽

Population Structuring ◽

The Impact ◽

Blue Whales

Knowledge of genetic diversity and structure is essential for developing conservation strategies for endangered species. The advances in museum genomics can assist in better understanding the effects of over-hunting on the genome by comparing historical to present-day samples. Blue whales were hunted to the point of near extinction in the mid-twentieth century. Herein, we use whole genome sequencing to elucidate the poorly understood population structure of North Atlantic (NA) blue whales (Balaenoptera musculus musculus). We generated a de novo genome assembly of 2.49 Mbp for a NA blue whale (N50 of 1.46 Mb) to analyze 19 whole genomic sequences and 28 complete mitochondrial genomes. We included present-day and historical samples (earliest from 1900) from the Atlantic and Antarctica to understand the impact of whaling on the genetic diversity. We found low population structuring, but high genetic diversity, suggesting a single, panmictic population in the NA. We identified gene flow from fin whale to blue whales, accounting for ~3.5% of the genome. Introgression between blue and fin whales was observed in all the present-day samples but were lacking in some whales sampled early in the 20th century, which suggests increasing disruption in mate choice concomitant with decline in blue whale population. We also assembled and analyzed the transcriptome and revealed positive selection of oncogenes, which may be involved in reduced cancer rates in this largest of mammals ever known. Our sequencing and population structuring studies provide a genomic framework to guide ongoing conservation strategies for this iconic species.

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Genetic variability and population structure of Saudi Arabia bread wheat (Triticum aestivum L.) by microsatellite markers

Genetika ◽

10.2298/gensr2003943a ◽

2020 ◽

Vol 52 (3) ◽

pp. 943-956

Author(s):

Ibrahem Almohisen

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Saudi Arabia ◽

Population Structure ◽

Genetic Variability ◽

Microsatellite Markers ◽

Bread Wheat ◽

Triticum Aestivum L ◽

Fixation Index ◽

Wheat Landraces

Almohisen A. Ibrahem (2020). Genetic variability and population structure of Saudi Arabia bread wheat (Triticum aestivum L.) by microsatellite markers- Genetika, Vol 52, No.3, 943-956. Wheat (Triticum aestivum L.) is an important cereal crop. Analysis of genetic diversity and population structure in local landraces would improve the wheat breeding program by more efficient use of genetic materials and management of genetic variation. To address this challenge, a set of thirteen Saudi Arabia wheat landraces was used to assess population structure and genetic diversity. Thirteen landraces were genotyped using eighteen microsatellite markers which revealed a clear polymorphism among these genotypes. In total, 136 alleles from a set of eighteen simple sequence repeats (SSRs) loci on a panel of thirteen wheat landraces were detected. All SSRs loci showed a wide range of allele numbers extended from 3 to 11 alleles with an average of 7.5. Genetic diversity, polymorphism information content and minor allele frequency ranged from 0.26 to 0.50, 0.23 to 0.37 and 0.15 to 0.46 with an average 0.43, 0.33 and 0.34, respectively. The results of principal coordinate analysis (PCoA) agreed with the structure analysis. Structure grouped the thirteen landraces into three clear subpopulations. The fixation index (Fst), a measure of population substructure, was 0.217, 0.432 and 0.541 for G2, G1, and G3, respectively. Furthermore, analysis of molecular variance recognized 35% variance among and 65% within populations. The present study showed a high genetic diversity between landraces which can be exploited to produce new bread wheat cultivars.

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Assessing Genetic Variability and Population Structure of Ziziphus Nummularia as Characterized by Phenotypic Traits and SSR Markers with Climatic Distribution

10.21203/rs.3.rs-432958/v1 ◽

2021 ◽

Author(s):

Nisar Uddin ◽

Noor Muhammad ◽

Niaz Ali ◽

Muhammad Khalil Ullah Khan ◽

Muhammad Nisar ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Ssr Markers ◽

Gene Diversity ◽

Important Variable ◽

Phenotypic Traits ◽

Migration Routes ◽

Precipitation Seasonality ◽

Ziziphus Nummularia

Abstract Genus of Ziziphus (family Rhamnaceae), approximately 170 species of prodigious economic and ecological importance. Studies on the genetic diversity within Pakistani Ziziphus species are limited, and to date, no single report on the application of DNA barcoding attempt for identification of Ziziphus species is available in the literature. Therefore, the current study was designed to biogeographic distribution, to assess diversity based on phenotypic traits, SSRs markers, and relationships among Ziziphus nummularia (Burm.f.) Wight & Arn. genotypes. For the first time we use ArcGIS modeling, and their cartographic function for the identification of diversity in climatic variables such as temperature, mean diurnal, humidity, precipitation, and precipitation seasonality and the using of these techniques to determine the important variable which is responsible for the recent distribution of the Ziziphus species. A total of 11 phenotypic traits were noted and have significant phenotypic variation among the traits. The study has used 40 simple sequence repeats (SSR) markers for gaining insights into the genetic diversity within 180 genotypes of Z. nummularia. Successful amplification was achieved with 27 SSRs and was applied for understanding the population structure and relationships among the genotypes. A total of 120 alleles were amplified from Z. nummularia genotypes collected from three districts of the Malakand division, alleles per locus ranged from 2 to 6, averaging 4.4286. whereas polymorphism information content (PIC) from 0.332 to 0.794 in locus JSSR-490 and JSSR-97, within mean value was 0.671 per locus, expected heterozygosity (He), was 0.575, observed heterozygosity (Ho), 0.6618 and average gene diversity 0.494. Flow estimates (6.415) indicated frequent gene flow within Z. nummularia genotypes. Analysis of molecular variance (AMOVA) revealed high genetic variability (80%). The genetic relationship inferred from the neighbor-joining (NJ) phylogeny separate genotypes into three clusters and Bayesian model-based STRUCTURE analyses and PCoA analysis resolved all genotypes and indicted that the KP, populations, Swat and Buner, represent excesses of two different migration routes, with one designated from Swat and Dir (L). The overall results indicated the prevalence of genetic variability and relationships among Z. nummularia across geographical boundaries has retained unique alleles and this may facilitate the development of agronomically desirable and genetically improved Ziziphus cultivars and collections that can help achieve efficient conservation.

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Genetic variability of sheep populations of Saudi Arabia using microsatellite markers

Indian Journal of Animal Research ◽

10.18805/ijar.b-775 ◽

2018 ◽

Author(s):

Ahmed H. Mahmoud ◽

Faisal M. Abou Tarboush ◽

Ahmed Rady ◽

Khalid M. Al-Anaz Mohammad Abul Farah ◽

Osama B. Mohammed

Keyword(s):

Genetic Diversity ◽

Saudi Arabia ◽

Genetic Variability ◽

Microsatellite Markers ◽

Population Differentiation ◽

Genomic Dna ◽

Mean Value ◽

Weinberg Equilibrium ◽

Expected Heterozygosity ◽

Hardy Weinberg Equilibrium

The present study was conducted to know the genetic diversity of three Saudi sheep populations; Naeimi (NM), Herri (H) and Najdi (NJ). Genomic DNA was extracted from 156 animals of sheep comprising 47 Naeimi, 47 Herri and 62 Najdi breeds using 18 microsatellite markers. A total of 212 alleles were generated with a mean value of 11.80 alleles per locus, with a range of observed and expected heterozygosity of 0.505 to 0.875 and 0.595 to 0.854, respectively. Eleven of the microsatellites loci studied in NM, three loci in H and fifteen loci in NJ were observed to be deviated from Hardy-Weinberg equilibrium. The fixation genetic indices (Fst) among the three sheep populations were very low, ranging from 0.017 (between NJ and H) to 0.033 (between NJ and NM), indicating low population differentiation among the three sheep populations studied. The present study showed that the microsatellite markers are powerful tool in determining genetic diversity among sheep populations.

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