High allelic diversity of the centromere-specific histone H3 (CENH3) in the legume sainfoin (Onobrychis viciifolia)

Abstract Mutations in KIT encoding the mast/stem cell growth factor receptor (MGF) are responsible for coat color variation in domestic pigs. The dominant white phenotype is caused by two mutations, a gene duplication and a splice mutation in one of the copies leading to skipping of exon 17. Here we applied minisequencing and pyrosequencing for quantitative analysis of the number of copies with the splice form. An unexpectedly high genetic diversity was revealed in white pigs. We found four different KIT alleles in a small sample of eight Large White females used as founder animals in a wild boar intercross. A similar number of KIT alleles was found in commercial populations of white Landrace and Large White pigs. We provide evidence for at least two new KIT alleles in pigs, both with a triplication of the gene. The results imply that KIT alleles with the duplication are genetically unstable and new alleles are most likely generated by unequal crossing over. This study provides an improved method for genotyping the complicated Dominant white/KIT locus in pigs. The results also suggest that some alleles may be associated with negative pleiotropic effects on other traits.

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Genetic Profiling Reveals High Allelic Diversity, Heterozygosity and Antigenic Diversity in the Clinical Isolates of the Theileria annulata From India

Frontiers in Physiology ◽

10.3389/fphys.2019.00673 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 1

Author(s):

Sonti Roy ◽

Vasundhra Bhandari ◽

Debabrata Dandasena ◽

Shweta Murthy ◽

Paresh Sharma

Keyword(s):

Allelic Diversity ◽

Theileria Annulata ◽

Clinical Isolates ◽

Genetic Profiling ◽

Antigenic Diversity ◽

High Allelic Diversity

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The effects of isolation and colonization history on the genetic structure of marine-relict populations of Atlantic cod (Gadus morhua) in the Canadian Arctic

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f06-085 ◽

2006 ◽

Vol 63 (8) ◽

pp. 1830-1839 ◽

Cited By ~ 30

Author(s):

David C Hardie ◽

Roxanne M Gillett ◽

Jeffrey A Hutchings

Keyword(s):

Gadus Morhua ◽

Atlantic Cod ◽

Allelic Diversity ◽

Canadian Arctic ◽

Environmental Stochasticity ◽

Arctic Lakes ◽

The Arctic ◽

Effective Population ◽

Eastern Canada ◽

High Allelic Diversity

The genetic consequences of extended periods at low population size are fundamental to the conservation of depleted species such as the Atlantic cod (Gadus morhua). We compared microsatellite genetic variability among cod populations in Canadian Arctic lakes with that of Gilbert Bay resident and inshore cod from eastern Canada. The Arctic populations had the lowest genetic diversity and were the most strongly genetically structured and distinct. By contrast, eastern Canadian samples expressed high allelic diversity and were not significantly genetically structured or distinct relative to each other, whereas Gilbert Bay resident cod were intermediate to the Arctic and eastern Canadian groups. Our results are consistent with the hypothesis that the Arctic populations were colonized between 8000 and 5000 years ago and have experienced little or no gene flow since that time. Despite isolation at the extreme of the species' range, the Arctic populations have retained relatively high heterozygosities and high genetic effective population sizes relative to census sizes (Ne–Nc ratios). Potential explanations for this include the absence of fishing pressure, allowing for the persistence of large, highly fecund individuals, as well as biotic (e.g., absence of planktivores) and abiotic (e.g., low environmental stochasticity) factors in the Arctic lakes that minimize individual variance in reproductive success.

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Targeted Ds-tagging strategy generates high allelic diversity at the Arabidopsis HY2 locus

Plant Molecular Biology ◽

10.1007/s11103-006-0035-6 ◽

2006 ◽

Vol 61 (4-5) ◽

pp. 603-613 ◽

Cited By ~ 3

Author(s):

Audrey Creff ◽

Bénédicte Léonard ◽

Thierry Desnos

Keyword(s):

Allelic Diversity ◽

High Allelic Diversity

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Geographical variation, population structure and gene flow between populations of Chrysophtharta agricola (Coleoptera: Chrysomelidae), a pest of Australian eucalypt plantations

Bulletin of Entomological Research ◽

10.1079/ber2003224 ◽

2003 ◽

Vol 93 (2) ◽

pp. 137-144 ◽

Cited By ~ 15

Author(s):

H.F. Nahrung ◽

G.R. Allen

Keyword(s):

Gene Flow ◽

Natural Enemies ◽

Chemical Control ◽

Genetic Resistance ◽

Allelic Diversity ◽

Native Forest ◽

Pest Species ◽

Eucalypt Plantations ◽

Pest Outbreaks ◽

High Allelic Diversity

AbstractChrysophtharta agricola (Chapuis) is a pest of commercial eucalypt plantations in Tasmania and Victoria. Vagility of pest populations may result in difficulty predicting temporal and spatial pest outbreaks, and influence genetic resistance to chemical control. Gene flow in this pest species was estimated to assess predicability of attack, the potential efficacy of natural enemies, and the likelihood of resistance build-up. Ten geographic populations of C. agricola (six from Tasmania, one from the Australian Capital Territory, one from New South Wales and two from Victoria) were examined for genetic variation and gene flow using cellulose acetate allozyme electrophoresis. Six enzyme systems (PGI, PGD, PGM, IDH, HEX and MPI) were consistently polymorphic and scorable and were used to quantify estimated gene flow between populations. FST values and analysis of molecular variance indicated that gene flow was restricted between populations. Chrysophtharta agricola exhibited high levels of heterozygosity, probably because of high allelic diversity, and because all loci examined were polymorphic. The southern-most population was the most genetically different to other Tasmanian populations, and may also have been the most recently colonized. Limited gene flow implies that outbreaks of C. agricola should be spatially predictable and populations susceptible to control by natural enemies. Our results also imply that genetic resistance to chemical control may occur under frequent application of insecticide. However, testing population movement between plantations and native forest also needs to be conducted to assess gene flow between forest types.

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AmpUMI: Design and analysis of unique molecular identifiers for deep amplicon sequencing

10.1101/288118 ◽

2018 ◽

Author(s):

Kendell Clement ◽

Rick Farouni ◽

Daniel E. Bauer ◽

Luca Pinello

Keyword(s):

Allelic Diversity ◽

Pcr Amplification ◽

Software Tool ◽

Amplicon Sequencing ◽

Dna Fragments ◽

Genomic Locus ◽

Sequencing Studies ◽

High Allelic Diversity ◽

Downstream Analysis ◽

User Friendly

AbstractMotivationUnique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments.ResultsBased on the total number of DNA fragments and the distribution of allele frequencies, we present a model for the determination of the minimum UMI length required to prevent UMI collisions and reduce allelic distortion. We also introduce a user-friendly software tool called AmpUMI to assist in the design and the analysis of UMI-based amplicon sequencing studies. AmpUMI provides quality control metrics on frequency and quality of UMIs, and trims and deduplicates amplicon sequences with user specified parameters for use in downstream analysis. AmpUMI is open-source and freely available at http://github.com/pinellolab/[email protected]

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Formation of novel PRDM9 allele by indel events as possible trigger for tarsier-anthropoid split

10.1101/047803 ◽

2016 ◽

Author(s):

Sacha Heerschop ◽

Hans Zischler ◽

Stefan Merker ◽

Dyah Perwitasari-Farajallah ◽

Christine Driller

Keyword(s):

Zinc Finger ◽

Hybrid Sterility ◽

Allelic Diversity ◽

Strand Break ◽

Zinc Finger Domain ◽

Reading Frame ◽

Allele Variant ◽

High Allelic Diversity ◽

And Function ◽

Zinc Finger Array

AbstractPRDM9 is currently the sole speciation gene found in vertebrates causing hybrid sterility probably due to incompatible alleles. Its role in defining the double strand break loci during the meiotic prophase I is crucial for proper chromosome segregation. Therefore, the rapid turnover of the loci determining zinc finger array seems to be causative for incompatibilities. We here investigated the zinc finger domain-containing exon of PRDM9 in 23 tarsiers. Tarsiers, the most basal extant haplorhine primates, exhibit two frameshifting indels at the 5’-end of the array. The first mutation event interrupts the reading frame and function while the second compensates both. The fixation of this peculiar allele variant in tarsiers led to hypothesize that de‐ and reactivation of the zinc finger domain drove the speciation in early haplorhine primates. Moreover, the high allelic diversity within Tarsius point to multiple effects of genetic drift reflecting their phylogeographic history since the Miocene.

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