scholarly journals Introgression of Eastern Chinese and Southern Chinese haplotypes contributes to the improvement of fertility and immunity in European modern pigs

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Hao Chen ◽  
Min Huang ◽  
Bin Yang ◽  
Zhongping Wu ◽  
Zheng Deng ◽  
...  
Keyword(s):  
Geographic Origin ◽  
Whole Genome Sequencing Data ◽  
Biological Functions ◽  
Sequencing Data ◽  
Phenotypic Characteristics ◽  
Large White ◽  
Wild Boars ◽  
Domestic Pigs ◽  
Southern Chinese ◽  
History Of

Abstract Background Pigs were domesticated independently from European and Asian wild boars nearly 10,000 years ago. Chinese indigenous pigs have been historically introduced to improve Europe local pigs. However, the geographic origin and biological functions of introgressed Chinese genes in modern European pig breeds remain largely unknown. Results Here we explored whole-genome sequencing data from 266 Eurasian wild boars and domestic pigs to produce a fine-scale map of introgression between French Large White (FLW) and Chinese pigs. We show that FLW pigs had historical admixture with both Southern Chinese (SCN) and Eastern Chinese (ECN) pigs ∼200–300 years ago. Moreover, a set of SCN haplotypes was shown to be beneficial for improving disease resistance and ECN haplotypes are favorable for improved reproductive performance in FLW pigs. In addition, we confirm human-mediated introgression events at the AHR locus, at which the haplotype of most likely ECN origin contributes to increased fertility of FLW pigs. Conclusions This study advances our understanding of the breeding history of global domestic pigs and highlights the importance of artificial introgression in the formation of phenotypic characteristics in domestic animals.

scholarly journals Characterization of Plastidial and Nuclear SSR Markers for Understanding Invasion Histories and Genetic Diversity of Schinus molle L.

Biology ◽  
2018 ◽  
Vol 7 (3) ◽  
pp. 43 ◽  
Author(s):  
Rafael Lemos ◽  
Cristiane Matielo ◽  
Dalvan Beise ◽  
Vanessa da Rosa ◽  
Deise Sarzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Invasive Plant ◽  
Whole Genome Sequencing Data ◽  
Natural Occurrence ◽  
Sequencing Data ◽  
Dispersal Capacity ◽  
Schinus Molle ◽  
High Dispersal ◽  
History Of

Invasive plant species are expected to display high dispersal capacity but low levels of genetic diversity due to the founder effect occurring at each invasion episode. Understanding the history of invasions and the levels of genetic diversity of such species is an important task for planning management and monitoring strategy for these events. Peruvian Peppertree (Schinus molle L.) is a pioneer tree species native from South America which was introduced in North America, Europe and Africa, becoming a threat to these non-native habitats. In this study, we report the discovery and characterization of 17 plastidial (ptSSR) and seven nuclear (nSSR) markers for S. molle based on low-coverage whole-genome sequencing data acquired through next-generation sequencing. The markers were tested in 56 individuals from two natural populations sampled in the Brazilian Caatinga and Pampa biomes. All loci are moderately to highly polymorphic and revealed to be suitable for genetic monitoring of new invasions, for understanding the history of old invasions, as well as for genetic studies of native populations in their natural occurrence range and of orchards established with commercial purposes.

scholarly journals Reconstructing Genetic History of Siberian and Northeastern European Populations

2015 ◽  
Author(s):  
Emily H.M. Wong ◽  
Andrey Khrunin ◽  
Larissa Nichols ◽  
Dmitry Pushkarev ◽  
Denis Khokhrin ◽  
...  
Keyword(s):  
Linguistically Diverse ◽  
Indigenous Populations ◽  
Whole Genome Sequencing Data ◽  
Eastern European ◽  
Sequencing Data ◽  
Hunter Gatherers ◽  
Human Genomes ◽  
History Of ◽  
New Evidence ◽  
Ancient Gene

Siberia and Western Russia are home to over 40 culturally and linguistically diverse indigenous ethnic groups. Yet, genetic variation of peoples from this region is largely uncharacterized. We present whole-genome sequencing data from 28 individuals belonging to 14 distinct indigenous populations from that region. We combine these datasets with additional 32 modern-day and 15 ancient human genomes to build and compare autosomal, Y-DNA and mtDNA trees. Our results provide new links between modern and ancient inhabitants of Eurasia. Siberians share 38% of ancestry with descendants of the 45,000-year-old Ust-Ishim people, who were previously believed to have no modern-day descendants. Western Siberians trace 57% of their ancestry to the Ancient North Eurasians, represented by the 24,000-year-old Siberian Malta boy. In addition, Siberians admixtures are present in lineages represented by Eastern European hunter-gatherers from Samara, Karelia, Hungary and Sweden (from 8,000-6,600 years ago), as well as Yamnaya culture people (5,300-4,700 years ago) and modern-day northeastern Europeans. These results provide new evidence of ancient gene flow from Siberia into Europe.

scholarly journals Differentiating Pigs from Wild Boars Based on NR6A1 and MC1R Gene Polymorphisms

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2123
Author(s):  
Anna Koseniuk ◽  
Grzegorz Smołucha ◽  
Małgorzata Natonek-Wiśniewska ◽  
Anna Radko ◽  
Dominika Rubiś
Keyword(s):  
Wild Boar ◽  
Wild Type ◽  
Large White ◽  
Allelic Discrimination Assay ◽  
Allelic Discrimination ◽  
Mc1r Gene ◽  
Wild Boars ◽  
Domestic Pigs ◽  
Larger Sample ◽  
Network Software

This preliminary study aimed to differentiate domestic pigs from wild boars based on MC1R and NR6A1 polymorphisms and to identify admixture between these genomes. We studied samples obtained from wild boars from two regions of Poland and five pig breeds: Polish Landrace, Polish Large White, Złotnicka White, Pulawska and Duroc. Along the MC1R gene sequence, we identified four polymorphic loci comprising three codons. The “wild type” allele was primarily found in wild boar but also in the Duroc and Złotnicka White breeds. Non-wild type alleles were identified in the vast majority of domestic pig samples and in two wild boar samples. Based on MC1R profiles, we conducted a population study, and revealed admixture between both genomes using STRUCTURE and NETWORK Software. Interestingly, an allelic discrimination assay with NR6A1 g.748C > T TaqMan probes revealed a clear separation of samples into two groups: wild boar samples representing the C allele and domestic breeds representing the T allele. Based on the obtained results, we conclude that NR6A1 g.748C > T is an effective marker for differentiating between wild boars and domestic pigs, where this is supported by MC1R data, to identify admixed profiles. We recommend that a larger sample of genomes is studied to verify this method.

A stochastic model to quantify the risk of introduction of classical swine fever virus through import of domestic and wild boars

2009 ◽  
Vol 137 (10) ◽  
pp. 1505-1515 ◽  
Author(s):  
B. MARTÍNEZ-LÓPEZ ◽  
A. M. PEREZ ◽  
J. M. SÁNCHEZ-VIZCAÍNO
Keyword(s):  
Stochastic Model ◽  
Classical Swine Fever Virus ◽  
Classical Swine Fever ◽  
Fever Virus ◽  
Prevention Programme ◽  
Recent History ◽  
Wild Boars ◽  
Domestic Pigs ◽  
History Of ◽  
Susceptible Populations

SUMMARYClassical swine fever (CSF) is a disease of pigs that imposes major hardship on the industry of infected regions. The recent history of CSF epidemics suggests that animal movements remain the main source of CSF virus (CSFV) infection for susceptible populations in Europe. This study presents an assessment of the risk of introducing CSFV into Spain through the importation of live susceptible animals. Results suggest that, if prevailing conditions persist, introduction of CSFV into Spain is likely to occur on average every 9 years and that introduction is almost three times more likely to occur via domestic pigs than through wild boars. The highest risk was concentrated in March and in the Northeastern provinces of Spain. Results were consistent with the time and location of previous CSFV introductions into the country. The methodology and the results presented here will contribute to improve the CSF prevention programme in Spain.

scholarly journals Insights on the historical biogeography of Philippine native pigs and its relationship with Continental domestic and wild boars

2021 ◽  
Author(s):  
John King Layos ◽  
Ronel Geromo ◽  
Dinah Espina ◽  
Masahide Nishibori
Keyword(s):  
Geographic Origin ◽  
The Philippines ◽  
Human Migration ◽  
Genetic Introgression ◽  
Effective Population ◽  
Loop Analysis ◽  
Wild Boars ◽  
Domestic Pigs ◽  
Sudden Decrease ◽  
Native Pigs

The Philippine archipelago was believed to have never been connected to the Asian continent, even during the severe Quaternary sea-level drops. As a result, the history of pig dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with some human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine native pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boars corresponding to their geographic origin. Results revealed a considerable genetic diversity (0.900±0.016), and a widespread Asian pig-ancestry (94.60%) were revealed in the phylogenetic analysis with admixed European pig-origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close genetic connection between the continental wild boars and domestic pigs present in the Philippine pigs corroborates our hypothesis of a genetic signal that could potentially be associated with the recently reported multiple waves of human migrations to the Philippines during the last 50,000 years. The high frequency of haplotypes (54.08%) that collapsed in the D7 haplogroup represent an interesting challenge as its distribution does not coincide with the hypothesized migratory route of the Neolithic Austronesian-speaking populations. We detected the first Pacific Clade signature and ubiquitously distributed D2 haplotypes which postulate the legitimate dispersal of pigs associated with the multiple waves of human migrations involving the Philippines. The multimodal mismatch and neutrality test statistics both Fu’s Fs and Tajima’s D correlates the long stationary period of effective population size revealed in the Bayesian skyline plot. While the sudden decrease in population was consistent with the pronounced population bottleneck of Asian and European pigs during the interglacial periods of the Pleistocene.

scholarly journals Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data

2020 ◽  
Vol 6 (11) ◽  
Author(s):  
Yuanwei Xu ◽  
Jessica E. Stockdale ◽  
Vijay Naidu ◽  
Hollie Hatherell ◽  
James Stimson ◽  
...  
Keyword(s):  
Mathematical Modelling ◽  
Disease Transmission ◽  
Machine Learning Techniques ◽  
Whole Genome Sequencing Data ◽  
Reconstruction Method ◽  
Sequencing Data ◽  
Patient Level ◽  
Learning Techniques ◽  
Level Data ◽  
History Of

Outbreaks of tuberculosis (TB) – such as the large isoniazid-resistant outbreak centred on London, UK, which originated in 1995 – provide excellent opportunities to model transmission of this devastating disease. Transmission chains for TB are notoriously difficult to ascertain, but mathematical modelling approaches, combined with whole-genome sequencing data, have strong potential to contribute to transmission analyses. Using such data, we aimed to reconstruct transmission histories for the outbreak using a Bayesian approach, and to use machine-learning techniques with patient-level data to identify the key covariates associated with transmission. By using our transmission reconstruction method that accounts for phylogenetic uncertainty, we are able to identify 21 transmission events with reasonable confidence, 9 of which have zero SNP distance, and a maximum distance of 3. Patient age, alcohol abuse and history of homelessness were found to be the most important predictors of being credible TB transmitters.

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract

2021 ◽  
Author(s):  
Johanna L. Jones ◽  
Mark A. Corbett ◽  
Elise Yeaman ◽  
Duran Zhao ◽  
Jozef Gecz ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Protein Interactions ◽  
Cholesterol Biosynthesis ◽  
Crystalline Lens ◽  
Whole Genome Sequencing Data ◽  
Mendelian Disease ◽  
Cataract Formation ◽  
Sequencing Data ◽  
Zebrafish Model ◽  
Paediatric Cataract

AbstractInherited paediatric cataract is a rare Mendelian disease that results in visual impairment or blindness due to a clouding of the eye’s crystalline lens. Here we report an Australian family with isolated paediatric cataract, which we had previously mapped to Xq24. Linkage at Xq24–25 (LOD = 2.53) was confirmed, and the region refined with a denser marker map. In addition, two autosomal regions with suggestive evidence of linkage were observed. A segregating 127 kb deletion (chrX:g.118373226_118500408del) in the Xq24–25 linkage region was identified from whole-genome sequencing data. This deletion completely removed a commonly deleted long non-coding RNA gene LOC101928336 and truncated the protein coding progesterone receptor membrane component 1 (PGRMC1) gene following exon 1. A literature search revealed a report of two unrelated males with non-syndromic intellectual disability, as well as congenital cataract, who had contiguous gene deletions that accounted for their intellectual disability but also disrupted the PGRMC1 gene. A morpholino-induced pgrmc1 knockdown in a zebrafish model produced significant cataract formation, supporting a role for PGRMC1 in lens development and cataract formation. We hypothesise that the loss of PGRMC1 causes cataract through disrupted PGRMC1-CYP51A1 protein–protein interactions and altered cholesterol biosynthesis. The cause of paediatric cataract in this family is the truncating deletion of PGRMC1, which we report as a novel cataract gene.

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