scholarly journals A detailed characteristics of bias associated with long runs of homozygosity identification based on medium density SNP microarrays

2020 ◽  
Vol 8 ◽  
pp. 43-48
Author(s):  
Tomasz Szmatoła ◽  
Artur Gurgul ◽  
Igor Jasielczuk ◽  
Weiwei Fu ◽  
Katarzyna Ropka-Molik
Keyword(s):  
Medium Density ◽  
Runs Of Homozygosity ◽  
Snp Microarrays

scholarly journals Calcium carbonate modified urea–formaldehyde resin adhesive for strength enhanced medium density fiberboard production

RSC Advances ◽  
2021 ◽  
Vol 11 (40) ◽  
pp. 25010-25017
Author(s):  
Li Lu ◽  
Yan Wang ◽  
Tianhua Li ◽  
Supeng Wang ◽  
Shoulu Yang ◽  
...  
Keyword(s):  
Calcium Carbonate ◽  
Urea Formaldehyde ◽  
Medium Density Fiberboard ◽  
Urea Formaldehyde Resin ◽  
Formaldehyde Resin ◽  
Medium Density ◽  
Ionic Bond ◽  
Resin Adhesive ◽  
Uf Resin ◽  
Modified Urea

Reactions between CaCO3 and CH2O2 during polycondensation of UF resin produce Ca2+. Ionic bond complexation binds Ca2+ with UF resin. The UF resin crystalline percentage decreases from 26.86% to 22.71%. IB strength of resin bonded fiberboard increases from 0.75 to 0.94 MPa.

The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations

Genomics ◽  
2021 ◽  
Author(s):  
Maryam Nosrati ◽  
Hojjat Asadollahpour Nanaei ◽  
Arash Javanmard ◽  
Ali Esmailizadeh
Keyword(s):  
World Wide ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

scholarly journals A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dora Henriques ◽  
Ana R. Lopes ◽  
Nor Chejanovsky ◽  
Anne Dalmon ◽  
Mariano Higes ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Large Scale ◽  
Medium Density ◽  
Nucleotide Polymorphisms ◽  
Functional Variation ◽  
Immune Genes ◽  
Wide Range ◽  
Scale Range ◽  
Innate Immune Genes

AbstractWith a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3’ and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee.

scholarly journals Long runs of homozygosity are associated with Alzheimer’s disease

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sonia Moreno-Grau ◽  
◽  
Maria Victoria Fernández ◽  
Itziar de Rojas ◽  
Pablo Garcia-González ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
European Ancestry ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Outbred Population ◽  
Whole Exome ◽  
Whole Exome Sequencing Data ◽  
Outbred Populations ◽  
Recessive Effects

AbstractLong runs of homozygosity (ROH) are contiguous stretches of homozygous genotypes, which are a footprint of inbreeding and recessive inheritance. The presence of recessive loci is suggested for Alzheimer’s disease (AD); however, their search has been poorly assessed to date. To investigate homozygosity in AD, here we performed a fine-scale ROH analysis using 10 independent cohorts of European ancestry (11,919 AD cases and 9181 controls.) We detected an increase of homozygosity in AD cases compared to controls [βAVROH (CI 95%) = 0.070 (0.037–0.104); P = 3.91 × 10−5; βFROH (CI95%) = 0.043 (0.009–0.076); P = 0.013]. ROHs increasing the risk of AD (OR > 1) were significantly overrepresented compared to ROHs increasing protection (p < 2.20 × 10−16). A significant ROH association with AD risk was detected upstream the HS3ST1 locus (chr4:11,189,482‒11,305,456), (β (CI 95%) = 1.09 (0.48 ‒ 1.48), p value = 9.03 × 10−4), previously related to AD. Next, to search for recessive candidate variants in ROHs, we constructed a homozygosity map of inbred AD cases extracted from an outbred population and explored ROH regions in whole-exome sequencing data (N = 1449). We detected a candidate marker, rs117458494, mapped in the SPON1 locus, which has been previously associated with amyloid metabolism. Here, we provide a research framework to look for recessive variants in AD using outbred populations. Our results showed that AD cases have enriched homozygosity, suggesting that recessive effects may explain a proportion of AD heritability.

Sign in / Sign up

Export Citation Format

Share Document