Unravelling the effect of environment on the genome of Sarda breed ewes using Runs of Homozygosity

2022 ◽  
Author(s):  
Alberto Cesarani ◽  
Giustino Gaspa ◽  
Fabio Correddu ◽  
Corrado Dimauro ◽  
Nicolò P. P. Macciotta
Keyword(s):  
Runs Of Homozygosity

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 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.

scholarly journals A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.)

2021 ◽  
Author(s):  
Tomas N Generalovic ◽  
Shane A McCarthy ◽  
Ian A Warren ◽  
Jonathan M D Wood ◽  
James Torrance ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Animal Feed ◽  
Repetitive Sequences ◽  
Genomic Variation ◽  
Runs Of Homozygosity ◽  
High Quality ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Chromosome Conformation ◽  
Important Species

Abstract Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome five. Release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterisation of genes of interest and genetic modification of this economically important species.

scholarly journals Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors

2013 ◽  
Vol 30 (9) ◽  
pp. 2209-2223 ◽  
Author(s):  
Iona M. MacLeod ◽  
Denis M. Larkin ◽  
Harris A. Lewin ◽  
Ben J. Hayes ◽  
Mike E. Goddard
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequence Errors

scholarly journals Excess of runs of homozygosity is associated with severe cognitive impairment in intellectual disability

2014 ◽  
Vol 17 (5) ◽  
pp. 396-399 ◽  
Author(s):  
Ilaria Gandin ◽  
Flavio Faletra ◽  
Francesca Faletra ◽  
Massimo Carella ◽  
Vanna Pecile ◽  
...  
Keyword(s):  
Cognitive Impairment ◽  
Intellectual Disability ◽  
Runs Of Homozygosity ◽  
Severe Cognitive Impairment

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced-representation sequencing data

2018 ◽  
Vol 49 (6) ◽  
pp. 579-591 ◽  
Author(s):  
Zhe Zhang ◽  
Qianqian Zhang ◽  
Qian Xiao ◽  
Hao Sun ◽  
Hongding Gao ◽  
...  
Keyword(s):  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Reduced Representation ◽  
Pig Breeds ◽  
Reduced Representation Sequencing

scholarly journals Correction to: Runs of homozygosity have utility in mammalian conservation and evolutionary studies

2018 ◽  
Vol 19 (6) ◽  
pp. 1309-1309
Author(s):  
Anna Brüniche-Olsen ◽  
Kenneth F. Kellner ◽  
Chase J. Anderson ◽  
J. Andrew DeWoody
Keyword(s):  
Runs Of Homozygosity ◽  
Evolutionary Studies

Genome‐wide scan for runs of homozygosity in the composite Montana Tropical ® beef cattle

2019 ◽  
Vol 137 (2) ◽  
pp. 155-165 ◽  
Author(s):  
Elisa Peripolli ◽  
Nedenia Bonvino Stafuzza ◽  
Sabrina Thaise Amorim ◽  
Marcos Vinícius Antunes Lemos ◽  
Laís Grigoletto ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Runs Of Homozygosity ◽  
Genome Wide ◽  
Genome Wide Scan
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