Directory of Open Access Journals (DOAJ)
Anna M. Hewett, Martin A. Stoffel, Lucy Peters, Susan E. Johnston, Josephine M. Pemberton,
The distribution of runs of homozygosity (ROH) may be shaped by a number of interacting processes such as selection, recombination and population history, but little is known about the importance of these mechanisms in shaping ROH in wild populations. We combined an empirical dataset ... the influence of each of these factors on ROH. We assessed ROH in a focal and comparison population to investigate ... and a genetic linkage map to search for ROH. We found differences in ROH distribution between both populations and map types indicating ...
Tópico(s): Wildlife Ecology and Conservation
2023 - Springer Nature | Heredity
Julie Colpitts, Philip D. McLoughlin, Jocelyn Poissant,
... of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length ... of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of ... between managed and unmanaged populations. Here we characterized ROH, inbreeding coefficients, and ROH islands in a feral horse population from Sable ... breeds to assess the impacts of isolation on ROH abundance, length, distribution, and ROH islands. Results ROH ...
Tópico(s): Veterinary Equine Medical Research
2022 - BioMed Central | BMC Genomics
Shen-he Liu, Xiaoya Ma, Faiz‐ul Hassan, Tengyun Gao, Tingxian Deng,
Runs of homozygosity (ROH) are a powerful tool to explore patterns of genomic inbreeding in animal populations and detect signatures of selection. The present study used ROH analysis to evaluate the genome-wide patterns of homozygosity, inbreeding levels, and distribution of ROH islands using the SNP data sets from 899 Mediterranean buffaloes. A total of 42,433 ROH segments were identified, with an average of 47.20 segments per individual. The ROH comprising mostly shorter segments (1-4 Mb) accounted ...
Tópico(s): Livestock Farming and Management
2022 - Elsevier BV | Journal of Dairy Science
Alberto Cesarani, Giustino Gaspa, Fabio Correddu, Corrado Dimauro, N.P.P. Macciotta,
... selection at genome-wide level, runs of homozygosity (ROH) are getting increasing popularity. In this paper, ROH distribution and features of a sample of 823 ... A total of 46,829 (33,087 unique) ROH were detected. OAR2 exhibited the largest average number of ROH per animal. The most frequent ROH (OAR27, 38.9-44.2 Mb) was shared by 327. ROH length was statistically affected (p < 0.001) by ... highest probability of a SNP falling in a ROH was observed for hill ewes, whereas the smallest ... 457 SNP exceeded the 99th percentile of the ROH count per SNP distribution and were considered significant. ...
Tópico(s): Cancer-related molecular mechanisms research
2022 - Wiley | Journal of Animal Breeding and Genetics
Yao Jiang, Xiaojin Li, Jiali Liu, Wei Zhang, Mei Zhou, Jieru Wang, Linqing Liu, Shiguang Su, Fuping Zhao, Hongquan Chen, Chonglong Wang,
Abstract Background Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable ... Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (F ROH ) and homozygosity (F HOM ). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein. Results The ...
Tópico(s): Cancer-related molecular mechanisms research
2022 - BioMed Central | BMC Genomics
Jiaxin Liu, Liangyu Shi, Li Yang, Liang Chen, Dorian J. Garrick, Lixian Wang, Fuping Zhao,
Abstract Background A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Genomic inbreeding can be quantified based on ROH. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. We carried out ROH analyses in five Chinese indigenous sheep breeds; Altay ... SNP BeadChip. Results A total of 18,288 ROH were identified. The average number of ROH per ...
Tópico(s): Cancer-related molecular mechanisms research
2021 - BioMed Central | Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology
Wim Gorssen, Roel Meyermans, Steven Janssens, Nadine Buys,
Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such ... of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in ... available. Results The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which ...
Tópico(s): Cancer-related molecular mechanisms research
2021 - BioMed Central | Genetics Selection Evolution
Zhong Xu, Shuqi Mei, Jiawei Zhou, Yu Zhang, Mu Qiao, Hua Sun, Zipeng Li, Lianghua Li, Binke Dong, Favour Oluwapelumi Oyelami, Junjing Wu, Xianwen Peng,
... to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore ... we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine ... of inbreeding coefficients, which were calculated based on ROHs (F ROH ) and homozygosity (F HOM ). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In ... has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on ...
Tópico(s): Cancer-related molecular mechanisms research
2021 - Frontiers Media | Frontiers in Genetics
Bayode O. Makanjuola, Christian Maltecca, F. Miglior, Gabriele Marras, Emhimad A. Abdalla, Flávio S. Schenkel, Christine F. Baes,
... aim was to identify unique run of homozygosity (ROH) genotypes present within a given genomic window that ... and to quantify the effects of these identified ROH genotypes. Methods In total, 50,575 genotypes based ... date between 2008 and 2018 were available. Unique ROH genotypes identified using a sliding-window approach were ... traits. Results In total, 133 and 34 unique ROH genotypes with unfavorable effects were identified for production ... genome-wise false discovery rate. Most of these ROH regions were located on bovine chromosomes 8, 13, ...
Tópico(s): Genetics and Plant Breeding
2021 - BioMed Central | Genetics Selection Evolution
Sindy Liliana Caivio Nasner, Albeiro López Herrera, Luis Gabriel González Herrera, Juan Carlos Rincón Flórez,
... Ne), genomic inbreeding for runs of homozygosity (F ROH ), genomic relation matrix (F GRM ), excess of homozygotes ( ... PEDCOMP ) and to characterize the runs of homozygosity (ROH), searching for selection signatures. A total of 419 ... and R programs were used to estimate LD, ROH, F ROH and F HOM . The SNeP v1.1 program ... with a mean of 18.35 ± 0.55 ROH/animal. Most of the genome was covered by long ROHs (ROH >8 Mb = 4.86%), indicating significant recent inbreeding. ... F PEDCOM , F GRM , F HOM and F ROH was 4.41%, 4.18%, 5.58% and ...
Tópico(s): Silkworms and Sericulture Research
2021 - Wiley | Journal of Animal Breeding and Genetics
Satish Kumar, Cecilia Deng, Martin Hunt, Chris Kirk, Claudia Wiedow, Daryl D. Rowan, Jun Wu, Lester Brewer,
Runs of homozygosity (ROH) have been widely used to study population history and trait architecture in humans and livestock species, but their application ... plants has not been reported. The distributions of ROH in 199 accessions representing Asian pears (45), European ... for genotype-phenotype analyses. The average number of ROH and the average total genomic length of ROH were 6 and 11 Mb, respectively, in Asian ... accessions. Significant associations between genomic inbreeding coefficients (F ROH ) and phenotypes were observed for 23 out of ...
Tópico(s): Plant Physiology and Cultivation Studies
2021 - Frontiers Media | Frontiers in Plant Science
Ying Zhao, Qi Zhang, Yunwu Li, Binlin Wang, Fangwu Ma,
... this article, a novel re-entrant octagonal honeycomb (ROH) with negative Poisson's ratio (NPR) configuration is ... of two-dimensional (2D) and three-dimensional (3D) ROHs under axial loading. Based on above, the predominant ... static mechanical properties and finite element model of ROH are validated by experiment and demonstrate high accuracy. Subsequently, to obtain dynamic responses of the ROH under dynamic impact loading, the relations among dynamic ... model. Besides, dynamic energy absorption models of the ROH under dynamic loading are acquired in consideration of ...
Tópico(s): Polymer composites and self-healing
2021 - Elsevier BV | Composite Structures
Sarah M. Adams, Martijn F. L. Derks, Bayode O. Makanjuola, Gabriele Marras, Benjamin J. Wood, Christine F. Baes,
... reduce inbreeding. The detection of runs of homozygosity (ROH), or contiguous stretches of homozygous marker genotypes, can ... coefficients can be calculated based on pedigree information, ROH, or the genomic relationship matrix. The aim of this study was to detect and describe ROH in the turkey genome and compare estimates of ... FPED) with genomic-based inbreeding coefficients estimated from ROH (FROH) and the genomic relationship matrix (FGRM). A ... 452 SNPs). The overall mean length of detected ROH was 2.87 ± 0.29 Mb with a ...
Tópico(s): Genetic diversity and population structure
2021 - Elsevier BV | Poultry Science
E. F. Dzomba, M. Chimonyo, Rian Pierneef, F. C. Muchadeyi,
... the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina ... more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global ... Helix SVS program was used to investigate the ROH islands. Results A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African ... Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category ( ...
Tópico(s): Livestock Farming and Management
2021 - BioMed Central | BMC Genomics
Giuseppina Schiavo, Samuele Bovo, María Muñoz, Anisa Ribani, E. Alves, J. P. Araújo, Riccardo Bozzi, Marjeta Čandek‐Potokar, Rui Charneca, Ana I. Fernández, M. Gallo, Fabián García, Danijel Karolyi, Goran Kušec, J.M. Martins, Marie-José Mercat, Yolanda Núñez, Raquel Quintanilla, Čedomir Radović, Violeta Razmaitė, Juliette Riquet, Radomir Savić, G. Usai, Valerio Joe Utzeri, Christoph T. Zimmer, C. Óvilo, Luca Fontanesi,
Summary ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 ... Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of ...
Tópico(s): Animal Nutrition and Physiology
2021 - Wiley | Animal Genetics
Matteo Cortellari, Arianna Bionda, Alessio Negro, S. Frattini, Salvatore Mastrangelo, Elisa Somenzi, Emiliano Lasagna, Francesca Maria Sarti, Elena Ciani, Roberta Ciampolini, Donata Marletta, Luigi Liotta, Paolo Ajmone‐Marsan, Fabio Pilla, Licia Colli, Andrea Talenti, Paola Crepaldi,
... pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management ... species in different rural areas.We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from ... Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern ( ... that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have ... which is attributable to their management and history. ROH are longer in breeds that are undergoing non- ...
Tópico(s): Genetic diversity and population structure
2021 - BioMed Central | Genetics Selection Evolution
Maryam Nosrati, Hojjat Asadollahpour Nanaei, Arash Javanmard, Ali Esmailizadeh,
Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data ... animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8. ... autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean ...
Tópico(s): Genetic diversity and population structure
2021 - Elsevier BV | Genomics
Xudong Wu, Ren Zhou, Wei Zhang, Bangji Cao, Jing Xia, Caiyun Wang, Xiaodong Zhang, Mingxing Chu, Zongjun Yin, Yueyun Ding,
Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess ... inbreeding levels and the genome regions with high ROH frequency.In a previous study, we obtained 501. ... We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in ... Black pigs and identified genomic regions with high ROH frequencies.In this work, 1,813 ROHs (837 ...
Tópico(s): Cancer-related molecular mechanisms research
2021 - Asian-Australasian Association of Animal Production Societies | Animal Bioscience
Seyed Mohammad Ghoreishifar, Hossein Moradi-Shahrbabak, Mohammad Hossein Fallahi, Ali Jalil Sarghale, Mohammad Moradi-Shahrbabak, Rostam Abdollahi-Arpanahi, Majid Khansefid,
... common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and ... 1) to estimate and compare inbreeding calculated using ROH (F ROH ), excess of homozygosity (F HOM ), correlation between uniting ... matrix (F GRM ); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results In this study, 9102 ROH were identified, with an average number of 21. ... KHZ, which was in contrast to the F ROH estimates. We identified 11 ROH islands (four in ...
Tópico(s): Livestock Farming and Management
2020 - BioMed Central | BMC Genomic Data
Sangang He, Jiang Di, Bing Han, Lei Chen, Mingjun Liu, Wenrong Li,
... number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the ... length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and ... the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, ...
Tópico(s): Genetic diversity and population structure
2020 - Multidisciplinary Digital Publishing Institute | Animals
Daniela del Gaudio, Marwan Shinawi, Caroline Astbury, Marwan K. Tayeh, Kristen Deak, Gordana Raca,
... presence of one or more regions of homozygosity (ROH) on the affected chromosome, but with retention of ... chromosome isodisomy based on obligatory presence of extensive ROH on the affected chromosome including its pericentromeric region, ... CMA testing based on its frequent association with ROH on the affected chromosome, generated by meiotic crossovers ... of molecularly confirmed UPD do not show extended ROH and are not detectable by CMA.27.Hoppman ... 2018; 20: 1522-1527Google Scholar Even when present, ROH associated with heterodisomy varies in size, and overlap ...
Tópico(s): Genomic variations and chromosomal abnormalities
2020 - Elsevier BV | Genetics in Medicine
Produção Nacional
Revisado por pares
Évelin Aline Zanardo, Fabíola Paoli Monteiro, Samar N. Chehimi, Yanca Gasparini, Alexandre Torchio Dias, Larissa A. Costa, Luiza Ramos, Gil Monteiro Novo‐Filho, Marília M. Montenegro, A. M. Nascimento, João Paulo Kitajima, Fernando Kok, Leslie Domenici Kulikowski,
... well as uniparental disomy and regions of homozygosity (ROH) in patients with a developmental delay and multiple ... loss and gain, respectively, and to consider an ROH a minimum size of 3 Mb and 500 ... software generated graphic representations of CNV breakpoints and ROHs for each sample. Moreover, the bead arrays supplied ... CNVs (224 deletions and 108 duplications) and 37 ROHs in the same samples. Thus, the detection rates ... WES)10,994,5567,984,948NANA, not applicable; ROH, regions of homozygosity; WES, whole-exome sequencing. Open ...
Tópico(s): Congenital heart defects research
2020 - Elsevier BV | Journal of Molecular Diagnostics
Leslie Matalonga, Steven Laurie, Anastasios Papakonstantinou, Davide Piscia, Elisabetta Mereu, Gemma Bullich, Rachel Thompson, Rita Horváth, Luis A. Pérez‐Jurado, Olaf Rieß, Marta Gut, Gert‐Jan B. van Ommen, Hanns Lochmüller, Sergi Beltrán, Alessandra Renieri, Ali Dursun, Antoni Matilla‐Dueñas, Bru Cormand, Carlo Rivolta, Carmen Ayuso, Carmen Espinós, Christian Scerri, Dilek Yalnızoğlu, Doriette Soler, Éva Morava, Fabrizio Barbetti, Francesca Forzano, Francesca Mari, Francesco Muntoni, Frederic Tort, Henry Houlden, María‐Isabel Tejada, Jan Senderek, Javier Benı́tez, Javier Corral De La Calle, Jordi Serra, José M. Millán, José Carlos Segovia, Juan Ramón Gimeno Blanes, Judith Armstrong, Rıza Köksal Özgül, Laura Vilarinho, Lluı́s Montoliu, Manuel Posada de la Paz, Maria Antonietta Mencarelli, Marina Mora, Paola Bianchi, Pavel Seeman, Perry Elliott, Alessandra Ferlini, Alexis Brice, Brunhilde Wirth, Francesco Muntoni, Michael G. Hanna, Sarah J. Tabrizi, Thomas Klockgether, Vincent Timmerman, Volker Straub, Semra Hız Kurul, Yavuz Oktay, Serdal Güngör, Ahmet Yaramış, Uluç Yiş, Alfons Macaya, Antònia Ribes, Aurora Pujol, Conxi Lázaro, Daniel Grinberg, Eduardo F. Tizzano, Francesc Cardellach, Francesc Palau, Montserrat Milà, P. Gallano, Rafael Artuch, Ramon MartiSeves, Gonzalo Villanueva, Silvia M. Vidal, Glòria Garrabou, Susana Balcells, Roser Urreizti, Estrella López‐Martín, Ivon Cuscó, Irene Valenzuela, María Sabater‐Molina,
... of detection of >1 Mbp runs of homozygosity (ROHs). A model was built to predict if an ... consanguinity ranges were established according to the total ROH size. Application of the model resulted in the ... consanguinity ranges provide, for the first time, specific ROH thresholds to estimate inbreeding within a pedigree on ... of detection of >1 Mbp runs of homozygosity (ROHs). A model was built to predict if an ... consanguinity ranges were established according to the total ROH size. Application of the model resulted in the ...
Tópico(s): Genetics and Neurodevelopmental Disorders
2020 - Elsevier BV | Journal of Molecular Diagnostics
Alberto Cesarani, Giustino Gaspa, Alfredo Pauciullo, Lorenzo Degano, D. Vicario, N.P.P. Macciotta,
Abstract The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, ... milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH‐based coefficient of inbreeding (F ROH ) were calculated for 3,845 Simmental bulls of ... Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered ...
Tópico(s): Genetics and Plant Breeding
2020 - Wiley | Journal of Animal Breeding and Genetics
Nicole Moody, Samuel Sesena, Dane W. deQuilettes, Benjia Dou, Richard Swartwout, Joseph T. Buchman, A. L. Johnson, Udochukwu Eze, Roberto Brenes, Matthew Johnston, Christy L. Haynes, Vladimir Bulović, Moungi G. Bawendi,
... the European Union (EU) Restriction of Hazardous Substances (RoHS) Directive2European Parliament and Council of the European UnionDirective ... files/2016-04/documents/55fr26986.pdfGoogle Scholar The RoHS Directive and RCRA both aim to reduce the ... perovskite films on glass and flexible substrates using RoHS Directive and RCRA mandated protocols, we find that ... flexible perovskite PV modules. In the EU, the RoHS Directive is the primary regulation that prevents the ... Fleet, D., and Salado, R. (2008). Study on RoHS and WEEE Directives. European Commission DG Enterprise and ...
Tópico(s): Quantum Dots Synthesis And Properties
2020 - Elsevier BV | Joule
Liangyu Shi, Ligang Wang, Jiaxin Liu, Tianyu Deng, Hua Yan, Longchao Zhang, Xin Liu, Hongmei Gao, Xinhua Hou, Lixian Wang, Fuping Zhao,
Runs of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability ... SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs (FROH), homozygosity (FHOM), genomic relationship matrix (FGRM) and ... FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.In total, ...
Tópico(s): Genetics and Plant Breeding
2020 - BioMed Central | Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology
Roel Meyermans, Wim Gorssen, Nadine Buys, Steven Janssens,
... for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art ... PLINK, the --homozyg function is used to perform ROH analyses and relies on several input settings. These ... array data. Guidelines for a robust and uniform ROH analysis in PLINK using medium density data are ... albeit these guidelines are vital for comparing different ROH studies. In this study, 8 populations of different ... low minor allele frequencies and linkage disequilibrium on ROH detection are shown.We introduce the genome coverage ...
Tópico(s): Genetic Associations and Epidemiology
2020 - BioMed Central | BMC Genomics