Evidence map›Paper›PMID 27342071›Full record

ArticleBMC genetics2016

A practical approach to detect ancestral haplotypes in livestock populations.

Enrique Sánchez-Molano, Dimitrios Tsiokos, Dimitrios Chatziplis, Hossein Jorjani, Lorenzo Degano, Clara Diaz, Attilio Rossoni, Hermann Schwarzenbacher, Franz Seefried, Luis Varona and 3 more

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In one paragraph

Article in BMC genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Enrique Sánchez-MolanoThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK. Enrique.Sanchez-Molano@roslin.ed.ac.uk.
Dimitrios TsiokosLaboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agricultural Technology, School of Agricultural Technology, Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki, Greece.
Dimitrios ChatziplisLaboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agricultural Technology, School of Agricultural Technology, Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki, Greece.
Hossein JorjaniInterbull Center, Uppsala, S-75007, Sweden.
Lorenzo DeganoAssociazione Nazionale Allevatori Bovini di razza Pezzata Rossa Italiana, Udine, Italy.
Clara DiazDepartamento de Mejora Genética Animal, INIA, Madrid, 28040, Spain.
Attilio RossoniAssociazione Nazionale Allevatori Bovini della Razza Bruna, Verona, Italy.
Hermann SchwarzenbacherZuchtData EDV-Dienstleistungen GmbH, Wien, Austria.
Franz SeefriedQualitas AG, Zug, Switzerland.
Luis VaronaDepartamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, Zaragoza, 50013, Spain.
Daniele VicarioAssociazione Nazionale Allevatori Bovini di razza Pezzata Rossa Italiana, Udine, Italy.
Ezequiel L NicolazziBioinformatics core facility, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. CascinaCodazza, Lodi, 26900, Italy.
Georgios BanosThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.

Funding

Biotechnology and Biological Sciences Research Council BB/J004235/1Biotechnology and Biological Sciences Research Council BBS/E/D/20211554
6 · The paper itself

Abstract

backgroundThe effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle.

resultsThe identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content.

conclusionIn agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations.

Indexed as

Evolution, MolecularHaplotypesAnimalsCattleFemaleGenetic VariationLivestockMaleModels, GeneticAncestral haplotypesCattlePopulation dynamicsSelection signatures

Identifiers

PMID27342071
PMCPMC4921009

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.