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MaGelLAn 1.0 : a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information

Ristov, Strahil; Brajković, Vladimir; Cubric Curik, Vlatka; Michieli, Ivan; Curik, Ino (2016) MaGelLAn 1.0 : a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information. Genetics Selection Evolution, 48 . 65-1-65-10. ISSN 0999-193X

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Abstract

Identification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis. Current research in our group focuses on acquiring the necessary mitochondria sequence information and analysing its influence on the phenotype of a quantitative trait. To facilitate these tasks we have produced software for processing pedigrees that is optimised for maternal lineage analysis. We present MaGelLAn 1.0 (maternal genealogy lineage analyser), a suite of four Python scripts (modules) that is designed to facilitate the analysis of the impact of mitogenome polymorphism on quantitative trait variation by combining molecular and pedigree information. MaGelLAn 1.0 is primarily used to: (1) optimise the sampling strategy for molecular analyses ; (2) identify and correct pedigree inconsistencies ; and (3) identify maternal lineages and assign the corresponding mitogenome sequences to all individuals in the pedigree, this information being used as input to any of the standard software for quantitative genetic (association) analysis. In addition, MaGelLAn 1.0 allows computing the mitogenome (maternal) effective population sizes and probability of mitogenome (maternal) identity that are useful for conservation management of small populations. MaGelLAn is the first tool for pedigree analysis that focuses on quantitative genetic analyses of mitogenome data. It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source code, along with the manual and the example files can be downloaded at http://lissp.irb.hr/software/magellan-1-0/ and https://github.com/sristov/ magellan.

Item Type: Article
Uncontrolled Keywords: mtDNA ; mitogenome ; software ; pedigree
Subjects: TECHNICAL SCIENCES > Computing
Divisions: Division of Electronics
Projects:
Project titleProject leaderProject codeProject type
Upotreba cijelog genoma mitohondrijske DNA u oplemenjivanju i konzervacijskoj genetici goveda-MitoTAUROmicsIno ĆurikIP-2013-11-9070HRZZ
Postupci strojnog učenja za dubinsku analizu složenih struktura podataka-DescriptiveInductionDragan GambergerIP-2013-11-9623HRZZ
Depositing User: Strahil Ristov
Date Deposited: 15 Nov 2017 09:35
Last Modified: 15 Nov 2017 09:35
URI: http://fulir.irb.hr/id/eprint/3670
DOI: 10.1186/s12711-016-0242-9

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