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

Abstract

BackgroundIdentification 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.ResultsWe 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.ConclusionsMaGelLAn 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0242-9) contains supplementary material, which is available to authorized users.

Analysis of the impact of cytoplasmic and mitochondrial inheritance on litter size and carcass in rabbits

“…Here, in addition to the models with maternal lineage of dam (does) effect, which is a classical approach used in a large number of studies (Boettcher et al, 1996;Boettcher et al, 1997;Snowder et al, 2004), we also modelled the maternal lineage of sire (bucks) effect. This decision was based on the established evidence that certain mitogenome mutations have strong impact on human male fertility (Ruiz-Pesini et al, 2000;John et al, 2005) and, consequently, can affect the litter size. We applied models 5, 6 and 7 to estimate the variance of the contribution of the difference between H1 and H2, applicable only in PW breed.…”

“…However, this is quite a relaxed assumption and, in order to obtain more accurate estimates, quantitative cytoplasmic genetic models have to be further extended to the association analyses of the mitogenome variation (polymorphism), from D-loop mitochondrial DNA (mtDNA) to complete mitogenome, with production traits. Good examples are provided in studies related to cattle (Boettcher et al, 1996a;Mezzadra et al, 2005), poultry (Li et al, 1998;Zhao et al, 2015), swine (Yen et al, 2007;Fernández et al, 2008;Yu et al, 2015, Tsai et al, 2016 and sheep (Chen et al, 2017) populations, as well as to humans (Ruiz-Pesini et al, 2000;Liu et al, 2012), where the association of certain mitogenome polymorphisms with quantitative traits have been analysed.…”

A Fast Method for the Selection of Samples in Populations with Available Genealogical Data

“…Clearly, the set of individuals that is expected to cover the largest variability is the set of mutually most distant individuals in a pedigree. The task of selecting the optimal set of K individuals for sampling is therefore translated into an algorithmic problem of selecting the K most distant individuals in a (pedigree) tree of size N. This problem was addressed in Magellan software for the analysis of maternal lines in a pedigree [4], where a transparent and user-friendly method was implemented to solve the (quasi)optimal set selection problem on the small and medium-sized pedigrees. However, the algorithm implemented in the Ref.…”

Estudo da influência genética da herança citoplasmática em características de interesse econômico de bovinos da raça Nelore

“…Devido as dificuldades enfrentadas para realizar as análises abrangendo os registros de pedigree, os dados fenotípicos e os genes mitocondriais, Ristov et al (2016) desenvolveram uma ferramenta para análise do pedigree, focada na análise quantitativa do mitogenoma e da genealogia materna.…”

“…A qualidade das informações de pedigree e dos fenótipos pode afetar as estimativas de parâmetros genéticos e predição de valores genéticos (RISTOV et al, 2016), bem como, é um problema associado com a menor seleção baseada em matrizes, sendo um dos principais pilares para obtenção de resultados acurados nas avaliações genéticas, devido à correta formação da matriz de parentesco e dados de produção. Em bovinos de corte, especialmente em condições de criação extensiva, as coletas de informações de pedigree são escassas e a estrutura do pedigree é insuficiente quanto às informações referentes às linhagens paternas e maternas.…”