Computational approach to utilisation of mitochondrial DNA in the verification of complex pedigree errors

Čačić, Mato; Čubrić-Ćurik, Vlatka; Ristov, Strahil; Čurik, Ino

doi:10.1016/j.livsci.2014.09.009

Cited by 5 publications

(4 citation statements)

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“…The results of this study were all higher than the standard value, which means that forest musk deer still exhibited high genetic diversity. We inferred with Chao 1 that there were 90 mtDNA CR haplotypes of captive forest musk deer in the Shaanxi province, including 90 maternal lines [ 44 ]. The reasons for the high genetic diversity of forest musk deer may be the abundant maternal lines with rich genetic resources and short breeding time.…”

Section: Discussionmentioning

confidence: 99%

mtDNA CR Evidence Indicates High Genetic Diversity of Captive Forest Musk Deer in Shaanxi Province, China

Wang

Gao

et al. 2023

Animals

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Forest musk deer (Moschus berezovskii) are endangered ruminants whose adult males secrete musk. China has been breeding forest musk deer artificially since the 1950s in an effort to restore wild populations, with Shaanxi and Sichuan provinces as the two main sites for captive breeding. Genetic diversity is a significant indicator that determines the long-term viability and status of a population, particularly for species at risk of extinction. In this study, we analyzed the current genetic makeup of seven captive forest musk deer populations in the Shaanxi province, using the mitochondrial DNA (mtDNA) control region (CR) as the molecular marker. We sequenced 604 bp of mtDNA CR, with an average content of A+T higher than G+C. We observed 111 variable sites and 39 different haplotypes from 338 sequences. The nucleotide diversity (Pi) and haplotype diversity (Hd) were 0.02887 and 0.908, respectively. Genetic differentiation between these populations was not significant, and the populations might not have experienced rapid growth. By combining our sequences with previous ones, we identified 65 unique haplotypes with 26 rare haplotypes and estimated a total of 90 haplotypes in Shaanxi province captive populations. The Shaanxi province and Sichuan province obtained 88 haplotypes, the haplotypes from the two populations were mixed together, and the two populations showed moderate genetic differentiation. Our findings suggested that captive forest musk deer populations in the Shaanxi province had high genetic diversity, with a rich founder population of about 90 maternal lines. Additionally, managers could develop genetic management plans for forest musk deer based on the haplotype database. Overall, our study will provide insights and guidelines for the conservation of genetic diversity in captive forest musk deer populations in the Shaanxi province.

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Section: Discussionmentioning

confidence: 99%

mtDNA CR Evidence Indicates High Genetic Diversity of Captive Forest Musk Deer in Shaanxi Province, China

Wang

Gao

et al. 2023

Animals

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“…The main functionality of this module is essentially the same as that of mag_con_demo , which is the initial tool for demonstration used in our previous work on computational pedigree analysis based on mtDNA [ 35 ]. Namely, mag_verif performs the verification of pedigree concordance with respect to mitochondrial haplotypes and maternal lines.…”

Section: Methodsmentioning

confidence: 99%

“…These descriptors are three indices denoted with HC (for haplotype counting or conflicts), IC (for informative counting or conflicts) and MISPLACED . The verification procedure and the meaning of indices are fully explained in [ 35 ]. Here we shall briefly repeat the main ideas.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2016

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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.

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“…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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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<p>The effects of mitogenome variation on economically important traits have been reported in a number of domestic animal species. In this study, the first of its kind on rabbits, we have performed the estimation of the contribution of cytoplasmic and D-loop mitochondrial DNA (mtDNA) sequence effects on the litter size and carcass traits in three Pannon rabbit breeds (Pannon Ka, Pannon Large and Pannon White). The observed effects of both estimates, coming from cytoplasmic or D-loop mtDNA variation, were negligible. The most likely explanation for the results obtained is the lack of mitogenome polymorphism in all three populations, as suggested from the analysis performed on the D-loop mtDNA sequence, here assigned to the two most frequent rabbit haplotypes. The extent of potential benefits of the introduction, or alteration, of mitogenome variation in rabbit breeding remains an open question for future research.</p>

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Computational approach to utilisation of mitochondrial DNA in the verification of complex pedigree errors

Cited by 5 publications

References 10 publications

mtDNA CR Evidence Indicates High Genetic Diversity of Captive Forest Musk Deer in Shaanxi Province, China

mtDNA CR Evidence Indicates High Genetic Diversity of Captive Forest Musk Deer in Shaanxi Province, China

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

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

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