Dataset Information

Mitochondrial DNA Diversity in Large White Pigs in Russia.

ABSTRACT: The Large White pig is the most commonly raised commercial pig breed in the world. The aim of this work was to investigate D-loop mtDNA in Large White pigs (n = 402) of various selections bred in the Russian Federation from 2000 to 2019. The general sample consisted of three groups: Old (n = 78) (Russian selection, 2000-2010); Imp (n = 123) (imported to Russia in 2008-2014); New (n = 201) (2015-2019). The synthesized score (Fz) was calculated by analyzing the main PCA (principal component analysis components). An affiliation to Asian or European haplogroups was determined according to the NCBI (National Center for Biotechnology Information). In the study, we defined 46 polymorphic sites and 42 haplotypes. Significant distinctions between groups Old, Imp and New in frequencies of haplotypes and haplogroups were established. The distribution of Asian and European haplotypes in the groups was Old: 50%/50%, Imp: 43%/57%, New: 75%/25%, respectively. The variety of haplotypes and haplogroups in the pigs of the group New is related to the farms in which they breed. Haplotype frequencies significantly differ between the clusters Old_Center, Old_Siberia and Old_South. This study will provide information on the genetic diversity of Large White breed pigs. The results will be useful for the conservation and sustainable use of these resources.

SUBMITTER: Getmantseva L

PROVIDER: S-EPMC7460241 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Mitochondrial DNA Diversity in Large White Pigs in Russia.

Getmantseva Lyubov L Bakoev Siroj S Bakoev Nekruz N Karpushkina Tatyana T Kostyunina Olga O

Animals : an open access journal from MDPI 20200806 8

The Large White pig is the most commonly raised commercial pig breed in the world. The aim of this work was to investigate D-loop mtDNA in Large White pigs (n = 402) of various selections bred in the Russian Federation from 2000 to 2019. The general sample consisted of three groups: Old (n = 78) (Russian selection, 2000-2010); Imp (n = 123) (imported to Russia in 2008-2014); New (n = 201) (2015-2019). The synthesized score (Fz) was calculated by analyzing the main PCA ...[more]

PMID: 32781729

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Project description:BACKGROUND: From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. METHODOLOGY/PRINCIPAL FINDINGS: The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals. CONCLUSIONS/SIGNIFICANCE: We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.

Project description:BackgroundMethane emissions from pigs account for 10% of total methane production from livestock in China. Methane emissions not only contribute to global warming, as it has 25 times the global warming potential (GWP) of CO2, but also represent approximately 0.1~3.3% of digestive energy loss. Methanogens also play an important role in maintaining the balance of the gut microbiome. The large intestines are the main habitat for the microbiome in pigs. Thus, to better understand the mechanism of methane production and mitigation, generic-specific and physio-ecological characteristics (including redox potential (Eh), pH and volatile fatty acids (VFAs)) and methanogens in the large intestine of pig were studied in this paper. Thirty DLY finishing pigs with the same diet and feeding conditions were selected for this experiment.ResultA total of 219 clones were examined using the methyl coenzyme reductase subunit A gene (mcrA) and assigned to 43 operational taxonomic units (OTUs) based on a 97% species-level identity criterion. The family Methanobacteriaceae was the dominant methanogen in colonic digesta of finishing pigs, accounting for approximately 70.6% of the identified methanogens, and comprised mainly the genera Methanobrevibacter (57%) and Methanosphaera (14%). The order Methanomassiliicoccales, classified as an uncultured taxonomy, accounted for 15.07%. The methanogenic archaeon WGK1 and unclassified Methanomicrobiales belonging to the order of Methanomicrobiales accounted for 4.57 and 1.37%, respectively. The Eh was negative and within the range - 297.00~423.00 mV and the pH was within the range 5.04~6.97 in the large intestine. The populations of total methanogens and Methanobacteriales were stable in different parts of the large intestine according to real-time PCR.ConclusionThe major methanogen in the large intestine of finishing pigs was Methanobrevibacter. The seventh order Methanomassiliicoccales and species Methanosphaera stadtmanae present in the large intestine of pigs might contribute to the transfer of hydrogen and fewer methane emissions. The redox potential (Eh) was higher in the large intestine of finishing pigs, which had a positive correlation with the population of Methanobacteriale.

Dataset Information

Mitochondrial DNA Diversity in Large White Pigs in Russia.

Publications

Mitochondrial DNA Diversity in Large White Pigs in Russia.

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