The pattern of genetic diversity of different breeds of pigs based on microsatellite analysis

Харзинова, В. Р.; Zinovieva, N. A.

doi:10.18699/vj20.669

Cited by 15 publications

(5 citation statements)

References 39 publications

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“…Therefore, breeders in Balkan countries, Austria, Switzerland, and Germany aim to conserve the original Mangalitsa without deleterious effects of inbreeding ( Egerszegi et al, 2003 ). There is a growing interest in the exploration of the genome resource of Mangalitsa pigs, relying on an array of genetic markers including microsatellites ( Zsolnai et al, 2006 ; Druml et al, 2012 ; Kharzinova and Zinovieva 2020 ), mitochondrial DNA D-loop sequences ( Marincs et al, 2013 ; Molnár et al, 2013 ; Frank et al, 2017 ), SNPs ( Bâlteanu et al, 2019 ; Bâlteanu et al, 2021 ; Zorc et al, 2022 ) and whole genome sequences ( Molnár et al, 2014 ). Previous studies have attempted to discriminate between Mangalitsa pigs of different colors, highlighting a rejection of the hypothesis that Mangalitsa individuals belong to one indistinguishable group ( Zsolnai et al, 2006 ).…”

Section: Discussionmentioning

confidence: 99%

An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs

Addo

Jung²

2022

Front. Genet.

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Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16–26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.

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Section: Discussionmentioning

confidence: 99%

An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs

Addo

Jung²

2022

Front. Genet.

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“…В другой российской работе [40] были даны матрицы парных GD между 11 породами свиней по 10 STR-локусам. В большинстве случаев (52 из 55) DEST-дистанции превышали FST (оценки DEST были выше в 1,3 раза).…”

Section: таблица 6 -треугольные матрицы парных генетических дистанций по Linfst(wandc) и F′st(wandc) G′′st(hed) и Dest мерам / Table 6 -Tunclassified

“…Коэффициент неопределённости, равный 0,31, указывал на наличие заметных отличий в структурах генетических взаимоотношений между породами при использовании двух мер. Это можно видеть и при сравнении приводимых в [40] Ординация быков на 2D диаграмме. Ординация -это упорядочение объектов вдоль некоторых осей методами многомерной статистики (PCA, PСoA и т.п.)…”

Assessment of genetic differentiation of populations by analysis of molecular variance (analytical review)

Kuznetsov

2021

Аграрная наука Евро-Северо-Востока

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Different approaches to using the analysis of molecular variance (AMOVA) to assess the genetic differentiation of populations have been compared in the research. Data on 11 microsatellite loci of 84 bulls of seven breeds were used. The results were compared for three options of the AMOVA module of the GenAlEx 6.502 program: the allele distance matrix (calculated FST(W&C)(=θ) statistics – variant AMOVA1); the genotype distance matrix (ΦPT– AMOVA2); and the allele size difference matrix (RST– AMOVA3). Similar summary estimates of the genetic differentiation of breeds were obtained: FST(W&C)= 0.108, ΦPT= 0.115, RST= 0.110 (all with pperm≤ 0.001). Between the estimates of FST(W&C)and ΦPTfor each locus, the correlation coefficient was 0.99 (pvalue<0.0001); no statistically significant correlations with RSTwere found. A high correlation of FST(W&C)and ΦPTwith the estimates of differentiation according to Nei’s (0.96) was found. Programs other than GenAlEx (Arlequin v.3.5, GenePop v.4.7.3, RST22) gave similar AMOVA estimates. The negative linear dependence of FST(W&C)and ΦPTon the level of the average heterozygosity of the breed samples was established (R2= 0.6, rS= -0.75 for pvalue < 0.02) and the absence of such dependence for RST(R2= 0.04, rS= -0.23 for pvalue= 0.47). The standardization of the FST(W&C)and ΦPTestimates according to Hedrick’s eliminated this dependence and raised the initial estimates to 0.35 and 0.37, respectively. The latter were comparable to the estimates obtained by the Nei-Hedrick’s (0.364-0.375), Jost’s (0.292), and Morisit-Horn’s (0.308) methods. The Mantel correlations between the matrices of paired genetic distances (GD) calculated by different measures were >0.9 in most cases. The projections of the GD matrices in the principal coordinate analysis (PCoA) on the 2D plane were generally similar. The PCoA identified a cluster of Holstein «ecotypes», a cluster of «Red» breeds, and a branch of the Jersey breed. In the two-factor AMOVA of data on clusters (as two «regions»), the interregional GD was 0.357; the differentiation of breeds within the «regions» did not exceed 0.027. Modeling the association of breeds with close to zero GD resulted in an increase in the number of alleles per locus in the «new» breeds by 29 %, and an increase in the combined estimate of genetic differentiation by 29-46 %. The results obtained can be used in the development of measures for the conservation of endangered breeds.

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“…Each breed or animal type shows some heterogeneity in morphological, productive and technological qualities. Microsatellite loci (short tandem repeat, STR) can be used to solve breedingtasksrelatedtothedeterminationofbreedaffiliation or breed type (Deniskova et al, 2018;Isakova et al, 2019Isakova et al, , 2021Kharzinova, Zinovieva, 2020;Nosova et al, 2020;Lemesh et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

A genogeographic study of the Kyrgyz mountain merino via microsatellite markers

Bekturov

Исакова²,

Kipen

et al. 2023

Vestn. VOGiS

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The aim was to ascertain the genetic and geographical structure of the Kyrgyz mountain merino (KMM). We analyzed DNA samples of 109 Kyrgyz mountain merino specimens, bred in three state breeding factories (STB), including“Orgochor” in the Issykul Province,“Katta-Taldyk” in the Osh Province and STb named after Luschikhin in the Talas Province. We identified 126 alleles in 12 microsatellite markers (McM042, INRA006, McM527, ETH152, CSRD247, OarFCB20, INRA172, INRA063, MAF065, MAF214, INRA005, INRA023). There were 6 to 16 alleles in each locus (mean 10.500 ± 0.957 alleles per locus). We identified 67 rare alleles (prevalence less than 5.0 %), which made up 53.2 % of all alleles found. The greatest number of rare alleles was found in STR-markers of CSRD247, INRA023, INRA005, INRA006, MAF214 and OarFCB20. For each group, there were individual differences in the distribution of allele frequencies across all the STR loci studied. The most significant of them were as follows: with regard to the McM042 locus, allele 87 was major in the TALAS and OSH groups (35.6 and 45.7 %, respectively), whereas allele 95 was major in the ISSYK-KUL group (36.2 %); allele 154 was major in all groups with regard to the INRA172 locus, but it was 1.25 times less prevalent in the ISSYK-KUL and 1.66 times less prevalent in the OSH groups compared to TALAS (55.2 and 41.4 %, respectively), whereas alleles 156 and 158 were found only in the ISSYK-KUL group. Considering the ETH152 locus, 186 allele prevalence in the TALAS group was 51.1 %, but allele 190 was also markedly prevalent in the ISSYK-KUL and OSH groups, 34.5 and 34.3 %, respectively. The genetic division of the studied groups of KMM (with K from 3 to 10) was homogeneous – the contribution of each subcluster was equivalent. The AMOVA analysis revealed that the groups are located equidistantly. To conclude, the genetic diversity of the Kyrgyz mountain merino in three state breeding factories of the Kyrgyz Republic was high and comparable with each other.

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The pattern of genetic diversity of different breeds of pigs based on microsatellite analysis

Cited by 15 publications

References 39 publications

An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs

An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs

Assessment of genetic differentiation of populations by analysis of molecular variance (analytical review)

A genogeographic study of the Kyrgyz mountain merino via microsatellite markers

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