scholarly journals Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1972
Author(s):  
Emil Krupa ◽  
Nina Moravčíková ◽  
Zuzana Krupová ◽  
Eliška Žáková
Keyword(s):  
Genetic Diversity ◽  
Correlation Coefficients ◽  
Pedigree Analysis ◽  
Minimum Size ◽  
Snp Analysis ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Snp Data ◽  
Inbreeding Rate

Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (n = 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (Ne) were evaluated. The correlations between inbreeding based on the runs of homozygosity (FROH) and pedigree (FPED) were also calculated. The average FPED for all animals was 3.44%, while the FROH varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The Ne, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49–0.54) were observed between FPED and FROH. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.

Pedigree analysis of Polish warmblood horses participating in riding performance tests

2015 ◽  
Vol 95 (1) ◽  
pp. 21-29 ◽  
Author(s):  
Alicja Borowska ◽  
Tomasz Szwaczkowski
Keyword(s):  
Genetic Diversity ◽  
Performance Test ◽  
Pedigree Analysis ◽  
Pedigree Information ◽  
Performance Tests ◽  
Effective Number ◽  
Horse Population ◽  
Inbreeding Coefficients ◽  
Discrete Generation ◽  
Inbreeding Rate

Borowska, A. and Szwaczkowski, T. 2015. Pedigree analysis of Polish warmblood horses participating in riding performance tests. Can. J. Anim. Sci. 95: 21–29. The aim of this study was to describe the population structure and genetic diversity in Polish warmblood horse population participating in the performance test. The reference population consisted of 596 stallions and 866 mares that participated in stationary performance tests conducted between 2002 and 2011 in Poland. The pedigree data contained 15 452 individuals. Completeness of pedigree information was assessed by two measures: percentage of animals with both parents known and discrete generation equivalent. Individual inbreeding coefficients, coancestry coefficient, individual increase in inbreeding, founder equivalent, founder genome equivalent, effective number of non-founders and genetic diversity loss were estimated to characterize the genetic diversity of the population. The average number of discrete generation equivalents reached 4.50 for observed stallions and 5.04 for mares, which shows good pedigree completeness. Pedigree analysis showed that 34% of the stallions and 44% of mares had inbreeding coefficients above zero. The average coancestry was 0.39% in the whole tested population. Average inbreeding rate of studied populations was very low (0.46%). The effective number of founders was 560. Generally, the inbreeding rate was low; genetic diversity was observed at a constant level for mares and only a small decrease was noticed for stallion. However, further studies are needed in this area.

EVALUATION OF BIODIVERSITY IN RUSSIAN LOCAL GOAT BREEDS BASED ON WHOLE-GENOME SNP ANALYSIS

2020 ◽  
pp. 434-436
Author(s):  
A. Dotsev ◽  
V. Volkova ◽  
M. Selionava ◽  
M. Fornara ◽  
H. Reyer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Pool ◽  
Snp Analysis ◽  
Whole Genome ◽  
Effective Population ◽  
Biodiversity Indicators ◽  
Snp Data ◽  
The World ◽  
Population Sizes ◽  
First Time

The genetic diversity of Russian local goats was estimated for the first time based on whole-genome SNP data. The tendencies of decrease in the effective population sizes were revealed, but the calculated biodiversity indicators are not inferior to the values obtained for the world goat breeds. The results indicate that there are still possibilities to preserve the valuable gene pool of local breeds.

scholarly journals Inbreeding pada Populasi Banteng (Bos javanicus d’Alton 1832) di Kebun Binatang Surabaya

2016 ◽  
Vol 18 (2) ◽  
pp. 84
Author(s):  
Reny Sawitri ◽  
Mariana Takandjandji
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Pedigree Analysis ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
Bos Javanicus ◽  
Individual Number ◽  
Hair Samples ◽  
Inbreeding Rate ◽  
The Impact

<p>Inbreeding Population of Banteng (Bos javanicus d&amp;rsquo;Alton 1832) at Surabaya Zoo. Reny Sawitry and Mariana Takandjandji. Banteng (Bos javanicus d&amp;rsquo;Alton 1832) is one of wildlife that is maintained in Surabaya Zoo, their mating system happened from a couples, and so overlap from generation to next generation. The purposed of this research was to determine effective population size, genetic diversity, and the change of physical and physiological of the herd. The methods used in this study were analysis DNA mitochondria from hair samples, description of physical and physiological change, and inbreeding coefficient. The results showed that effective populations size of herd in Surabaya Zoo tended to decline from productive age of banteng. Haplotype diversity of herd population was very low, the distance of genetic intra population zerro, and it&amp;rsquo;s genetic diversity was very homogen. This occured caused change in sex ratio of which male dominated the offspring population. Subsequently, the impact of inbreeding was the change of physic and physiology of banteng such as skin colour, sterile and infertile. Inbreeding that happened in Surabaya Zoo affected extinction of third population because of individual number of live sex less than one. The inbreeding coeficient was calculate using of pedigree analysis and inbreeding rate per generation based on the population structure. The calculation result of inbreeding coeficient was 0.42, while the inbreeding rate was 4.3% per generation. Finally, it&amp;rsquo;s needed to supply banteng from nature to fix offsprings and it&amp;rsquo;s genetic diversity.</p><p> </p><p><strong>Abstrak</strong></p><p>Banteng (Bos javanicus d&amp;rsquo;Alton 1832) merupakan salah satu satwa liar yang dipelihara di Kebun Binatang Surabaya (KBS). Sistem perkawinan banteng di lokasi ini dimulai dari bibit tunggal dan overlap antar generasi. Tujuan penelitian adalah untuk mengetahui keragaman genetika banteng di KBS melalui analisis DNA mitokondria, deskripsi perubahan fisik dan fisiologi banteng, gambaran nilai koefisien dan laju inbreeding per generasi. Metode yang digunakan adalah penghitungan ukuran populasi efektif, deskripsi perubahan fisik dan fisiologi serta koefisien dan laju inbreeding. Hasil penelitian menunjukkan bahwa ukuran populasi efektif banteng cenderung menurun dilihat dari umur produktif. Diversitas haplotipe populasi banteng di KBS sangat rendah, sehingga jarak genetik dalam populasi = 0 dan dapat dikatakan keragaman genetiknya sangat homogen. Rata-rata nilai koefisien inbreeding adalah 0,42 dan laju inbreeding 4,3% per generasi. Hal ini dapat dilihat dari keturunan jantan daripada betina. Perkawinan secara inbreeding penurunan fisik serta fisiologi banteng di KBS, seperti terjadinya kemandulan dan ketidaksuburan. Inbreeding juga mengakibatkan kepunahan pada populasi yang ada karena pada generasi ketiga jumlah individu tiap kelamin yang hidup kurang dari satu. Dengan demikian diperlukan pasokan banteng dari alam untuk memperbaiki keturunan dan keragaman genetik.</p>

scholarly journals The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
N. Z. Gebrehiwot ◽  
E. M. Strucken ◽  
H. Aliloo ◽  
K. Marshall ◽  
J. P. Gibson
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Large Population ◽  
Bos Indicus ◽  
Principal Component ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
African Cattle ◽  
Snp Data

Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

Nuclear and cytoplasmic genetic diversity reveals long-term population decline in Abies semenovii, an endemic fir of central Asia

2012 ◽  
Vol 42 (12) ◽  
pp. 2142-2152 ◽  
Author(s):  
Svetlana A. Semerikova ◽  
Martin Lascoux ◽  
Vladimir L. Semerikov
Keyword(s):  
Genetic Diversity ◽  
Central Asia ◽  
Population Decline ◽  
Population Expansion ◽  
Nuclear Marker ◽  
Effective Population ◽  
Species Status ◽  
Siberian Fir ◽  
Low Genetic Diversity

The genus Abies is one of the largest conifer genera and many of the marginal species remain poorly characterized. Abies semenovii B. Fedtsch. is a rare mountain fir species from central Asia, and its species status is still disputed. We used both nuclear (allozymes and AFLP) and chloroplastic (cpSSR) markers to show that A. semenovii deserves to be considered as a species and that its low genetic diversity justifies more a proactive conservation policy. First, A. semenovii was significantly differentiated from the Siberian fir Abies sibirica Ledeb. and we did not detect gene flow between the two species. Second, A. semenovii has a very low nuclear genetic diversity, suggesting a prolonged restricted effective population size. Abies semenovii had low cpSSR diversity too but the identification of seven closely related haplotypes suggests that these mutations accumulated recently during a phase of population expansion. This agrees well with the palynological record and is in contrast with the situation observed in another rare Eurasian fir endemic to Kamchatka, Abies gracilis Kom., which was devoid of variation in cpSSRs but that also had a more substantial nuclear marker diversity than A. semenovii, thereby suggesting a more recent but less severe population bottleneck.

scholarly journals Improving short and long term genetic gain by accounting for within family variance in optimal cross selection

2019 ◽  
Author(s):  
Antoine Allier ◽  
Christina Lehermeier ◽  
Alain Charcosset ◽  
Laurence Moreau ◽  
Simon Teyssèdre
Keyword(s):  
Genetic Diversity ◽  
Genomic Selection ◽  
Genetic Gain ◽  
Family Selection ◽  
Breeding Programs ◽  
Short And Long Term ◽  
Inbreeding Rate ◽  
Genetic Value ◽  
Optimal Set

AbstractThe implementation of genomic selection in recurrent breeding programs raised several concerns, especially that a higher inbreeding rate could compromise the long term genetic gain. An optimized mating strategy that maximizes the performance in progeny and maintains diversity for long term genetic gain on current and yet unknown future targets is essential. The optimal cross selection approach aims at identifying the optimal set of crosses maximizing the expected genetic value in the progeny under a constraint on diversity in the progeny. Usually, optimal cross selection does not account for within family selection, i.e. the fact that only a selected fraction of each family serves as candidate parents of the next generation. In this study, we consider within family variance accounting for linkage disequilibrium between quantitative trait loci to predict the expected mean performance and the expected genetic diversity in the selected progeny of a set of crosses. These predictions rely on the method called usefulness criterion parental contribution (UCPC). We compared UCPC based optimal cross selection and optimal cross selection in a long term simulated recurrent genomic selection breeding program considering overlapping generations. UCPC based optimal cross selection proved to be more efficient to convert the genetic diversity into short and long term genetic gains than optimal cross selection. We also showed that using the UCPC based optimal cross selection, the long term genetic gain can be increased with only limited reduction of the short term commercial genetic gain.

scholarly journals Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection

2022 ◽  
Vol 8 ◽  
Author(s):  
Michela Ablondi ◽  
Alberto Sabbioni ◽  
Giorgia Stocco ◽  
Claudio Cipolat-Gotet ◽  
Christos Dadousis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dairy Cattle ◽  
Population Size ◽  
Genomic Selection ◽  
Effective Population Size ◽  
Genomic Data ◽  
Future Market ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Snp Data

Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (FROH). The average pedigree inbreeding was 0.07, while the average FROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for Fped and FROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.

scholarly journals Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations

2021 ◽  
Vol 19 (2) ◽  
Author(s):  
Josiane Ribolli ◽  
Evoy Zaniboni-Filho ◽  
Carolina Barros Machado ◽  
Tailise Carolina de Souza Guerreiro ◽  
Patrícia Domingues de Freitas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Anthropogenic Impacts ◽  
Species Conservation ◽  
Migratory Fish ◽  
Effective Population ◽  
Long Distance ◽  
Management Actions ◽  
Population Structure Analysis ◽  
Salminus Brasiliensis

Abstract Life-history, geographical barriers, and damming can shape the genetic diversity of freshwater migratory fish, which are particularly vulnerable to anthropogenic impacts. We investigated the genetic diversity of Salminus brasiliensis, a long-distance migratory species that is recognized as an important provider of ecosystem services. We implemented microsatellite analyses to assess genetic diversity and simulate future scenarios for evaluating the long-term viability of dammed and non-dammed populations from the Uruguay River. High levels of genetic diversity were detected for all sampled populations. However, effective population sizes were lower in the uppermost river stretches, where the landscape is highly fragmented. Population structure analysis indicated two spatial genetic populations. It is suggested that this genetic structure preserves populations partially isolated by an ancient natural barrier, instead of being a result of the presence of dams. The simulated genetic scenarios indicated that genetic variability of S. brasiliensis populations from upstream dams could collapse over the years, mainly due to the reduction in the number of alleles. Therefore, besides helping to better understand issues related to the influence of dams on the genetic diversity of migratory fish, our results are especially relevant for driving local fishery policies and management actions for the species conservation.

scholarly journals Evaluation of the Romosinuano cattle population structure in Mexico using pedigree analysis

2020 ◽  
Vol 33 (1) ◽  
pp. 44-59
Author(s):  
Rafael Núñez-Domínguez ◽  
Ricardo E Martínez-Rocha ◽  
Jorge A Hidalgo-Moreno ◽  
Rodolfo Ramírez-Valverde ◽  
José G García-Muñiz
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Pedigree Analysis ◽  
Effective Population ◽  
Genetic Management ◽  
Generation Interval

Background: Romosinuano cattle breed in Mexico has endured isolation and it is necessary to characterize it in order to facilitate sustainable genetic management. Objective: To assess the evolution of the structure and genetic diversity of the Romosinuano breed in Mexico, through pedigree analysis. Methods: Pedigree data was obtained from Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). The ENDOG program (4.8 version) was used to analyze two datasets, one that includes upgrading from F1 animals (UP) and the other with only straight-bred cattle (SP). For both datasets, three reference populations were defined: 1998-2003 (RP1), 2004-2009 (RP2), and 2010-2017 (RP3). The pedigree included 3,432 animals in UP and 1,518 in SP. Demographic parameters were: Generation interval (GI), equivalent number of generations (EG), pedigree completeness index (PCI), and gene flow among herds. Genetic parameters were: Inbreeding (F) and average relatedness (AR) coefficients, effective population size (Nec), effective number of founders and ancestors, and number of founder genome equivalents. Results: The GI varied from 6.10 to 6.54 for UP, and from 6.47 to 7.16 yr for SP. The EG of the UP and SP improved >63% from RP1 to RP3. The PCI increased over time. No nucleus or isolated herds were found. For RP3, F and AR reached 2.08 and 5.12% in the UP, and 2.55 and 5.94% in the SP. For RP3, Nec was 57 in the UP and 45 in the SP. Genetic diversity losses were attributed mainly (>66%) to genetic drift, except for RP3 in the SP (44%). Conclusions: A reduction of the genetic diversity has been occurring after the Romosinuano breed association was established in Mexico, and this is mainly due to random loss of genes.Keywords: effective population size; gene flow; genetic diversity; genetic drift; generation interval; inbreeding; pedigree; population structure; probability of gene origin; Romosinuano cattle. Resumen Antecedentes: La raza bovina Romosinuano ha estado prácticamente aislada en México y requiere ser caracterizada para un manejo genético sostenible. Objetivo: Evaluar la evolución de la estructura y diversidad genética de la raza Romosinuano en México, mediante el análisis del pedigrí. Métodos: Los datos genealógicos provinieron de la Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). Los análisis se realizaron con el programa ENDOG (versión 4.8) para dos bases de datos, una que incluyó animales en cruzamiento absorbente (UP) a partir de F1 y la otra con sólo animales puros (SP). Para ambas bases de datos se definieron tres poblaciones de referencia: 1998-2003 (RP1), 2004- 2009 (RP2), y 2010-2017 (RP3). El pedigrí incluyó 3.432 animales en la UP y 1.518 en la SP. Los parámetros demográficos fueron: intervalo generacional (GI), número de generaciones equivalentes (EG), índice de completitud del pedigrí (PCI), y flujo de genes entre hatos. Los parámetros genéticos fueron: coeficientes de consanguinidad (F) y de relación genética aditiva (AR), tamaño efectivo de la población (Nec), número efectivo de fundadores y ancestros, y número equivalente de genomas fundadores. Resultados: El GI varió de 6,10 a 6,54 para la UP, y de 6,47 a 7,16 años para la SP. El EG de la UP y la SP mejoró >63%, de RP1 a RP3. El PCI aumentó a través de los años, pero más para la SP que para la UP. No se encontraron hatos núcleo o aislados. Para RP3, F y AR alcanzaron 2,08 y 5,12% en la UP, y 2,55 y 5,94% en la SP. Para RP3, Nec fue 57 en la UP y 45 en la SP. Más de 66% de las pérdidas en diversidad genética se debieron a deriva genética, excepto para RP3 en la UP (44%). Conclusiones: una reducción de la diversidad genética ha estado ocurriendo después de que se formó la asociación de criadores de ganado Romosinuano en México, y es debida principalmente a pérdidas aleatorias de genes.Palabras clave: consanguinidad; deriva genética; diversidad genética; estructura poblacional; flujo de genes; ganado Romosinuano; intervalo generacional; pedigrí; probabilidad de origen del gen; tamaño efectivo de población. Resumo Antecedentes: A raça bovina Romosinuano tem estado praticamente isolada no México e precisa ser caracterizada para um manejo genético sustentável. Objetivo: Avaliar a evolução da estrutura e diversidade genética da raça Romosinuano no México, através da análise de pedigree. Métodos: Os dados genealógicos vieram da Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). As análises foram feitas com o programa ENDOG (versão 4.8) para duas bases de dados, uma que incluiu animais em cruzamento absorvente (UP) a partir da F1 e a outra base de dados somente com animais puros (SP). Para ambas bases de dados foram definidas três populações de referência: 1998-2003 (RP1), 2004-2009 (RP2) e 2010-2017 (RP3). O pedigree incluiu 3.432 animais na UP e 1.518 na SP. Os parâmetros demográficos foram: intervalo entre gerações (GI), número de gerações equivalentes (EG), índice de completude do pedigree (PCI), e fluxo de genes entre rebanhos. Os parâmetros genéticos foram: coeficiente de consanguinidade (F) e da relação genética aditiva (AR), tamanho efetivo da população (Nec), número efetivo de fundadores e ancestrais, e número equivalente de genomas fundadores. Resultados: O GI variou de 6,10 a 6,54 para a UP, e de 6,47 a 7,16 anos para a SP. EG da UP e a SP melhorou >63%, de RP1 a RP3. O PCI aumentou ao longo dos anos, mas mais para a SP do que para o UP. Não se encontraram rebanhos núcleo ou isolados. Para RP3, F e AR alcançaram 2,08 e 5,12% na UP, e 2,55 e 5,94% na SP. Para RP3, Nec foi 57 na UP e 45 na SP. Mais de 66% das perdas em diversidade genética foram ocasionadas pela deriva genética, exceto para RP3 no UP (44%). Conclusões: Depois que a associação da raça Romosinuano foi estabelecida no México, tem ocorrido uma redução da diversidade genética, principalmente devido a perdas aleatórias de genes.Palavras-chave: consanguinidade; deriva genética; diversidade genética, estrutura populacional; fluxo de genes; intervalo entre gerações; pedigree; probabilidade de origem do gene; Romosinuano; tamanho efetivo da população.

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