Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis
Abstract
Genetic variability and relationships among six native French cattle breeds (Abondance, Tarentaise, Villard de Lans, Montbéliarde, Limousin, and Charolais) and one foreign breed (Holstein) were investigated using 23 microsatellite markers. These breeds were also compared with four Swiss breeds genotyped in a previously published study. Interestingly, the French alpine breeds have smaller population sizes but showed higher genetic variability than the larger Holstein breed. Neighbor-joining trees and PCA (principal components analysis) showed that alpine breeds tend to cluster together. Abondance and Tarentaise breeds were closely related, whereas the Holstein was highly differentiated from all breeds analyzed. Two different assignment tests for determining the breed of origin of individuals were compared: "direct" and "exclusion-simulation" approaches. The exclusion-simulation significance test correctly assigns fewer individuals than the direct approach but provides a confidence level (e.g., P < 0.01) for each individual being assigned. Accurate assignment with high statistical confidence is required for animal traceability. Unfortunately, the accuracy of assignment greatly decreases as the threshold level of confidence of assignment increases (e.g., from P < 0.05 to P < 0.001). Assignment accuracy also greatly declines as the level of population differentiation decreases below the level often found between related breeds (e.g., F(ST) < 0.1).
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The Holstein breed has much lower genetic variability than other cattle breeds based on microsatellite DNA analysis.
“It is known that domestication generally decreases the genetic diversity of strains and that the Holstein breed has much lower genetic variability than other cattle breeds based on microsatellite DNA analysis [14].”
From Lunar Cycle Influences Spontaneous Delivery in Cows (2016) · cites this paper as [14]
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“…1998) and is used as effective molecular markers in genetic diversity analysis for animal populations (Gaouar et al., 2016; Maretto et al., 2012; Maudet et al., 2002; Peelman et al., 1998), parental identification (Gamarraa et al., 2015) and wild animal protection (Paetkau et al., 1995; Xia et…”
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Genetic Characterization of Albanian Sheep Breeds by Microsatellite Markers
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BackgroundGenetic characterization of Gaddi goat breed of Western Himalayas using microsatellite markers
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Evaluation of Genetic Variability in Kenkatha Cattle by Microsatellite Markers
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Development of a model webserver for breed identification using microsatellite DNA marker
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BackgroundAssociation of microsatellite markers with fiber diameter trait in Peruvian alpacas (Vicugna pacos)
Paredes, M., Membrillo, A., Gutiérrez, J. P., et al. (2013) · Livestock Science · doi:10.1016/j.livsci.2013.12.008 · Cited by 16 · see citing works
“…population sub-structuring, shortage of samples, low levels of polymorphism, the presence of non-amplified alleles (Sun et al., 2012) and the lack of neutrality relative to selection (selection favouring homozygotes) (Maudet et al., 2002), which may also causes a reduction in the heterozygosity.”
BackgroundMOLECULAR APPLICATIONS OF CANDIDATE GENES IN GENETIC IMPROVEMENT PROGRAMS IN LIVESTOCK
Khalil, M. H. (2020) · Egyptian Journal of Animal Production · doi:10.21608/ejap.2020.97954 · Cited by 15 · see citing works
“Among all types of the molecular markers, the microsatellites are used as the most widely used markers for the analysis of genetic diversity and population structure in poultry(Maudet et al., 2002).”
BackgroundAnalysis and Selection of Microsatellites Markers for Individual Traceability System in Hanwoo
임현태 (2005) · Journal of Animal Science and Technology · doi:10.5187/jast.2005.47.4.491 · Cited by 14 · see citing works
Detecting SNP markers discriminating horse breeds by deep learning
Manzoori, S., Farahani, A. H. K., Moradi, M. H., & Kazemi‐Bonchenari, M. (2023) · Scientific Reports · doi:10.1038/s41598-023-38601-z · Cited by 14 · see citing works
“Maudet, et al. 32 found out that, by using 23 microsatellite loci, they could be assigned more than 90% of individuals to their breed.”
MethodResultDistinguishing industrial meat from that of indigenous chickens with molecular markers
Soglia, D., Sacchi, P., Sartore, S., et al. (2017) · Poultry Science · doi:10.3382/ps/pex077 · Cited by 13 · see citing works
“The membership value, Q, of the correctly allocated individuals is not a trivial problem (Maudet et al., 2002; Mateus and RussoAlmeida, 2015).”
BackgroundPhylogenetic relationships of native Turkish cattle breeds using microsatellite markers
Özşensoy, Y., Kurar, E., Doğan, M., Bulut, Z., Nizamlıoğlu, M., Altunok, V., & IŞIK, A. (2019) · TURKISH JOURNAL OF VETERINARY AND ANIMAL SCIENCES · doi:10.3906/vet-1805-10 · Cited by 13 · see citing works
Genetic diversity of native Turkish cattle breeds: Mantel, AMOVA and bottleneck analysis
Özşensoy, Y., & Kurar, E. (2014) · Journal of Advanced Veterinary and Animal Research · doi:10.5455/javar.2014.a21 · Cited by 12 · see citing works
“In another study in France, an important correlation (r=0.70; p=0.012) was recorded between geographic and genetic distance (Maudet et al., 2002).”
InfluentialEndogenous JSRV-like proviruses in domestic cattle: Analysis of sequences and transcripts
Va, M., Morozov, A. V., & Lagaye, S. (2007) · Virology · doi:10.1016/j.virol.2007.05.018 · Cited by 12 · see citing works
MICROSATELLITE MARKERS FOR PEDIGREE VЕRIFICATION IN CATTLE
Adamov, N., Mickov, L., Petkov, V., & Adamov, M. (2011) · Macedonian Journal of Animal Science · doi:10.54865/mjas111009a · Cited by 12 · see citing works
Analysis of genetic diversity in B olivian llama populations using microsatellites
Barreta, J., Gutiérrez‐Gil, B., Iñiguez, V., et al. (2012) · Journal of Animal Breeding and Genetics · doi:10.1111/jbg.12009 · Cited by 11 · see citing works
“In a population, several factors can contribute to identify a lower heterozygosis than expected, including inbreeding, the presence of null alleles and lack of neutrality relative to selection, with selection in favour of homozygotes (Maudet et al. 2002).”
BackgroundMolecular Markers Allow to Remove Introgressed Genetic Background: A Simulation Study
Amador, C., Toro, M. Á., & Fernández, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049409 · Cited by 11 · see citing works
“, disease resistance, adaptation to harsh conditions) not shown in other breeds [15,16].”
BackgroundGenome-wide selection of discriminant SNP markers for breed assignment in indigenous sheep breeds
Moradi, M. H., Farahani, A. H. K., Khodaei‐Motlagh, M., et al. (2020) · Annals of Animal Science · doi:10.2478/aoas-2020-0097 · Cited by 11 · see citing works
Inference of admixture in the endangered Blanca Cacereña bovine breed by microsatellite analyses
Padilla, J. A., Sansinforiano, E., Parejo, J. C., et al. (2008) · Livestock Science · doi:10.1016/j.livsci.2008.09.016 · Cited by 11 · see citing works
Patterns of genetic diversity of local pig populations in the State of Pernambuco, Brazil
da Silva, E. C., Júnior, W. M. D., Ianella, P., et al. (2011) · Revista Brasileira de Zootecnia · doi:10.1590/s1516-35982011000800010 · Cited by 11 · see citing works
“Several factors may have contributed for the low Ho/He ratio in the studied populations, such as inbreeding, population subdivision, presence of null alleles or even the selection in favor of homozygous, which leads to heterozygous losses (Maudet et al., 2002).”
BackgroundAssessment of genetic structure in Mexican charolais herds using microsatellite markers
Sifuentes‐Rincón, A. M., Puentes-Montiel, H., & Parra‐Bracamonte, G. M. (2007) · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) · doi:10.4067/s0717-34582007000400002 · Cited by 11 · see citing works
Gamarra, D., Lopez-Oceja, A., & de Pancorbo, M. M. (2016) · animal · doi:10.1017/s1751731116001063 · Cited by 11 · see citing works
Application of DNA markers in animal industries
Jeon, J. T., Lee, J. H., Kim, K. ‐., et al. (2006) · Australian Journal of Experimental Agriculture · doi:10.1071/ea05191 · Cited by 11 · see citing works
Teneva, A., Todorovska, E., Tyufekchiev, N., et al. (2007) · Biotechnology in Animal Husbandry · doi:10.2298/bah0701227t · Cited by 10 · see citing works
Molecular characterization of camel breeds of Gujarat using microsatellite markers
Patel, A. C., Jisha, T. K., Upadhyay, D., et al. (2015) · Livestock Science · doi:10.1016/j.livsci.2015.10.007 · Cited by 10 · see citing works
“52) (Maudet et al., 2002), buffalo (MNA1⁄45.”
Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes
Gamarra, D., Taniguchi, M., Aldai, N., et al. (2020) · Animals · doi:10.3390/ani10091584 · Cited by 10 · see citing works
“an assignment success between 67% and 100% using 6 to 23 STR data from 4 to 7 cattle breeds [6,44].”
BackgroundMethodKaraket, T., Poompuang, S., Na‐Nakorn, U., et al. (2010) · Aquaculture · doi:10.1016/j.aquaculture.2010.11.042 · Cited by 10 · see citing works
Movahedin, Amirinia, C., Noshary, A., et al. (2010) · AFRICAN JOURNAL OF BIOTECHNOLOGY · Cited by 10 · see citing works
de Oliveira, A. P. F., de Carvalho, J. H., Miretti, M. M., Lara, M. A. C., & Contel, E. P. B. (2012) · Revista Brasileira de Zootecnia · doi:10.1590/s1516-35982012001100003 · Cited by 9 · see citing works
“…of inbreeding within native cattle populations, in line with records in native breeds from Portugal, Spain and France (Beja-Pereira et al., 2003; Maudet et al., 2002), in Romosinuano Creole from Colombia (Barrera et al., 2006), Creole breeds from Argentina and Bolivia (Lirón et al., 2006) and…”
BackgroundSartore, S., Soglia, D., Maione, S., et al. (2014) · Italian Journal of Agronomy · doi:10.4081/ija.2014.605 · Cited by 9 · see citing works
“…et al., 2014), sheep (Bramante et al., 2011; Lasagna et al., 2011), pig (Boitard et al., 2010; Wilkinson et al., 2011; Oh et al., 2014), cattle (Maudet et al., 2002; Moioli et al., 2004; Ciampolini et al., 2006; Orrù et al., 2006; Dalvit et al., 2008; Rodríguez-Ramírez et al., 2011;…”
Utilization of a 17 microsatellites set for bovine traceability in Czech cattle populations.
Putnová, L., Vrtková, I., Šrubařová, P., et al. (2011) · Iranian journal of applied animal science · Cited by 9 · see citing works
Decision making in animal breeding programs and their consequences for animal production
McManus, C., Cobuci, J. A., Neto, J. B., et al. (2011) · Cited by 9 · see citing works
- Authors
- Maudet, C., Luikart, G., & Taberlet, P.
- Corresponding author
- Maudet, C.
- Venue
- Journal of Animal Science
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-04-01
- Volume
- 80
- Issue
- 4
- Pages
- 942-950
- ISSN
- 0021-8812 (ISSN-L)
- 1525-3163
- OpenAlex
- W195462802
- Cited by
- 164
- References
- 0
- Citations by year
- 2025: 1 · 2024: 4 · 2023: 4 · 2022: 3 · 2021: 1 · 2020: 6 · 2019: 8 · 2018: 6 · 2017: 4 · 2016: 6 · 2015: 9 · 2014: 12 · 2013: 10 · 2012: 12
- FWCI
- 1.59
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Animal Science (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- cattle breeds, genetic diversity, breed assignment, microsatellite markers, Tarentaise, Montbéliarde, Limousin, Charolais, Holstein, genetic differentiation, animal traceability, breed relationships
- MeSH terms
- Animals, Breeding, Cattle, Computer Simulation, DNA, Satellite, France, Gene Frequency, Genetic Markers, Genotype, Heterozygote, Genetic Linkage, Mutation, Phylogeny, Polymorphism, Genetic, Genetic Variation, Polymerase Chain Reaction, Microsatellite Repeats
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