Evaluating Evolutionary Divergence with Microsatellites

Paszek, A. A.; Flickinger, Gail H.; Fontanesi, Luca; Beattie, Craig W.; Rohrer, G. A.; Alexander, L. J.; Schook, Lawrence B.

doi:10.1007/pl00006279

Cited by 29 publications

(22 citation statements)

References 28 publications

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“…Since the average number of alleles per locus is sensitive to the sample size and microsatellites used, expected and observed heterozygosity should be preferred for comparisons. The Chinese Erhualian showed higher expected heterozygosity than some published data on pigs (Laval et al, 2000;Kim & Choi, 2002), suggesting higher gene diversity in the Erhualian pigs, which correspondents to the results on the Meishan pigs (Paszek et al, 1998). The observed heterozygosity was higher in other pig breeds (Kim & Choi, 2002;Laval et al, 2000) than in the Chinese breed.…”

Section: Discussionsupporting

confidence: 82%

“…Research efforts in Europe and the USA have been aimed at explaining the mechanisms underlying the high fecundity and lower embryonic mortality of the Meishan pigs (Rothschild & Ruvinsky, 1998). A study carried out in the USA showed that the allelic diversity of the imported Meishan pigs was higher than that of some commercial breeds (Paszek et al, 1998). A PCR-RFLP analysis of calcium-releasechannel (CRC) gene showed that the frequency of the T allele associated with stress susceptibility was zero in Meishan pigs (Knorr et al, 1994).…”

Section: Introductionmentioning

confidence: 99%

“…Paszek et al, 1998;Laval et al, 2000;Kim & Choi, 2002). However, molecular studies on the Erhualian pigs are just beginning (Fan et al, 2002;Jiang et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

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Molecular genetic analysis of the Chinese Erhualian pig breed

Yue¹,

Gl²

2004

SA J. An. Sci.

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The Chinese Erhualian is one of the most prolific pig breeds in the world, but it is in danger of being replaced by other exotic pig breeds because of its slow growth rate and high fat content in the body. To obtain some genetic information for conservation, we analysed the Erhualian pigs by using a PCR-RFLP for the calcium-release-channel (CRC) gene, nine polymorphic microsatellites and the complete mtDNA D-loop sequences, and compared these data with those from other pig breeds from Europe and Asian. The PCR-RFLP analysis of the CRC gene showed that the frequency of the C allele associated with stress resistance was 100% in the Erhualian pigs. Neighbour-Joining trees constructed on the basis of mtDNA D-loop sequences and the microsatellite analysis clearly showed that the Erhualian pigs were located in a separate branch. These data suggest that the Erhualian pigs are different from other breeds. Microsatellite analysis showed that the average allele number (5.3/locus) in the Erhualian pig was intermediate as compared with that (4.8-7.0/locus) in the three European pig breeds. The expected heterozygosity was higher in the Erhualian pig (0.78) than that in these European pig breeds (0.59-0.72), whereas the observed heterozygosity was higher in the European breeds (0.51-0.64) than in the Erhualian pig (0.46). In the Erhualian pig, the fixation index (F IS ) was as high as 0.41. These data suggest a high level of inbreeding and/or subpopulation in the Erhualian pigs. For conservation of the germplasm in the Erhualian pigs, it is necessary to take measures to reduce inbreeding and/or subpopulation.

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Section: Discussionsupporting

confidence: 82%

Section: Introductionmentioning

confidence: 99%

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Molecular genetic analysis of the Chinese Erhualian pig breed

Yue¹,

Gl²

2004

SA J. An. Sci.

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“…This trend was anticipated because the Landrace breed was originally a cross between a native Danish pig and the Large White, whereas the Duroc represents a distinct breed. Results by Paszek et al (1998) and (Lemus-Flores et al, 2001), using linked microsatellites, also showed that Duroc animals were distant from other commercial populations, including the Large White. Among the indigenous populations, F ST and R ST values showed that the Kolbroek was slightly more differentiated from the Namibian and Mozambican populations, compared to differentiation between the latter two populations.…”

Section: Discussionmentioning

confidence: 85%

Microsatellite-based characterization of Southern African domestic pigs (<i>Sus scrofa domestica</i>)

Swart¹,

Kotzé²,

Olivier³

et al. 2010

SA J. An. Sci.

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________________________________________________________________________________ AbstractThis paper details genetic characterization and trends from a microsatellite-based study of genetic diversity on southern African pig populations. A total of 351 pigs from three commercial breeds and three indigenous populations were genotyped at 39 loci. Differences among the levels of genetic diversity in populations correlated well with known population histories. In commercial breeds, heterozygosity was higher in the well established SA Landrace and Large White breeds (0.580 and 0.636) compared to the Duroc breed, established more recently (0.531). In indigenous populations, the highest heterozygosity levels were found in the Mozambican and South African populations (0.692 and 0.634) with a lower value of 0.531 in a smaller Namibian population. A hierarchical division of total genetic diversity revealed a high betweenpopulation component of 17.9%. F ST -and R ST -based analysis confirmed high levels of differentiation, with pair-wise comparisons between breeds indicating significant differentiation in 20 out of 21 comparisons.Results from an assignment test confirmed results from F ST and R ST and suggested a true genetic structure with significant differentiation between most populations sampled, but with little differentiation among the commercial SA Landrace and Large White breeds. The results are discussed with reference to known historical information on commercial and indigenous pig populations. This paper also presents new data on the optimization of microsatellite markers for application in Sus scrofa domestica.

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“…In order to measure the genetic distances between closely related populations like breeds, it is desirable to use highly polymorphic markers such as microsatellites [3,4,9,15,18,24,37,40,53,59,60,70].…”

Section: Introductionmentioning

confidence: 99%

Measuring genetic distances between breeds: use of some distances in various short term evolution models

2002

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-Many works demonstrate the benefits of using highly polymorphic markers such as microsatellites in order to measure the genetic diversity between closely related breeds. But it is sometimes difficult to decide which genetic distance should be used. In this paper we review the behaviour of the main distances encountered in the literature in various divergence models. In the first part, we consider that breeds are populations in which the assumption of equilibrium between drift and mutation is verified. In this case some interesting distances can be expressed as a function of divergence time, t, and therefore can be used to construct phylogenies. Distances based on allele size distribution (such as (δµ) 2 and derived distances), taking a mutation model of microsatellites, the Stepwise Mutation Model, specifically into account, exhibit large variance and therefore should not be used to accurately infer phylogeny of closely related breeds. In the last section, we will consider that breeds are small populations and that the divergence times between them are too small to consider that the observed diversity is due to mutations: divergence is mainly due to genetic drift. Expectation and variance of distances were calculated as a function of the Wright-Malécot inbreeding coefficient, F. Computer simulations performed under this divergence model show that the Reynolds distance [57] is the best method for very closely related breeds. microsatellites / breeds / divergence / mutation / genetic drift

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Evaluating Evolutionary Divergence with Microsatellites

Cited by 29 publications

References 28 publications

Molecular genetic analysis of the Chinese Erhualian pig breed

Molecular genetic analysis of the Chinese Erhualian pig breed

Microsatellite-based characterization of Southern African domestic pigs (<i>Sus scrofa domestica</i>)

Measuring genetic distances between breeds: use of some distances in various short term evolution models

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