A highly polymorphic horse microsatellite locus: VHL20

AbSTRAcT. The genetic variability for a sample of 227 animals from three populations of Pantaneiro horses was estimated using data from 10 microsatellite loci. The number of alleles and the proportion of heterozygosity indicated high variability. A total of 91 alleles were found, with a significantly high mean number of alleles. The mean polymorphic information content was 0.7 and the paternity exclusion probability was 99.3%. The inbreeding coefficient (F IS ) was low for the three populations: Ipiranga (F IS = 0.147), Nova Esperança (F IS = 0.094) and Promissão (F IS = 0.108). Genetic differentiation among all three populations was low (F ST = 0.008 to 0.064). Three methods were used to test for a recent bottleneck effect. The graphical method and the Wilcoxon test using the stepwise mutation model showed no bottleneck pattern for any of the populations. The test by two-phase mutation model showed genetic signatures of bottleneck for Ipiranga and Promissão. When we consider standard deviation value for Nova Esperança, the M-statistic detected a bottleneck pattern, but this result could be explained by a sample size effect. Therefore, there is no immediate cause for concern regarding loss of variation within the breed.

Section: Microsatellitesmentioning

confidence: 99%

Genetic diversity in the Pantaneiro horse breed assessed using microsatellite DNA markers

Giacomoni¹,

Fernández²,

Freitas³

2008

“…PCR mixtures were prepared with 5.0 µL Phusion Flash Master Mix Enzyme, 1.0 µL ultrapure water, 3.0 µL primer mix, and 1.0 µL extracted DNA. The genotyping panel consisted of 14 microsatellite markers: AHT4 and AHT5 (Binns et al, 1995), ASB2 and ASB17 (Breen et al, 1997), HTG4 and HTG6 (Ellegren et al, 1992), HMS3, HMS6, and HMS7 (Guérin et al, 1994), ASB23 (Irvin et al, 1998), HTG7 and HTG10 (Marklund et al, 1994), LEX33 (Coogle et al, 1996) and VHL20 (van Haeringen et al, 1994). Three multiplex panels were used for PCR: one with an annealing temperature of 60°C (AHT4, AHT5, ASB17, ASB23, HMS6, HMS7, HTG4, and VHL20), one with an anealing temperature of 56°C (ASB2, HMS3, and HTG10), and one with an annealing temperature of 60°C (LEX33, HTG6, and HTG7).…”

Section: Methodsmentioning

confidence: 99%

Genetic relationship between the Nordestino horse and national and international horse breeds

Pires

Coelho

Melo³

et al. 2016

ABSTRACT. Knowledge of genetic diversity and relationships between breeds is very important for conservation programs. Hair samples were collected from 393 individual Nordestino horses and genotyped using 14 microsatellite markers in order to investigate the genetic relationship between this breed and 66 international horse breeds. There was high allelic diversity and inbreeding coefficient within population values were not significant, which was probably due to crossbreeding. Despite the Nordestino horse population being in Hardy-Weinberg equilibrium, a global deficit of heterozygotes was observed. This may represent evidence of repeated use of the same stallions for breeding, which is consistent with the high number of castrated males found. Campolina, Mangalarga Marchador, and Mangalarga were the Brazilian horse breeds most closely related to the Nordestino horse, which is a reflection of recent introgressions. Among Iberian horse breeds, the Sorraia breed appears to have had an important influence on the genetics of the Nordestino horse. Those results provide important information that can guide future conservation programs.

“…The microsatellite loci tested were ASB3 (Breen et al, 1997), ECMPZ001 (Breen et al, 1994), LEX014, LEX017 and LEX019 (Coogle et al, 1996a), LEX031 (Coogle et al, 1996b), SGCV23 (Godard et al, 1997), TKY321 (Tozaki et al, 2001), VHL20 (van Haeringen et al, 1994), and VIASH39 (Ewen and Matthews, 1994).…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity and population structure in Brazilian Mangalarga Marchador horses

DeAssis¹,

DeLaat²,

Peixoto³

et al. 2009

ABSTRACT. One hundred and fifteen unrelated Mangalarga Marchador horses were sampled from three geographically distinct regions of Minas Gerais State, Brazil (South, Southeast, and Northeast) and tested for 10 microsatellite loci. Genetic diversity and population structure parameters were estimated with ARLEQUIN 3.0, CERVUS 2.0, POPGENE 1.31, GENEPOP on the web, STRUCTURE 2.0, and SPAGEDI 1.2 software packages. Under Hardy-Weinberg assumptions, seven markers were at equilibrium (LEX014, LEX017, LEX019, SGCV23, TKY321, VHL20, and VIASH39), while two (ASB3 and LEX031) presented significant homozygote excess. Seventy-four alleles were identified in these nine markers, with a mean of 8.22 alleles. Mean heterozygosity was 0.637 and polymorphism information content was 0.662. Markers ASB3, LEX019, SGCV23, TKY321, and VHL20 were highly informative (PIC >0.7) and may be useful for eventual expansion of parentage test panels. The F ST value (0.0562) indicated relatively little geographical structure. However, based on a Bayesian-based cluster analysis under a three-cluster model, 94% of the 115 individuals were correctly assigned to the subpopulations from where they were sampled. Mean pairwise f was relatively high (0.11), and in spite of the efforts towards non-consanguineous sampling, 1% of the pairs of individuals shared over 50% of the alleles. These results strongly suggest that the population is genetically structured. Under a conservation genetics approach, two strategies are recommended: avoidance of crosses between highly endogamic individuals and stimulation of crosses between individuals from those regions for which low genetic flow was identified.