Multiple paternity in domestic pigs under equally probable natural matings – a case study in the endangered Gochu Asturcelta pig breed

Menéndez, Juan Antonio Lázaro; Álvarez, Isabel; Roza, B. de la

doi:10.5194/aab-58-217-2015

Cited by 9 publications

(9 citation statements)

References 9 publications

(13 reference statements)

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“…Considering the high mean F of the pedigree analyzed, lower N e values would be likely. However, after a sudden increase of F during the first stages of the breeding programme due to wrong breeding practices including full-sib matings (Menendez et al 2015), the breeding policy avoided matings between close relatives as much as possible ( Figure 2). This led to minimizing the increase in AR and even to a decrease in mean ΔF i in the last few years of pedigree recording.…”

Section: Discussionmentioning

confidence: 99%

Genealogical analysis of the Gochu Asturcelta pig breed: insights for conservation

Menéndez¹,

Álvarez²,

Fernández³

2016

CZECH J ANIM SCI

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ABSTRACT:The Breeders Association of Gochu Asturcelta (ACGA) initiated a recovery programme with six founders (three boars and three sows) in 2002. Information provided by a total of 3156 records (515 litters, 109 boars, and 309 sows) with father and mother known included in the Gochu Asturcelta herdbook was analyzed. The aim of the analyses was to assess if the mating policy implemented by the breeders association ACGA has been successful in preserving the genetic background of the founders in the present population. Two reference populations were defined: 232 individuals born in 2013 and 2014 (PopO), and 18 individuals born in 2012 and 2013 and kept for reproduction (PopR). Mean inbreeding was very high (0.230 ± 0.078 for the whole pedigree) with mean individual increase in inbreeding (ΔF i ) of 0.067 ± 0.021 for PopO and PopR. However, mean ΔF i tended to keep steady values (around 0.07) after 2009. The number of founders identified for PopO and PopR was 4 and 5, respectively. The ratio between the effective number of ancestors (f a ) and effective number of founders (f e ) was roughly 1 for both PopO and PopR. This suggests that the ACGA's mating policy has avoided an extreme bottleneck in the population. However, drift caused noticeable losses of genetic diversity: ratio between the founder genome equivalents (f g ) and f e was around 0.6 for the two reference populations. The current results highlight the need of unbalancing further genetic contributions to the population towards descendants of a very poorly represented founder (Fema 1).

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Section: Discussionmentioning

confidence: 99%

Genealogical analysis of the Gochu Asturcelta pig breed: insights for conservation

Menéndez¹,

Álvarez²,

Fernández³

2016

CZECH J ANIM SCI

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“…A set of 17 microsatellites (IGF1, S0002, S0026, S0071, S0101, S0155, S0225, S0226, S0227, SW240, SW632, SW857, SW911, SW936, SW951, S0005, and S0090) used in paternity testing and diversity analyses (Menéndez et al. , ) were typed in a representative sample of the available individuals. Most microsatellites used were included in the ISAG–FAO panel (http://www-lgc.toulouse.inra.fr/pig/panel/panel2004.htm).…”

Section: Methodsmentioning

confidence: 99%

Assessing performance of single‐sample molecular genetic methods to estimate effective population size: empirical evidence from the endangered Gochu Asturcelta pig breed

Menéndez¹,

Álvarez

Fernández

et al. 2016

Ecology and Evolution

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Estimating effective population size (N e) using linkage disequilibrium (LD) information (N e( LD )) has the operational advantage of using a single sample. However, N e( LD ) estimates assume discrete generations and its performance are constrained by demographic issues. However, such concerns have received little empirical attention so far. The pedigree of the endangered Gochu Asturcelta pig breed includes individuals classified into discrete filial generations and individuals with generations overlap. Up to 780 individuals were typed with a set of 17 microsatellites. Performance of N e( LD ) was compared with N e estimates obtained using genealogical information, molecular coancestry (N e(M)) and a temporal (two‐sample) method (N e( JR )). Molecular‐based estimates of N e exceeded those obtained using pedigree data. Estimates of N e( LD ) for filial generations F3 and F4 (17.0 and 17.3, respectively) were lower and steadier than those obtained using yearly or biannual samplings. N e( LD ) estimated for samples including generations overlap could only be compared with those obtained for the discrete filial generations when sampling span approached a generation interval and demographic correction for bias was applied. Single‐sample N e(M) estimates were lower than their N e( LD ) counterparts. N e(M) estimates are likely to partially reflect the number of founders rather than population size. In any case, estimates of LD and molecular coancestry tend to covary and, therefore, N e(M) and N e( LD ) can hardly be considered independent. Demographically adjusted estimates of N e( JR ) and N e( LD ) took comparable values when: (1) the two samples used for the former were separated by one equivalent to discrete generations in the pedigree and (2) sampling span used for the latter approached a generation interval. Overall, the empirical evidence given in this study suggested that the advantage of using single‐sample methods to obtain molecular‐based estimates of N e is not clear in operational terms. Estimates of N e obtained using methods based in molecular information should be interpreted with caution.

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“…Due to their highly polymorphic nature, the use of microsatellite typing for parentage control and solving the problems of questionable paternity had been advocated in almost all livestock species (Behl et al 2007, Souza et al 2012, Monies et al 2011, Jakhesara et al 2012, Kathiravan et al 2012, Brenig and Schulz 2016. Due to multiple mating nature of sows and so the probability of multiple paternity of the litter makes the use of such unambiguous paternity exclusion methodology absolutely necessary for pigs (Aguilera-Reyes 2006, Menéndez et al 2015.…”

Section: Resultsmentioning

confidence: 99%

Evaluation of 24 microsatellite markers for parentage exclusion in three indigenous pig types of India

Behl

Tantia

et al. 2017

Indian J of Anim Sci

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A set of 24 FAO recommended microsatellite markers was evaluated for parentage exclusion (PE) in three Indian pig types of Assamese, North-Indian and Ankamali. The genomic DNA from these three Indian pig types was amplified at these loci by polymerase chain reaction and resolved for alleles. The allelic frequency data was analysed to calculate the probability of paternity exclusion when one of the parents is to be excluded (PE1), when both the parents are to be excluded (PE2) and when only one parent is known and that is to be excluded (PE3) in these three Indian pig types using a set of minimum 5 loci and then increasing the number of loci in increments of 5 upto maximum of 24 loci. The cumulative PE1 values taking into consideration all the 24 loci varied from 1-2.07×10-10 in North Indian pigs to 1-3.95×10-11 in Ankamali pigs. The cumulative PE2 values taking into consideration all the 24 loci varied from 1-4.57×10-16 in Assamese pigs to 1-3.17×10-18 in Ankamali pigs. Similarly, cumulative PE3 values for all the 24 loci varied from 0.9999968 in Assamese pigs to 0.99999955 in Ankamali pigs. The cumulative PE values obtained, even with a set of 15 loci (CGA, IGF1, S0005, S0026, S0068, S0090, S0155, S0178, S0215, S0218, S0228, S0355, SW122, SW911, SW936), were clearly more than the required value of 0.9995 in all the three breeds with the minimum value of 0.99985 for PE3 in Assamese pigs. Clearly, this set of 15 loci or the sets with 20 or 24 loci can be safely employed for parentage exclusion purposes in the Indian pigs.

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Multiple paternity in domestic pigs under equally probable natural matings – a case study in the endangered Gochu Asturcelta pig breed

Cited by 9 publications

References 9 publications

Genealogical analysis of the Gochu Asturcelta pig breed: insights for conservation

Genealogical analysis of the Gochu Asturcelta pig breed: insights for conservation

Assessing performance of single‐sample molecular genetic methods to estimate effective population size: empirical evidence from the endangered Gochu Asturcelta pig breed

Evaluation of 24 microsatellite markers for parentage exclusion in three indigenous pig types of India

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