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Hannah Santos
October 31, 2013
Biology 303H
Dr. Bert Ely
Loss of Genetic Diversity in the Sorraia Horse Breed
Genetic diversity is very significant for the survival of many species. A lack of
genetic diversity can be problematic when the current genetic viability of a species is no
longer supported by the conditions of the environment; in other words, the species will
lack the ability to adjust to new conditions. However, a lack of genetic diversity can
reinforce the genetic viability if the current conditions remain the same. This lack of
genetic diversity is usually the case in the selective breeding of domesticated animals.
Although, the main goal is to maximize genetic viability, a breeding program must be
able to eliminate all the detrimental versions of a gene by first maintaining a high level of
genetic diversity and while doing so, having a low level of inbreeding within the animal
population (Vozzi et al. 2007). Inbreeding can lead to the loss of founder alleles, the
alleles that the breed begins with, which is the case for the research conducted by
Pinheiro, Kjollerström, and Oom on the Sorraia horse breed. By analyzing the genetic
variability and the demographic structure of the breed, a future plan can be developed for
the conservation of the Sorraia horse.
The Sorraia horse breed is native to Portugal and has the ability to survive in
harsh conditions. It is best known for its primitive markings specifically the yellow or
mouse markings, black dorsal stripe, and zebra marks (Pinheiro et al. 2013). However,
this breed of horse is considered critical-maintained and there are approximately 280
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horses left worldwide (Pinheiro et al. 2013). With such a small population size, this breed
shows low levels of genetic diversity and high levels of inbreeding, which in this case, is
detrimental to the genetic viability of the breed. One reason for the inbreeding is that the
Sorraia horse breed began in 1937 with 10 founders and although an additional 3 horses
were introduced in later years, the low level of genetic input limited the genetic diversity
of this breed (Luís et al. 2007).
For the researched conducted by Pinheiro and his group, the complete pedigree
(lineage of the breed) was analyzed in order to determine the genetic variability and
demographic structure of the Sorraia horse breed. This dataset includes 653 registered
horses since the breed foundation in 1937 until 2006 (Pinheiro et al. 2013). The
demographic parameters used to calculate the completeness of the pedigree included the
generation intervals, the average age of parents when they had offspring, maximum
number of generations and the genetic importance of the male horses. In addition to the
demographic parameters, the genetic parameters used to determine the genetic diversity
included the following: the effective number of founders (fe) and their contribution to
genetic diversity to the descendant population, the inbreeding coefficient (the probability
for an individual to have two genes identical by descent), and the average relatedness
coefficient which is the probability of an allele to be randomly chosen from the entire
population and belonging to a specific animal (Pinheiro et al. 2013). Furthermore, the
pedigree analysis can be checked for consistency with the microsatellite analysis of the
horse breed conducted by Luîs, Cothran, and Oom in 2007.
Generation length is an important factor in the rate of genetic progress and
conservation (Pinheiro et al. 2013). Normally horses have generation lengths between 9
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and 11 years; however, the long generation length depends on the management of the
breed (Valera et al. 2005). In the demographic analysis, the generation average length
was found to be 7.94 years (Pinheiro et al. 2013). As shown in Table 1 below, the
generation length is considerably lower than average.
Table 1: Generation Intervals and Average Age of Parents
Pathways
Generation interval
Average age
N
Years
N
Years
Sire–son
55
7.65
310
8.27
Sire–daughter
168
7.28
330
7.73
Dam–son
55
8.61
310
9.02
Dam–daughter
168
8.48
330
8.57
Average
7.94
8.39
The generation interval and average age for each of the parent-offspring pathway of the
Sorraia horse breed.
Additionally, the Sorraia breed shows shorter generation length for the sires (male
horses) than the dam (female horses) as shown in Table 1. In other words, the dams are
kept longer for reproduction, while sires are replaced more frequently. From this, it can
be concluded that the management of the breed has a short recreational use and an early
reproductive life, especially for male horses. In the Andalusian horse pedigree (an older
breed native to both Portugal and Spain), the generation average length was found to be
10.11 years (11.50 for Carthusian strain), which is significantly higher than the Sorraia as
shown in Table 2 below (Valera et al. 2005).
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Table 2: Generation Intervals of Andalusian Breed and Carthusian Strain
Pathway
Whole pedigree
Carthusians
N
Years
N
Years
Stallion–son
5474
10.39
640
11.99
Stallion–daughter
15,862
10.36
1,457
11.24
Mare–son
5477
9.99
634
11.35
Mare–daughter
15,830
9.80
1470
11.62
Average
10.11
11.50
The generation intervals for the Andalusian horse breed and for the Carthusian strain. As
shown, the Carthusian strain has a higher generation interval than the breed as a whole.
Breeders for the Andalusian horses spend a longer time to selecting a descendant for
breeding; therefore, the loss of genetic diversity is generally less than the Sorraia horse
breed. Lastly, regular substitution of the horses for breeding helps minimize loss of
genetic diversity as well.
Despite the Carthusian strain having a longer generation interval, the Carthusian
strain has a higher average inbreeding coefficient of 9.08% compared to the entire
Andalusian horse population of 8.48% (Valera et al. 2005). The Carthusian strain is most
preferable for reproduction by breeder. As a result, the Carthusian strain has higher levels
of inbreeding. As shown in Figure 1 below, the Carthusian strain has a lower percentage
of horses used for breeding compared to the entire horse population.
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Figure 1: Percent of Horses Used for Reproduction
The percent of horses used for breeding for the whole Andalusian breed compared to the
Carthusian strain. The solid white bars represent the Carthusian strain.
The higher average inbreeding coefficient for the Carthusian Strain compared to the
Andalusian breed is also a result of the unbalance and selection of horses used for
breeding. In order to increase the genetic variability of the Carthusian strain, there has to
be wider selection of horses used for reproduction. The same proposal for the Carthusian
strain can be applied to the Sorraia breed in order to increase genetic diversity.
In the genetic analysis, the effective number of founders was found to be 7.46 for
the entire population of the Sorraia horse breed; nearly half of the 13 founders (Pinheiro
et al. 2013). Based on this knowledge, loss of initial genetic variability is observed due to
unequal amount of genetic information contributed from each founder as shown in Figure
2 below.
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Figure 2: Genetic Contribution of the Founders of the Sorraia Horse
The genetic contribution of each of the founders for the current Sorraia population.
Ideally, the genetic contribution for each founder should be equal in order to maintain
genetic diversity in the population. Yet, 52.9% of genetic variability was contributed by
three founders: Gaivota, Baio, and Cunhal (Pinheiro et al. 2013). Furthermore, as shown
in Figure 1, three of the founders (Vigilante, Freire, and Anselma) are all under 0.5% and
are no longer represented in the current population; the alleles of these three founders are
lost in the genetic pool. Despite the fact that the effective number of founders is nearly
half of the actual number, this ratio is quite high compared to that of other horse species.
For example, the Andalusian horse breed has an fe of 39.6 even though the initial number
of founders estimated to be between 1000-2000 and the studbook for this breed has
75,389 individuals (Valera et al. 2005). Overall, the success of the breed depends on the
viability of the breed despite the large loss of genetic diversity.
The values of inbreeding for the Sorraia horse breed were found to be extremely
high with an average inbreeding coefficient to be 26.99% (Pinheiro et al. 2013). After
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five years since the foundation of the horse breed in 1937, inbred animals began to appear
in 1942 with a linear increase since then as shown in Figure 3.
Figure 3: Average Values of Inbreeding and Relatedness of the Sorraia Breed
This graph shows a linear increase for both average values of inbreeding and relatedness
(AR) since the beginning of Sorraia horse breed.
The early inbreeding of the Sorraia horse breed is a result of having very few founders, a
reduced population size, lack of introduction of new alleles, and poor breeding
management. Overall, the inbreeding in this case is detrimental to the viability of the
breed. When inbreeding arises, harmful recessive genes can begin to appear; in this
research, inbreeding inhibits the reproduction performance and juvenile survival of the
Sorraia horse breed (Luís et al. 2007). In an earlier research study conducted by Luís,
Conthran, and Oom, heterozygosity was used to determine the fitness and the inbreeding
level of the Sorraia breed. As shown in Figure 4 below, there was significant negative
correlation between inbreeding coefficient and heterozygosity (Luís et al. 2007).
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Figure 4: Comparison of Heterozygosity and Inbreeding Coefficient
124 Sorraia horses were typed for up to 22 loci and the correlation between
heterozygosity and inbreeding coefficient was r=-0.268, p<0.005 (Luís et al. 2007).
It can be clearly seen from Figure 3 that individual heterozygosity is considerably low
within the population, which complements the high average inbreeding coefficient of the
breed found by Pinheiro and his team. Overall, inbreeding levels of the Sorraia horse
breed needs to be reduced in order to increase the fitness of the breed; in order to do so, a
possible plan is for each generation to choose the fittest horse to be used for each
breeding year. Doing so would increase the genetic viability of the breed and reduce the
risk of inbreeding within the population.
Overall, in the artificial selection of domesticated animals, the main focuses in
these programs must be on minimizing inbreeding and conserving the genetic diversity of
the species. By following such goals, breeders will be able to remove harmful alleles
from the gene pool and select for the most optimal versions of the genes. Ideally, if all the
harmful alleles were to be removed from the gene pool, genetic diversity would no longer
be needed (as long as the environmental conditions remain the same) and inbreeding
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would help reinforce the genetic viability of the population. For the Sorraia horse breed,
genetic diversity has to be preserved in such a small population and the individual
heterozygosity needs to be increased. Lastly, individual heterozygosity provides a more
effective measurement than evaluating a population by its inbreeding coefficient if the
population is small. We can use individual heterozygosity as a method for selecting
certain horses for breeding and effectively conserve and/or maximize the genetic
diversity of the breed.
Work Cited
1. Luís C, Conthran E.G, Oom M. 2007. Inbreeding and Genetic Structure in the
Endangered Sorraia Horse Breed: Implications for its Conservation and
Management. Journal of Heredity 98: 232-237.
<http://jhered.oxfordjournals.org.pallas2.tcl.sc.edu/content/98/3/232.full>
2. Mokhtari M.S., Shahrbabak M, Esmailizadeh A, Abdollahi-Arpanahi R,
Guitierrez J.P. 2013. Genetic diversity in Kermani sheep assessed from pedigree
analysis. 2013. Small Ruminant Research 114: 202-205. <
http://www.sciencedirect.com.pallas2.tcl.sc.edu/science/article/pii/S09214488130
02265?np=y#bbib0090>
3. Pinheiro M, Kjöllerström H.J, Oom M. 2013. Genetic diversity and demographic
structure of the endangered Sorraia horse breed assessed through pedigree
analysis. Livestock Science 152: 1-10
http://www.sciencedirect.com.pallas2.tcl.sc.edu/science/article/pii/S18711413120
04386
4. Valera M, Molina A, Gutiérrez J.P, Gómez J, Goyache F. 2005. Pedigree analysis
in the Andalusian horse: population structure, genetic variability and influence of
the Carthusian strain. Livestock Production Science 95: 57-66. <
http://www.sciencedirect.com.pallas2.tcl.sc.edu/science/article/pii/S03016226040
02854?np=y>