I marcatori microsatelliti per l'indagine di popolazioni animali antiche e moderne
Author(s)
Gargani, Maria
Date Issued
July 7, 2010
Type
Doctoral Thesis
Abstract
The aim of this study was to apply microsatellite markers to two different studies. The first
concerned the analysis of the genetic structure of six water buffalo populations from Turkey
(Anatolian water buffalo). This is the first study in these populations that need special attention because 1) the proximity of Turkey to the center of domestication and possible spread of species to Italy, and 2) the drastic decrease in the number of individuals that occurred in recent decades.
Anatolian water buffalo greatly contributes to agriculture economy through milk, meat and draught
power. Although the number of Anatolian buffalo has decreased from 1,117,000 to 110,000 head
over the past three decades, farming of this species has survived in order to promote productive system in agreement with sustainable rural development.
In the present study, microsatellite markers were used to analyse the relationships among six
Turkish water buffalo populations. One hundred and fifty-four animals were sampled in six
different Turkish districts belonging to four regions that represent the most important sites of water buffalo breeding. We chose 26 bovine heterologous microsatellites primers listed in the BOVMAP database and recommended by FAO for diversity studies in cattle. The six populations analyzed showed a moderate level of genetic variability, mainly due to variations within populations. In 44 locus–population combinations, we found a deviation from Hardy-Weinberg due to a
heterozygosity deficit.
Some factors, such as inbreeding and occurrence of population substructure (Wahlund effect), could
be the reasons for heterozygote deficiency in populations. We hypothesize that inbreeding is the
most likely cause. The values of the coefficient of inbreeding in fact was positive and significant, in particular, the Merzifon population showed the highest value of FIS.
The Principal Coordinates Analysis (PCA) and the Bayesian clustering approach revealed a high
differentiation of Merzifon and Danamandira populations. In the Merzifon district, the buffalo
population size is shrinking and the breeding territory is now confined to a small area. This could have caused a reduction in breeding animals, which led to an increase of inbreeding as previously shown by FIS. In the Danamandira population, belonging to Istanbul province, husbandry is very popular and most of the farmers rear few heads for family consumption. The other populations represented one single cluster. In particular Coskun individuals were not assigned to a unique group but were distributed with most of the other buffalo populations. This could reflect the heterogeneity of the breeding stock, which is probably because of farmers buying animals from other regions.
These preliminary results could be useful for developing conservation strategies for the Turkish
buffalo, which represents an important resource for small villages that are far away from the big
cities. In particular, the Merzifon population deserves special attention to prevent further increases in population inbreeding.
The second study concerned the identification of suitable microsatellites that can be used in ancient livestock remains. The study of ancient DNA could allow to interpret the population structure of ancient animal populations, including their demography, geographical origin, migration and the similarity to modern breeds. Furthermore, allele scoring can help archaeozoologists, often collecting
more remains in the same excavation site, in attributing remains to specific individuals and to
obtain information on the populations the remains belong to. The majority of studies conducted on
ancient populations at molecular level mostly concerned mitochondrial DNA (mtDNA). mtDNA is
present in cells in hundreds of copies, therefore it is easier to analyse as it is preserved, though
damaged, after hundreds of thousands of years. However, nuclear marker like microsatelliteas are
more informative than mtDNA because of higher polymorphism level. In this study we selected
from FAO list a total of 15 microsatellites for which we redesigned, on the basis of the reference
sequences, specific primers able to amplify fragments shorter than the original ones. Microsatellite loci were analyzed on medieval cattle bones from Ferento, an archaeological site near Viterbo, central Italy. Two important results need to be mentioned:
1) It was possible to extract DNA from all 13 samples
2) Among the 15 microsatellites tested, 5 loci amplified successfully in our samples.
Furthermore we compared the microsatellite data obtained from this study with those for 72 cattle
breeds modern. Ferento population showed a reduced level of variability compared to modern
breeds, as demonstrated by heterozygosity values and the average number of alleles. Ancient cattle
showed a surprising level of homozygosity probably due to inbreeding. This could reflect a
condition in which the livestock trade was very low, as well as the number of animals for breeding.
Alternatively we could hypothesized that inbreeding was wanted to retain specific characteristics of animals arrived at the place by chance (e.g. following up invading armies)
The second hypothesis could also be suggested by the likelihood values which showed that some
remains were close to foreign breeds (German, Dutch and British).
The positive results obtained demonstrated the feasibility of using microsatellites for the study of ancient cattle which could be very powerful given the existence of a large database containing genotypes from widely sampled extant cattle.
Additional information
Dottorato di ricerca in Ecologia e gestione delle risorse biologiche
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