Tuesday, 22 April 2014

Basics on animal genetic resources

Farm animal genetic resources, or simply AGR, refers to the genetic material we currently have in live animals and frozen in sperm banks, and which is of economical, cultural and scientific importance. Genetic diversity, both within and between breeds, is vital. Diversity
  • helps the animals to adapt to their environment
  • is the basis for animal breeding
  • allows adaptation to changes and new breeding targets
  • prevents inbreeding depression
  • keeps the frequency of harmful allelels low.
Domestication has already reduced genetic diversity in farm animal species (and artifical insemination has reduced it even further). Domestication is the process by which captive animals adapt to man and the environment provided, and it is achieved through genetic changes. Genetic factors affecting domestication are inbreeding, genetic drift and selection.  

Impact of domestication on milk yield of dairy cows.
Inbreeding is necessary when selecting a desired trait, but it reduces heterozygosity and thus diversity, although it does not affect allele frequencies. Genetic drift causes alleles to become fixed or deleted randomly, and its direction cannot be estimated. Selection, both natural and artificial, has altered the fitness of certain traits. For example, in domestication species the distance to flee and fearfulness have been decreased, even though they are vital for a wild animal. These are both behavioral changes. Physiological changes involve changes in hormone levels, reproduction cycle and production traits (e.g. the increased milk yield of cows and the all-year farrowing of sows). Morphological changes have also occurred, as animals have grown larger and developed colors unseen in the wild (especially white). For an example of scientific study on domestication, see Giuffra et. al (2000) or Kantanen et al. (1999).

Studying domestication

Domestication can be studied in several methods. Paternal transmission of Y-chromosome shows traits have developed from sire to offspring. It's counterpart is the study of mtDNA (mitochondrial DNA), which is always inherited from the dam to all her offspring. mtDNA haplotypes are sequenced and aligned, and dendrograms or cladograms are drawn based on the multiple-sequence-alignment (MSA) results. The haplotypes can be further divided into groups, which helps to draw a network. For more information visit the blog The Genealogical World of Phylogenetic Networks and their post on interpreting rooted networks.

The most common method by far is still studying microsatellite markers. Usually 20-30 microsatellites are studied, but FAO has published recommendations for each animal species (FAO). Polymorphic loci with 4 or more alleles are recommended to eliminate false positives by identical-by-state -alleles. Unlike mtDNA and Y-chromosome, microsatellites are inherited from both parents to all offspring. Genotyping and aligning SNP-markers is similar to microsatellies, but requires the use of thousands or hundreds of thousands of SNP-markers. Microchip arrays are readily available for several species for SNP-analysis.

Practical application of genetic domestication studies.
(c) ILRI 2006

Studying ancestral DNA is tedious, but can yield valuable information on extinct species. Ancestral DNA can be thousands or tens of thousands of years old. It is collected either from animal remains such as fossils, teeth, wools, hides or bone pieces, or from the ground ("dirty DNA"). Ancestral DNA also helps to chart the spread of different animal and plant species and to determine temporal changes in their genetics. The problem with ancestral DNA is that the concentration of desired DNA is often low, while the concentration of microbial DNA is high. Contamination risk is very high indeed. Sterile environment must be maintained whenever possible when working with ancestral DNA. Another problem is that the ancestral DNA has been fragmented, and many chemical bonds have been broken. C > T and G > A mutations in PCR are common due to deamination. The results must be confirmed in several independent laboratories. In addition, all results derived from ancestral DNA must fit in to earlier context.

Retroviruses have been used as a study method on sheep. Retroviruses are viruses, which insert their RNA to the sheep's system, and with reverse-transcriptase produce DNA from the RNA. The viral DNA is then integrated as a part of the sheep's own genome. The viral DNAs which have infected germline cells are hereditary, and thus provide a tool for studying the evolution of sheep. The original virus infections happened 5-7 million years ago, and have continued to branch even during the last 10 000 years. Studies of retrovirus-DNA has shown that originally all sheep in Europe were used for meat production. A meat-and-wool producing breed was introduced later,  and replaced the old breed nearly completely. Still existing breeds originating from the first migration are Soay sheep, Gutesheep and Finnsheep.  

Determining the level of endangerment and the value of a breed

There are thousands of animal breeds in the world. FAO's DAD-IS -information system classifies breeds into four categories:
  • local breeds, which exists in one country or area only
  • transboundary breeds, which exists in several countries
  • regional transboundary breeds, which exists in several countries but only in one continent
  • international transboundary breeds, which exists in many continents.
Each breed is also classified based on the level of endangerment. There are five levels, which are determined by the population size and number of breeding males and females. Other classification systems also consider the direction of population size (growing or decreasing), the purity of the species and the number of populations (e.g. herds). FAO's five levels are
  1. Extinct
  2. Critical (with or without a conservation program)
  3. Endangered
  4. Not at risk
  5. No information on the population size.
Currently DAD-IS lists (among others) 3093 cattle breeds, 2558 chicken breeds/lines and 1283 pig breeds. Altogether there are 14544 breeds listed for 38 animal species. Of the listed local cattle breeds, 181 are extinct (209 in 2006) and only 399 are not at risk. For pigs there are 110 extinct breeds (140 in 2006) and 206 not at risk. The numbers from the year 2006 are larger, probably due to renewal of the concept of breed or improved methods of separating breeds and collecting information. Below are a few examples of the tables created from DAD-IS system, showing the status of cattle, pig and sheep breeds in different regions.

The level of endangerment is the likelihood of the breed going extinct in the current circumstances within a certain time period. It can be used to estimate how much there is time to save a breed. The level depends on demographic factors (population size and its changes) and genetic variation. Genetic variation is calculated from effective population size Ne, which again is deduced from the change of inbreeding (Ne = 1/2 ΔF). Growth factor can be calculated from r = anti-log (( logN2–logN1) / t ), where N1 and N2 are the population size at two different measurements (generation 1 and 1+n), and t is time in years. The growth factor depends on animal births and deaths, cullings, changes in market prices and agricultural politics and on epidemics.

Method of estimation impacts the value of  ΔF. Pedigree-based studies give consistently lower estimated of ΔF than SNP-based evaluation. In one study, pedigree analysis found that 15 % of animals had F > 6.25 %, while in an SNP-study the percentage was 25 %. For pairwise kinship coefficients both methods are equally reliable for close relatives. For more distant relatives the pedigree analysis gives higher estimates than SNP-analysis. (Li et al. 2011)

However, Ne, ΔF and the growth factor are only single meters. To estimate the value of a breed for genetic conservation requires a more holistic approach. In addition to the meters mentioned before, the breed value depends on several factors. The factors, and examples related to them, are listed below.
  •  its ability to adapt to a certain environment (Yakutian cattle, goat breeds in arid African countries)
  • economically important traits (the excellent cheese-making qualities of the milk of Finncattle)
  • unique traits (breed-specific mutations, alleles and gene combinations)
  • cultural heritage, historical value (Yakutian cattle)
  • unique genetics.
One must remember that the breed must be able to cope even in the future, and to continue being useful for the herders. It is not a viable option to maintain breeds which cannot survive for example after global warming or if their surroundings change due to industrialization. 

Yakutian cattle (c) EPFL / Anu Osva

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