Genetic markers offer some important applications in animal breeding. The first is parentage control. It is based on the fact that a sire and a dam pass one of the two alleles of a genetic marker to its offspring. Thus, from the two alleles you establish in a son or daughter, one should be present in the sire and one in the dam (see example).
Mistakes in pedigrees may be caused by interchanges of parents (or semen) at mating, unnoticed matings, interchange of young animals shortly after birth or administrative mistakes. From experiences in parentage control it is known that 2 – 10 per cent of the animals have a wrong pedigree. In breeding programs with high costs, parentage control is highly recommended, especially when animals are kept in large numbers in a breeding unit, where mistakes easily may pop up.
Example: parentage control with 18 microsatellites in dogs (source: “Het fokken van rashonden”, Kor Oldenbroek and Jack Windig, Raad van Beheer op Kynologsich gebied in Nederland) .
Two female dogs named Marjolein and Martha are born on the same day in the same kennel. The kennel owner considered Marjolein to be the daughter of the female dog Lianne and the male dog Boris. In his view Martha has as parents the female dog Lieneke and the male dog Bart. The two males, Borus and Bart, are owned by a neighbouring breeder. Lianne was mated to Boris on the same day that Lieneke was mated to Bart. As usual, before printing the official pedigree, parentage control with 18 micro-satellite markers was carried out to verify the pedigree.
...
Microsatellite
...
Marjolein
...
Lianne
...
Borus
...
Martha
...
Lieneke
...
Bart
...
1 AHT 121
...
102/102
...
102/102
...
97/102
...
97/102
...
97/102
...
102/102
...
2 AHT 137
...
149/151
...
147/151
...
128/147
...
147/149
...
149/151
...
149/151
...
3 AHTH 171
...
219/225
...
219/225
...
212/233
...
227/233
...
227/229
...
219/219
...
4 AHTH 260
...
254/252
...
254/246
...
252/250
...
252/244
...
244/244
...
252/244
...
5 AHTK 211
...
93/93
...
93/95
...
91/95
...
91/93
...
93/93
...
93/97
...
6 AHTK 253
...
284/288
...
288/290
...
288/288
...
288/288
...
286/288
...
284/288
...
7 CXX 279
...
126/126
...
126/128
...
124/128
...
124/128
...
126/128
...
124/126
...
8 FH 2054
...
152/152
...
152/164
...
152/156
...
156/160
...
152/160
...
152/156
...
9 FH 2848
...
230/234
...
234/234
...
230/230
...
230/230
...
230/230
...
230/234
...
10 INRA 21
...
97/101
...
97/101
...
95/101
...
95/101
...
95/97
...
95/101
...
11 INU 005
...
126/126
...
126/126
...
126/128
...
132/128
...
132/126
...
130/126
...
12 INU 030
...
144/144
...
144/150
...
144/144
...
144/144
...
144/150
...
144/144
...
13 INU 055
...
210/214
...
210/218
...
210/212
...
210/216
...
212/216
...
214/216
...
14REN162C04
...
202/204
...
200/202
...
200/204
...
202/204
...
200/202
...
200/204
...
15REN169D01
...
212/218
...
212/212
...
218/218
...
214/218
...
214/218
...
216/218
...
16REN169O18
...
162/164
...
162/162
...
164/170
...
164/170
...
164/168
...
164/168
...
17 247M23
...
268/268
...
268/270
...
268/272
...
268/268
...
268/274
...
268/274
...
18 54P11
...
226/226
...
226/236
...
226/232
...
226/226
...
226/232
...
226/234
Marjolein has for microsatillite 1 (AHT 121) allele 102 in twofold. This allele is present in Lianne as well in Borus. For microsatellite 2 (AHT 137) Marjolein has the alleles 149 and 151. Allele 151 can be traced back to her dam Lianne, but her sire Borus (and her dam Lianne!) does not have allele 149! For microsatellite 3 (AHTH 171) Marjolein has the alleles 219 en 225, similar as her dam Lianne, but her sire Borus has the alleles 212 and 233. When you continue to check in this way all alleles for the 18 microsatellites present in the six animals, you can conclude that Borus cannot be the sire of Marjolein on base of the microsatellites 2, 3, 5, 6, 7, 13. On base of the alleles of Bart for the 18 microsatellites it may be very reasonable that Bart is the sire of Marjolein.
Considering the alleles of Martha and Lieneke you can conclude that it may be very reasonable that they are daughter and dam. But Bart cannot be the sire of Martha based on the alleles for the microsatellites 2, 3, 5, 11, 13 and 16.
A comparison of the alleles of Marjolein with the alleles of Lianne and of Bart indicate that Marjolein may be born out of a mating of Lianne and Bart and that Martha is born out of a mating of Lieneke and Boris. Apparently, something has been going wrong during the matingsThis marker consists of a repeat in sequence of a few (2 or 3) bases. For example, the sequence of the bases T and A can result in a TATATATA, which is a four times repeat of TA. Microsatellite markers (micros) generally have 8 to 30 or even up to 40 repeats. They are also called tandem repeats. Each different number of repeats is considered an allele of the micro. Micros can have very many alleles and are, therefore, useful to describe genetic differences between animals (and homologous chromosomes). There are very large numbers (thousands) of micros available in many domestic animal species. In theory, these micros would be ideal for most of the purposes that genetic markers are used for.
However, it takes a lot of time and effort to genotype animals for many different micros. The reason is that the alleles of these markers differ in length and that is how they are genotyped: identify differences in length. Each micro has a distinct start and end code and based on that the part of the DNA is identified with specific primers that find those distinct bits of DNA on the genome. So for each different micro, different primers are required and a new analysis needs to be performed.
For large-scale genotyping single nucleotide polymorphism (SNP) markers are developed and much easier to automate for large-scale genotyping.