Haplotypes: What are they?
A haplotype is a segment of the DNA that is inherited together from a single parent. Each animal carries two copies of a haplotype segment, one inherited from the dam and another from the sire. The individual is said to be homozygous for a gene or haplotype when both inherited DNA segments or alleles have the same genotype and heterozygous when the two copies have different genotypes.
The figure on the left shows an example of a sire and a dam that are both heterozygous polled which means they have an allele for the polled trait and an allele for the horned trait. You can see that if these animals are mated, they have a 25% chance of producing a homozygous polled progeny, 50% chance of producing a heterozygous polled progeny, and a 25% chance of producing a homozygous horned progeny.
Haplotype vs Genetic Marker
DNA is inherited from parents to progeny in segments which are called haplotypes. These haplotypes are not constant in size or number in the population and change over time.
we can find a marker or gene test to pinpoint the actual genetic variant within a haplotype that we are interested in. Once these markers (SNPs) are identified, they would be in a complete linkage with the causal mutation, as such more accurate in comparison to a haplotype genomic test where the association of a segment of DNA with the actual genetic variant might change over generations.
Inheritance of Haplotypes
Most genetic disorders are related to recessive trait expression patterns. A recessive trait is a trait that is only expressed in progeny when inherited from both parents. Disorders will be manifested only in homozygous individuals as it is required for an animal to have two copies of a gene with a specific genotype. Individuals carrying one single copy of the recessive genotype will not manifest the phenotype, but as a carrier, has a 50% of chance of transmitting the recessive copy to its progeny, spreading the undesirable gene among the herd.
Holstein:
Embryonic Haplotypes
Embryonic Haplotypes exclusive to the holstein breed.
Holstein Haplotype 1
Stylised as HH1 / HH1T free, HH1C carrier.
Holstein Haplotype 1 (HH1) is a genetic marker which causes spontaneous abortions throughout gestation of homozygous embryos. It is seen in around 1.28% of the holstein population.
Popular sires which carried the HH1 genetic marker include O-Bee Krusader (Planet x Shottle x Marshall) and Charpentier LFG Spectrum (FBI x Talent x Formation).
Holstein Haplotype 2
Stylised as HH2 / HH2T free, HH2C carrier.
Holstein Haplotype 2 (HH2) is a haplotype which can be tested as per a standard CDCB evaluation and causes abortion before 100 days of gestation of homozygous embryos. It is seen in around 1.21% of the holstein population.
Popular sires which carried the HH2 haplotype include Claynook Tennessee (Mr Burns x Goldwyn x Allen) and his father Dudoc Mr Burns (Thunder x Storm x Starbuck).
Holstein Haplotype 3
Stylised as HH3 / HH3T free, HH3C carrier.
The third Holstein Haplotype (HH3) is a genetic marker causes abortion before 60 days of gestation of homozygous embryos. It one of the more prevalent of the group, seen in around 2.64% of the holstein population.
Popular HH3 carriers were sires such as Mainstream Manifold (O Man x Marshall x Emory) and O Man (Manfred x Elton x Melwood).
Holstein Haplotype 4
Stylised as HH4 / HH4T free, HH4C carrier.
Holstein Haplotype 4 (HH4) is one of the lesser seen in comparison to its contemporaries, at 0.23% of the holstein population being affected. HH4 causes abortion in early gestation of homozygous embryos.
Holstein Haplotype 5
Stylised as HH5 / HH5T free, HH5C carrier.
The fifth Holstein Haplotype (HH5) is more prominent in the holstein population, affecting 2.39% of it, however we assume this to be higher in the UK. HH5 causes abortion before 60 days of gestation of homozygous embryos.
Infamous carriers of HH5 include Picston Shottle (Mtoto x Aerostar x Inspiration), Val-Bisson Doorman (Bookem x Shottle x Goldwyn) and Ms Atlees SHT Aftershock (Shottle x Durham x Storm).
Holstein Haplotype 6
Stylised as HH6 / HH6T free, HH6C carrier.
Holstein Haplotype 6 (HH6) is a genetic marker which causes abortion before 35 days of gestation of homozygous embryos. HH6 is seen in approximately 0.44% of the holstein population, however again we predict this to rise.
There are a lot of sires available now which carry HH6, mostly coming from Peak AltaZazzle, other carriers include Bomaz AltaTopshot (Supershot x Embassy x Robust) and RMD-Dotterer SSI Elvin (Rayshen x Barcelona x Frazzled) sons.
Jersey:
Embryonic Haplotypes
Embryonic Haplotypes exclusive to the jersey breed.
Jersey Haplotype 1
Stylised as JH1 / JH1F free, JH1C carrier.
Jersey Haplotype 1 (JH1) is a genetic marker which causes abortion before 60 days of gestation of homozygous embryos. It is seen in around 9.21% of the jersey population.
Jersey Neuropathy
Stylised as JNS / JNSF free, JNSC carrier.
JNS (Jersey Neuropathy with Splayed Forelimbs) is a haplotype which can be tested as per a standard CDCB evaluation and causes a neurological symptoms including spasticity of head and neck and convulsive behavior. Calves affected are unable to stand and show rigidity of forelimbs and/or excessive lateral abduction. It is seen in around 3.04% of the jersey population.
Ayrshire:
Embryonic Haplotypes
Embryonic Haplotypes exclusive to the ayrshire breed.
Ayrshire Haplotype 1
Stylised as AH1 / AH1T free, AH1C carrier.
Ayrshire Haplotype 1 (AH1) is a genetic marker which causes abortion in early gestation of homozygous embryos or stillbirth. It is seen in around 11.16% of the ayrshire population.
Ayrshire Haplotype 2
Stylised as AH2 / AH2T free, AH2C carrier.
Ayrshire Haplotype 2 (AH2) is a genetic marker and causes Abortion in early gestation of homozygous embryos or stillbirth. It is seen in around 10.5% of the ayrshire population.
Arthogryposis Multiplex AM
Stylised as AMC / AMF free, AMC carrier.
Arthogryposis Multiplex (AM) causes stillbirth or calves are born deformed with stiffness in multiple joints and/or joints that are curved or hooked and die shortly after birth.
