Haplotypes and Genetic Markers

Haplotypes and Genetic Markers: What are they and why are they important to herd profitability?

A study published in the Journal of Dairy Science in 2016 reported that $11 million of economic losses could be avoided in the U.S. alone if mating pairs were avoided that produced embryos affected by haplotypes causing reduced fertility and perinatal calf death (Cole, 2016). Identifying haplotypes through genomic testing is a critical piece to the genetic strategy in your herd because propagating these haplotypes in your herd could have negative consequences including loss of profitability from mating carriers of the same negative haplotypes. Understanding the haplotype and marker data in your female genomic evaluations as well as the bulls you select for breeding is essential to make informed management decisions to avoid loss of profits and promote animal welfare.

What is a haplotype?

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. Figure 1 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.

Why is it important to screen these genes in my herd?

Genomic technology has enabled the screening of genes within your herd to identify animals carrying undesirable alleles. By genomic testing your females, you can make strategic breeding and selection decisions by controlling and eradicating undesirable genes which can improve the health, fertility and productivity of your herd.
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. In Figure 2, a female carrying the Holstein Cholesterol Deficiency (HCD) haplotype is mated to a bull that is also a carrier of HCD. This means that this mating pair has a 25% chance of producing progeny that would express HCD. An HCD calf would die within months of birth which would affect profitability and diminish animal welfare. The only way to know the haplotype frequency of animals in your herd is to genomic test your animals.

How can I best manage my herd based on recessive genes and haplotypes screening?

The first step of managing haplotypes in your herd is to genomic test your females. This will allow you to assess the genetic dynamics of your herd including production, type, and health traits along with EcoFeed to determine which animals you will breed to sexed semen. Some of the females that you select to make replacements may be carriers of negative haplotypes which means that you should not mate these females to bulls with the same negative haplotype. By utilizing the Chromosomal Mating® program, you can ensure that carriers of the same negative haplotype will not be mated, so the negative haplotype will not be expressed in the next generation of your herd.

What is the difference between a marker and a haplotype?

A haplotype is a stretch of DNA that is inherited together whereas a marker or SNP test is the actual mutation that is causing the abnormality. A marker or SNP test that is pinpointing the actual causal mutation is more accurate in comparison to a haplotype where the association with the causal mutation might fade over generations. Identifying negative haplotypes is an excellent tool to screen animals for possible carriers, but a gene or marker test provides a more complete identification of carriers. Genetic Visions-ST’s Vision 75 genomic test includes a number of marker tests to better detect carriers of negative traits including the only marker test available on the market for HH5, a Holstein haplotype affecting fertility, Jersey Neuropathy with Splayed Forelimbs (JNS), and Arthrogryposis Multiplex (AM) or Curly Calf Syndrome in Ayrshires.

Which haplotypes should I be looking for in my herd?

Negative haplotypes can occur in all breeds of cattle, but some can be more common in certain ones (as shown in the tables below). They are usually linked to poor fertility and health status. Other traits like coat color and polledness are also related to recessive alleles. In order to interpret the genomic results of the haplotypes in your animals or bulls that you see in a sire catalog, please use the tables below.

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