Solving the genetic jigsaw

They are using LIC Jersey and Holstein-Friesian bulls to build a genetic map of New Zealand dairy cattle.

Improving the genetic reference sequence is expected to help in identifying disease genes and speed up the delivery of breeding worth traits, among other things, LIC says. This will lead to more efficient cows and thus environmental benefits, and may help researchers to breed diseases out of the livestock population. 

Improvements in genetic gain reward farmers and so help the NZ economy.

In 2009, after a six-year effort, the US Department of Agriculture (USDA) and 300 scientists from 25 countries published the first cattle genome sequence of a female Hereford cow called Dominette. Though now dead, this cow ‘lives on’ in research laboratories worldwide where researchers have used her DNA sequence for other genetics discoveries. Improved genome sequencing is enabling researchers to overhaul Dominette’s sequence to improve accuracy.

LIC’s work in charting the DNA differences between beef and dairy cattle will help scientists understand what role different genes play in milk production, fertility and body condition, and the potential these genetic markers might have for the country’s dairy herd. Each DNA sequence makes up a piece of this jigsaw puzzle.

This research was funded by the Transforming the Dairy Chain (TDVC) Primary Growth Partnership programme, a seven-year, $170 million innovation programme led by commercial partners including LIC, DairyNZ and Fonterra, and partnered by MPI.

LIC’s acting chief scientist, Dr Bevin Harris, says the work with the USDA will bring benefits for the NZ dairy herd.

The bovine genome has three billion base pairs (the building blocks of the DNA double helix) containing 22,000 genes, 80% of which are shared with humans. Within these 22,000 genes there are genetic variants. 

To use a book analogy, each cow has the same number of chapters, i.e. 22,000. But there are a number of word and spelling changes (variants) in each chapter of each book.

You could read any book and be able to broadly describe what each is about, but there would be slightly different contextual differences with different interpretations. 

This is what leads to diversity within a species. Put crudely, everybody looks the same (the same book of 22,000 genes) but there are slight differences in most traits or characteristics.

By the end of this year, genomes from 1000 dairy cattle will have been sequenced. Through this sequencing, LIC has identified about 19 million variations that exist within the NZ dairy cattle population.

These will be compared to Dominette’s and the new dairy cattle reference genomes, and the next job will be to identify which of these genes affect the traits that dairy farmers are interested in. 

This information can then be used to improve the ability to predict how well animals will perform at birth based on their genome sequence.

DNA progress

In the last three years, improvements in DNA sequencing technology have cut the cost of sequencing a new genome and newer technology is allowing genomes to be sequenced more quickly.

A once-massive, costly exercise (US$50 million when Dominette’s genome was sequenced in 2006) now costs NZ$1000 per genome.

Harris says if genome sequencing had to be done manually, it would take someone typing 60 words per minute eight hours a day for 50 years to type the bovine genome.

“The entire DNA sequence would fill 200 one-thousand-page telephone directories,” he explains.

“The knowledge gained from this sequencing project will enable us to identify the potential benefits of genetic gains for the NZ dairy herd, and this will increase the accuracy of bull selection which will increase the national rate of genetic gain.” 

NZ Animal Evaluation (NZAEL), a subsidiary of DairyNZ, estimates that improvements in genetic merit are worth $300m profit a year to the dairy sector.