NZ innovation underpins global probe of sheep genome

New Zealand science has made a key contribution to international research which has laid open the genetic history of sheep — one of the world’s most important livestock species — with the potential to garner economic benefits for sheepfarmers.

The new study, published today in  PLoS Biology, maps out how humans bred  sheep for specialised production of meat, wool and milk in a range of environments, and showed frequent mating and strong gene flow between animals of different breeds had retained high levels of genetic diversity in modern sheep.

“The key finding was there was a high diversity retained in most breeds with evidence that divergence was largely  related to geographic dispersal from a domestication centre but with considerable evidence (of) crossing and recrossing among the diverging breeds,” said one of the authors, John McEwan, a senior scientist at AgResearch’s Invermay campus. “In this way sheep differ significantly from cattle and dogs [species subjected to large amounts of interbreeding],” he told the SMC.

A key implication of that genetic diversity is the prospect of continued breeding to further boost wool and food production  and food production:  NZ taxpayers last month handed a local consortium nearly $14.6 million to develop genomic and diagnostic selection tools targeting  genes controlling traits such as coat colour, body size,  and reproduction. But there may also be gains in resistance to disease and parasites.

The team compared 49,000 DNA sites across the genome in 2819 sheep from 74 breeds to pin down the genetic consequences of domestication and evolution of hundreds of breeds, said Mr McEwan, a pioneer in creation of high-density SNP chips and their use to allow faster genetic improvement in sheep, via a technique called whole genome selection. Single nucleotide polymorphisms (SNP) are point mutations or genetic variations that occur when a single nucleotide in a genome is altered. Two decades of work by New Zealanders have led to creation of SNP chips able to quickly and cheaply screen sheep for useful genes.

The sequencing of 6 sheep in a SNP discovery project in 2007 created an initial genome assembly of the sheep genome which led to the Beadchip used in the latest research to  deeply probe for the first time how the world’s sheep breeds are related.  Initial work into what regions of the genome had been selected for as part of the domestication and breed creation process including two regions already known as “positive controls”  to harbor major genes affecting traits that differed between breeds. This included horns and meat yield but the work also identified many other interesting  regions for follow- up in further studies. Interestingly 11 of the 31 regions listed also appeared have been targeted in the breeding of  domesticated cattle, “suggesting common responses to domestication in these ruminants”  said Mr McEwan.

New Zealand animals represented in the study included Romney, Wiltshire, Texel, Arapawa, Dorset Horn breeds,  and the  total resource will now provide  reference for all future studies in sheep worldwide, including any work done in New Zealand.

The work validated the use of SNP chips, which have been widely used by Ovita (a consortium of Beef and Lamb New Zealand and AgResearch) on thousands of leading New Zealand rams, leading to development of  genomic selection in NZ flocks —  based on DNA variation — for an expanding variety of production traits. Technology is being commercialised by animal health company Pfizer.

Underpinning the commercial innovation was the new knowledge about  genetic diversity: some of these  genotypes have been  investigate the origin of the Arapawa Island breed of feral  sheep “with some evidence it represents a novel breed imported into New Zealand over 150 years ago and could therefore act as a reservoir of  genetic variants not present in other New Zealand breeds,” said Mr McEwan.  The work also allowed clarity on what other breeds may harbour useful variants which don’t exist in New Zealand.

In response to SMC questions, Mr McEwan said:

“”Some of the regions under selection reported in this study are related to wool characteristics, milking ability and reproduction (especially early puberty) and as such may have a direct impact on New Zealand sheep breeding. However, other regions will be related to the presence of lack of wool (hair sheep) or the presence of a fat tail and coat coloration and as such will have less impact in New Zealand. The hope is some regions will be associated with disease resistance especially to internal parasites and footrot, but much further work remains to be done in this regard and this was not the major  emphasis of this study.

“I am not at all surprised that Texels from Germany, Scotland and New Zealand clustered together given the historical record. Perhaps what may surprise many is just how close Romney, and Border Leicester (and presumably Cheviot) are to this breed but given that these English breeds forebears were probably imported by Anglo-Saxons from the region of Texel anyway and there is  recorded evidence of Texels being upgraded using English breeds around 100 years ago this is not surprising. It does suggest though that we actually have a rather restricted sampling of sheep genetic variation present in New Zealand.

“The work to initially map the sheep genome was done by many people, but in New Zealand it was Allan Crawford, Grant Montgomery and Tom Board that did most of the heavy lifting in the early years with George Davis proving examples of reproduction variants that could be usefully mapped.  This early work set the scene and identified that major variants affecting performance could be mapped and without that work NZ would not have either the staff capability nor the funding support that led to this work.

“The high levels of genetic diversity remaining in sheep mean that this species has considerable ability to respond top selection in any desired direction and also that many closely related breeds probably contain most of the variability of the related breeds.

The full list of breeds sampled is given at this site and  it also includes 9 Argali sheep – a breed of huge wild animals which some NZ farmers have eyed because they grow to 180kg — but the results of wild sheep were not reported in today’s paper.