Using Genomics to See the Forest for the Trees

How to get past the destructive Mountain Pine Beetle using genomics

Most of the presentation was spent discussing policy implications of the impact of the Mountain Pine Beetle, containment challenges faced in limiting its expansion and the potential to mitigate economic impact on a limited budget. As is being done in livestock, genomics can be used to investigate tree resistance to disease and pests. The result in this case was discovering how drought impacts gene expression in various species of trees, reducing their ability to fend off Mountain Pine Beetle attacks.

Similarly, newly-developed genomic signatures for various populations of Mountain Pine Beetles enabled experts to determine the geographic areas from which they were invading new territories. In turn, this allowed an improved risk assessment process to feed into forestry policy due to a better understanding of range expansion and spread dynamics.

The research on gene expression showed that degree of drought has a significant impact on a tree’s resistance or ability to repel a Pine Beetle attack. Combined with the latter work on genomic signatures, this led to policy development directing resource use towards activites that defend vulnerable forest areas in times of drought and target the reduction of beetle populations from where they are most likely to invade.

From there, the discussion shifted to tree improvement, pointing out that, as is the case with breed improvement in livestock, the three main areas of investigation are end-product quality, health and efficiency. This was more accurately summarized as wood and pulp characteristics, growth and yield, drought tolerance, nutrient use or efficiency, and pest and pathogen resistance. Just like cows!

Up next was an overview of the importance of an accurate and efficient system of forestry traceability. Industry-wide, half a billion seedlings are grown each year as part of Canadian reforestation efforts. This involves massive efforts in cone collection and seed extraction (among others) as part of the transplantation back into sensitive natural environments where an unintended species can have a significant impact on the environment and equally significant financial consequences for the corporation responsible for introducing them. Genomic traceability initiatives have already played a major role as a fail-safe means of determining that the intended genetics are delivered into the intended stands

In closing, the discussion turned to the future and how in forestry, as in medicine and agriculture, the promise is in the emergence of genomics-led precision initiatives as conservation tools as well as a means to advance high-value areas of the Canadian forestry industry … or better said, as a means to better the Canadian environment, outdoor experience and economy.

Postcards from Brazil

From Brazil’s fierce milkers to Canada’s placid eaters


“These are Girolandos,” says Valente. “They’re a cross between Holsteins and Gyr, more adapted to hot climates and ectoparasites. The down side is that they produce less and are more… uhm… reactive during handling than the European breeds.”

Valente’s main interest is the genetic approach to behaviour in farm animals, focusing on temperament in cattle. In Brazil, one of the projects he is involved in relates to milking temperament in Girolando and associating the trait with production and health and welfare aspects. These pictures were taken at one of the farms involved in the project, the Fazenda Floresta in Sao Paolo State, which has a large herd of Gyr and Girolando. Valente’s visit had one key objective: training the heifers.

“First milking is a big problem. Sometimes they go absolutely crazy, break everything and hurt themselves,” he admits. “So we try to get the heifers used to the parlour facilities ahead of time.”

The idea is to reduce their reaction (their flight zone) and teach them about their new lives. Brave volunteers guide them into the parlour without restraints, walk around them, introduce them to new noises and new equipment. The pictures below show the “novel object test” to assess the Girolandos’ general fear of novelty.

“In this picture,” says Valente, “a group of us from Sao Paulo State University are at Girolando Bulls’ Performance Centre in Uberaba, State of Minas Gerais, measuring the bulls for temperament.”

Due to the cost of collecting semen from Girolando bulls (and, no doubt, the danger to life and limb!), a preselection test is done instead. Since 2014, bulls are measured once a month for four months for temperament, which comprises 10 percent of the selection index. The other factors are andrological parameters and body capacity measurements.

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In Canada, nothing nearly so adrenalin-pumping. As a postdoc, Valente works with Gentec CEO Graham Plastow and Gentec-associated researchers John Basarab (Alberta Agriculture and Forestry), and John Crowley (Canadian Beef Breeds Council) on feed efficiency as it relates to feeding behaviour in beef cattle.

“We know some animals spend more time at the feed bunk but are not more efficient than those animals that spend less time” he says. “So we’re looking at two traits: one for time at the bunk (duration) and the other for ‘head down’. The second one means they are eating not just hanging around.”

Valente found Graham Plastow and Gentec through another Canadian. Karen Schwartzkopf-Genswein (Agriculture and Agri-Food Canada, Lethbridge R&D Centre) is a visiting professor at Sao Paolo State University, where Valente was doing his PhD under Mateus José R. Paranhos da Costa (Faculty of Agricultural and Veterinary Sciences). There, the two developed a close professional relationship and co-authored a publication. When he was searching for an internship for his PhD, he asked her where he might study genomic tools applied to beef cattle in Canada. She recommended Gentec.

“Graham is an excellent connection,” he says. “He helped improve the quality of my PhD thesis, invited me for the postdoc, and now I have an opportunity to build a bridge between two like-minded organizations.”

Indeed, Plastow is keen to collaborate with the Empresa Brasileira de Pesquisa Agropecuária (Embrapa), the Brazilian agricultural research corporation, which has precious datasets from breed associations and phenotypes that could be useful in the Canadian context.

“Travelling between Canada and Brazil, especially to work on different projects… it’s quite gratifying,” concludes Valente.

Can enriching the lives of pigs improve their health?

Combining genetics and enriched environments could improve pig welfare in commercial systems.

Yolande Seddon became fascinated in the alteration of behaviour through genes and that some behaviour is “hard-wired” while studying animal behaviour and welfare as an undergraduate student in the UK. For her Master’s, she began to focus on pigs, investigating the effects of long-distance transport.

“I was amazed by how many factors there are to consider—and this is just one aspect of one industry in a much larger sector,” she says. “I decided to specialize to help make real improvements.”

Today, Seddon’s mandate is to improve pig welfare in current production systems, with a particular interest in fully-slatted systems. She admits that a number of welfare improvements could be made by moving away from slatted systems but the reality of sustainable production and affordable meat ensure their survival. She was recently awarded nearly $2 million from NSERC, USask and industry for a 5-year program to explore, among other things, how enriched environments and positive welfare can influence health and resilience to disease (see media coverage here and here).

Good pig welfare concerns how the animal is feeling and copes with its environment. So, good physical and mental health, no fear, not in want of anything, and able to respond effectively to challenges. In Canada, we want good well-being and good production to be efficient. However, if pigs fail to cope with challenges, chronic stress can develop, which can influence susceptibility to disease

“Generally, producers are aware of the link between welfare and meat quality. The challenges come when we look at behavioural needs,” says Seddon. “Animals are driven to perform some behaviours even when domesticated. When a sow is about to farrow, for example, she still wants to build a nest. However, space is at a premium, and bedding isn’t often used for hygiene reasons, so the sow’s ability to express nest building behaviour fully can be reduced.”

Seddon’s Alberta Agriculture Funding consortium funding will piggy-back (no pun intended) onto Gentec-associated researcher Michael Dyck’s current Genome Canada project.

On entering the nursery, 50% of pens will serve as controls and 50% will receive an enrichment routine that will continue as they enter the disease challenge, recover and exit the finisher. Individuals and pens will be compared for susceptibility to disease, immune response and genetic expression.

Every two days, the pigs will be exposed to new objects that have properties known to be attractive and can be destroyed, manipulated and chewed—but not eaten (pigs like to eat their enrichment). Examples include cotton ropes for chewing, rubber mats and jute sacks for rooting, Porcichew hanging enrichment, a sheet of tarpaulin for group interaction, and rubber hoses. To help the novelty (don’t forget—pigs are pretty smart!), items are removed and rotated so they won’t see them again for another two weeks.

study in the Netherlands showed that enrichment increases resistance to disease. In this study, pigs had more space, comingling, shavings, branches and peat moss. After a challenge with PRRS virus and Actinobacillus pleuropneumoniae (APP), the pigs with enrichment cleared the PRRS virus sooner and only 7% had APP lung lesions vs 57% of pigs in the barren environment.

However, because the pigs may have been eating their enrichment, the effect on the microbiome is unknown. Seddon’s project will help break that down by identifying whether non-edible enrichment that brings novelty to the pens and offers pigs an opportunity to investigate can influence disease resistance.

So what does enrichment cost?

“The cost/benefit needs to be identified,” says Seddon. “But, a specific enrichment routine could be targeted at a specific time of production to enhance immune response. Or, if you’re building a new barn, you might invest in an overhead rail to automate enrichment rotation. You can buy purpose-built systems for that. But if production quality is important, you just make it happen.”

11th WCGALP (2018) Summary

The premier event for researchers and professionals involved in the genetic improvement of livestock

Over 10 Gentec members attended this important conference. Gentec CEO Dr Graham Plastow chaired the fantastic session on gene editing which is a hot topic in livestock genomics in recent years. Over five days, workshops updated the genomics progress in both research and application in livestock, which significantly renewed my knowledge in genomics. The one-day field trip (sheep/deer farm) gave me a better understanding about animal breeding and production in New Zealand. The excellent conference program and social activities did wonders for my professional networking with people from academia and industry.

For me, the most attractive session was the genomics methods and tools program which spread over all five days. Powerful statistical methodology and tools have been well developed and improved in recent years, driven by the rapid increase number of phenotypes and genotypes. Single step GBLUP (SSGBLUP) is considered the most popular one in practical breeding since it can handle large pedigree, genotypes and various types of phenotypes simultaneously. SSGBLUP + APY (algorithm-proven young for easier G inversion) is widely used in the US to evaluate beef cattle and by pig-breeding companies (e.g. Topigs Norsvin and Genesus Inc.). However, SSGBLUP still needs to improve minor issues, such as the weighting of SNPs.

Another valuable session was on how to improve genomic prediction accuracy especially with whole genome sequence data, which has been a main research topic in Gentec under several projects in cattle and pigs in collaboration with our industry partners. According to a discussion with Drs Mike Goddard and Ben Hayes, they both thought that, theoretically, by adding the TOP SNPs selected from whole sequence, the accuracy of GEBV should be better or at least remain the same.

As many reports in the conference demonstrated, results from practice data are not always consistent. We faced a similar situation as described in the paper we published recently (Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants). We all agreed that possible solutions include increasing the number of training animals especially including the target breed, increasing the number of SNPs especially the causal ones, using Bayesian methods (e.g. BayesRC) and multi-omic data (gene expression and annotations).

Another interesting area was genomic studies in pigs. Several presentations talked about GWAS and/or genomic prediction for economically important traits in pigs we have studied widely at Gentec. Their results were quite comparable with ours. For example, important QTL were reported for the number of stillborn (SSC9) and the number of born alive (SSC2, 5, 9, 14). Many putative lethal haplotypes associated with sow fertility were detected, and the region on SSC14 was also detected in our Duroc pigs. There were also a few talks in hot-topic areas such as novel predictors or selection criteria for pig growth, pork quality and reproduction, such as hemoglobin levels and gut microbiome. We have investigated these topics in recent projects to improve resilience to disease through genomics.

Genome Editing in Livestock

As a beef cattle producer and the Chief Scientific of Acceligen, the livestock food subsidiary of Recombinetics, Tad Sonstegard is in a position to offer a moderate, informed opinion of this technology while standing at the water cooler.

Tad provides tangible examples of how gene editing has already shown it can benefit the livestock sector through the potential for “precise cross-breeding.”

One example discussed as an introduction to gene editing is the potential to select for polled dairy cattle, which removed the need for de-horning and improved animal welfare. These genetics have been selectively bred (the old-fashioned way) for generations via the polled beef breeds and, as such, have been part of the human food chain for thousands of years. One positive signal towards the potential acceptance of this technology is that the Humane Society of the United States has endorsed the use of gene editing technology to select for polled animals on the grounds that it reduces pain and suffering for livestock. More importantly, it also agreed to evaluate and endorse the application of gene editing on a case by case basis depending on its impact on animal welfare.

CRISPR is also being used to mitigate the greenhouse gas impacts of food production, with the most potential for use in the developing world through improving heat tolerance. Heat affects the disease resistance, nutrition, productivity and health of animals. Tad talks of how it takes nine dairy cows in India to produce the milk of one dairy cow in the US, with much of this difference due to lower productivity due to heat stress. If this technology eliminated this productivity gap, the GHG emissions and environmental impact of up to eight cows could be removed with no corresponding loss of milk production while also freeing up the food, water and other inputs currently directed to those eight animals. One application of selective breeding is showing great promise. It takes advantage of animals, referred to as “slick,” which have a hide comprised of hair that is less dense and half the normal length in addition to possessing larger, more active sweat glands. This combination allows “slick” animals to maintain a lower body temperature in more heat-stressful conditions.

In closing, Tad talks of future applications for gene editing and where the greatest economic benefits may lie, which appears to be in addressing disease resistance. More work does need to be done here as we don’t yet understand which areas of the genome are important when it comes to health. With a better basic understanding however, comes the ability to select for innate immunity as well as using rational design techniques that allow animals to better defend against bacteria and viruses. While the means discussed here differ, the ends are similar to those currently being pursued via more traditional methods in the Genome Canada Pig Resilience Project led by UAlberta’ Mike Dyck.

Watch the video summary for a more in-depth look at these and other editing applications

Temple Grandin speaks at 2018 Livestock Care Conference

Many of our readers will know Temple Grandin as the Colorado State University Animal Science Professor who despite (or perhaps because of) her autism has had a hand in designing livestock facilities around the world, working with corporations such as McDonald’s, Chipotle and Whole Foods. She has appeared on Larry King Live, 60 Minutes, a TED Talk, and was named one of Time Magazine’s 100 Most Influential people.

Taking to the stage, Dr. Grandin decided that the world had had enough of her “Improving Cattle Stockmanship 2nd Edition” presentation and instead delivered a wide-ranging, very entertaining and largely off-the-cuff presentation that moved through a number of topics that perhaps can be best described as exploring the theme of unintended consequences.

The first was in relation to “bad becoming normal.” Often, when we set out to solve a problem, we focus too narrowly and end up with unanticipated results. Think genetic selection or breed for a single trait. Examples she gave include the “Rapist Roosters” that Grandin spoke of in her book “Animals in Translation,” where breeding programs intended to select for larger breasts and white meat resulted in hyper-aggressive roosters with poor courtship skills. A more benign example involves how, as a result of selecting cattle for docility, the industry has dialed back the fear response to the extent that we are now able to observe a much wider range of emotions in cattle (such as curiosity).

From this, she expressed two frustrations: 1) while a lot of great research is being done, genetic and otherwise, to improve the livestock industry, unfortunately much of it is done privately and thus proprietary, and can result in said unintended consequences spreading when they should be contained; and 2) very positive results are prevented from wider adoption when they would benefit animals and people. As an aside, Grandin also noted the prevalence of the myopic expectation that advances in genetics, engineering, and/or equipment will solve our problems when in fact they account for only half of the solution. The other half falls to us; it is management that must step forward to solve the other half.

Grandin’s second overarching theme was that “big is fragile,” which has led society to worry about sustainability. Locally-sourced food is comforting because deep down on a psychological level, we know that big is fragile and we wonder what will happen to us if “the Walmart truck doesn’t arrive.”. Local, sustainable food provides security.

And finally, we should be careful of what we wish for. The future holds all sorts of potential but we need to step into it with our eyes wide open: CRISPR technology that allows us to select for “no horns” may, as in the roosters example, select for something that looks similar but results in unintended consequences; a) synthetic meat may provide a “humane” alternative to livestock production but b) it’s probably a GMO, c) may require huge energy inputs to achieve, and d) as a monoculture grown in vats, holds enormous potential for diseases to flourish during production.

Stepping forward isn’t bad in and of itself but we should be careful about how we do it and what we wish for. Bad becomes normal… and big is fragile!