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Next generation genetic evaluation
AWI Program Manager Genetics and Animal Welfare Advocacy, Geoff Lindon.
What are the current trends in genetic evaluation and what might the industry be doing a generation from now? In this article, read about the prediction of AWI’s Geoff Lindon that genetic evaluation will provide many opportunities to keep the Merino a viable and profitable enterprise for farmers in the decades to come.
The Balmoral Breeders Association requested that Geoff Lindon, AWI Program Manager Genetics and Animal Welfare Advocacy, give a presentation on ‘Where to with Genetic Evaluation’ at the recent dinner associated with its February Field Days. Geoff has worked at AWI for nearly 15 years, managing AWI’s investments in genetics research.
In the presentation, Geoff firstly described what genetic evaluation looks like now and what breeders are aspiring to do. He then tantalisingly provided the audience with his thoughts of what the industry might be doing new in a generation’s time, 30 years into the future, and what additional traits might be important.
Genetic evaluation today in 2022
Geoff began the presentation by summarising the present situation, in which on-farm assessments are currently dominated by young post weaner and yearling age traits.
“A quarter of woolgrowers breed their own rams. 31% of growers use a sheep classer, while 44% class their own sheep and 25% don’t class at all. The national average joining rate is 2.1 rams per 100 ewes,” Geoff said.
“Each year in Australia, about a quarter of a million ewes, mostly Merino, are inseminated using laparoscopic artificial insemination (Lap AI).”
Geoff pointed out that there is a broad range and difference in size of ram sellers.
“One third of ram sellers are members of MERINOSELECT and they sell approximately 50% of all Merino rams and 70% of Merino semen,” he said.
“Sire Evaluation is the lead progeny testing regime but mostly up until hogget or early adult age for wool, carcass, visual and welfare traits.
“However, half of Stud Merino ram breeders sell a relatively small number of rams. For them, ASBV technology can add considerable cost to their business and their management, and contemporary groups are small for evaluation. They buy rams and semen with classer support and genetic evaluation information. They tend to provide their ram buyers with raw data or within mob variance information on the rams they sell.”
Today’s trends in genetic evaluation
Geoff said that there had been a long-term trend to class and sell animals at younger and younger ages but one of the current trends is that many ram sellers are increasingly interested to see how they can evaluate and class at older ages.
“Although rams are often classed from 6 to 12 months of age with most sales occurring at 12 to 14 months of age, many ram breeders class their sires and ewes carefully on an annual basis,” he said.
“Most studs are aware that the long-term genetics advice is a two-stage objective selection process, evaluating ewes at one year old and two years old, but they tend to be cautious or resistant to the cost and they need evidence of the benefits.
“Phenotyping for welfare traits, condition score, worm and fly parasites are increasing significantly along with 50K DNA genotyping. The Merino breed trends for these traits are gathering momentum.”
Geoff noted there are some very impressive genetic trends occurring at the individual ram breeder level.
“Some of these gains are more difficult to see at the macro level where differing type trends cancel each other out at the whole of Merino breed level, but nonetheless even at the macro level there are some clear solid gains being made,” he said.
Reproduction is an increasing focus with the rise in lamb and surplus sheep prices. There are three new component traits of conception, litter size and ewe rearing ability, along with greater focus on lambing ease, scrotal circumference and udder soundness.
“The ever-increasing body weight is creating concerns on shearing and efficiency fronts. How we can have productive yet more moderate adult ewe weight is one of a range of topics to be fine-tuned in pending index reviews,” Geoff advised.
“Sire Evaluation continues to grow and there is interest in more reproduction assessments and future feed efficiency and methane assessments.
“The use of MateSel to optimise genetic gain with controlled line breeding to minimise culls is increasing. Big outcrosses can provide quick gains, but they can increase off types and culling rates until stabilised. Having a well thought out breeding objective and sticking to it works,” he said.
“Sheep Genetics has just updated its old databases; all data is in one database opening a range of new analysis opportunities. MERINOSELECT phenotypes amount to four terrabytes of data, the genomics database another four terrabytes, totaling an incredible eight terrabytes, which is analysed every fortnight. The recent computer upgrades are able to conduct the analysis with much greater speed.
“In addition, Sheep Genetics is about to release a Data Quality Score that will highlight to ram buyers which ram sellers are collecting a broad range of data and following best practice protocols. This is a major step forward and will give more confidence to semen and ram buyers.”
What the industry might be doing new in 30 years
It was at this point in the presentation that Geoff warned he was moving from evidence to conjecture. “So here is my crystal ball for 2052,” he boldly stated!
“Well informed and experienced visual classing will remain a cheap and effective way of evaluating sheep across their lifetime, especially when visual traits are the key traits in a breeding objective. How to get the balance in combining visual and the ever expanding and more expensive objective assessments will remain an ongoing challenge.
“Finding the truly elite individual and breeding from them will remain the mix of science, observation and gut know-how. The use of progeny testing will continue to support and reward those who can find the individuals among the masses and population genetics approach.”
Geoff predicted that combining production data with feed intake and whole-body energy will have big financial returns but warned it is a complex area.
“Other extensive and intensive livestock species have made enormous gains in the area. Sire Evaluation sites and some larger ram breeders will be assessing individuals and sires for feed intake and whole-body energy. And the CO2 and methane data gained is likely to be viewed as essential to meet global obligations.”
Geoff revealed that the Merino Lifetime Productivity (MLP) project today is pointing to a large variation in lifetime survival of 35% between the extremes, and around 20% between the top 20% and bottom 20% of sires.
“Survival is an important trait with significant financial consequence, but needs to be included in indexes,” he said.
Geoff noted that the industry has been artificially breeding now for 40 years with less natural selection on semen quality and libido.
“A byproduct of the MLP project is some information on natural ram mating success; some sires are getting 150 progeny in a five-week natural joining, others are getting 10. This is supporting findings in other sheep breeds where the heritability of the trait is as high as 0.3. Through the use of pedigree DNA in natural matings, selecting for ram mating success could lead to the ram joining percentages moving to around 1%, with the benefits shared between ram buyer and seller.
“Genomics will assist with the hard to measure traits of lifetime production, reproduction, survival, feed intake, minimising the impacts of parasites and resilience. The MLP project is showing there are rams that can do it all and this will continue despite the additional traits.
“Full pedigree and electronic identification (EID) will be required along with lifetime roll calls and full data collection at the top tier of ram breeders.”
Geoff said every genetic evaluation site depends on the use of a web of link sires, via frozen semen and Lap AI, but warned that the technology has “head winds”.
“It is an invasive practice and involves use of fluid from another species, pregnant mare serum, which is banned in many European countries.
“So we need to find a way to use frozen thawed semen by cervical AI in unsynchronized programs. From many hundreds of proteins, the University of Sydney has isolated the four proteins damaged on freezing that lead to 20% conception via cheaper cervical AI, but more work is needed to find the solution.
“The EU inseminates 10 times the number of ewes per year that we do here in Australia, all with fresh semen and there has been extensive collaboration with R&D efforts in France. With a breakthrough, there will be much greater use of AI using elite frozen/thawed semen and use of sexed semen.”
Geoff philosophically noted that everyone likes progress, but no one likes change.
“So there needs to be a motive and a profit for ram sellers to have the head time to investigate these options, invest in their adoption and find ways to do so profitably. Equally, ram buyers need to create the time to absorb the advantages for them, find sellers with the same breeding objectives and invest prudently in the new genetics,” he concluded.
How will these changes be affordable?
“How will these changes be affordable, you might ask,” Geoff said.
“I have already mentioned improvements in survival that will increase sheep sales and culling rates, and could lead to the halving of the number or rams required to around 1 ram per 100 ewes. Breeding for feed efficiency could lift stocking rates by 10 to 20% and more, if we follow the success of other breeds.”
Geoff noted that MateSel will most likely be expanded to all important objective and visual traits.
“So culls will be minimalised and rams sold to rams left entire at marking, could return to 65 to 70% which has major profitability consequences.”
Geoff also predicted that there will be streamlined processes to collect, send, validate and return analysed data and there will be improved analysis for indexes and a wider range of traits.
“I predict that the most profitable arrangement will be for five to 10 studs with similar breeding objectives, in a similar production environment with 1,000 to 1,500 fully pedigreed and measured ewes, forming more collective business arrangements having combined semen and elite ram auctions.
“The supply chain will have significant transparent access to these groups and their practices, encouraging price advantages along the supply chain and sale of surplus sheep.”
Some perspective and optimism
In reflecting what might be achievable in the next 30 years, by 2052, Geoff noted that it is worth reflecting on what has happened in the past 30 years, since 1992.
“The Reserve Price Scheme was teetering, faxes were new, so was scanning for fat and muscle. There were no laptops and no mobile phones, no commercial internet, no EID and no software packages. Merino Sire Evaluation had just started as had the first across flock analysis, Merino Benchmark, doing just two runs per year, compared today’s one per fortnight.
“My father used to say to me as a teenager, sometimes you sit and think but sometimes you just sit,” Geoff continued. “Perhaps today, I have over thought, but humankind’s drive for progress and advantage always pushes boundaries.
“Given the changes in genetic evaluation over the past 30 years and the escalating pace of change in general, the next 30 years will provide many more opportunities to keep the Merino a viable and profitable enterprise.”
This article appeared in the June 2022 edition of AWI’s Beyond the Bale magazine. Reproduction of the article is encouraged.