12 minute read
New inbreeding calculator on the way
Inbreeding is something which concerns some breeders more than others, but which, arguably, all breeders should be paying attention to at some level.
As Society technical and data services manager Ed Smith explains: “Inbreeding is essentially the mating of related individuals or of individuals with shared ancestors.
“And while linebreeding can be used to establish desirable traits within a family or flock, it is a form of inbreeding and the offspring should be carefully monitored for any undesirable characteristics.
“A balance needs to be maintained between selecting animals to optimise rates of genetic gain and minimise levels of inbreeding,” he says.
While some level of inbreeding cannot be avoided for most pedigree breeds and inbreeding risk should not be the only selection consideration, reducing the inbreeding load in a population is a valuable goal, says Dr Smith.
An individual animal’s level of inbreeding is reported as a percentage and presented in iTexel as the Inbreeding coefficient (or F) value. A minimum of five generations are required to give confidence in the calculated inbreeding coefficients.
“This is one of the benefits of the pedigree flock book and iTexel registry service provided by the Society and another reason to maintain accurate records.
“In general, the lower the level of inbreeding the better, though a threshold value of 7% has been determined to be an acceptable level of inbreeding within a breeding programme,” he explains.
The percentage estimate of inbreeding is based on the relatedness of individuals in a pedigree and examples of percentage inbreeding values for different matings are presented in Table 1.
Table 1. Expected level of inbreeding from example matings “Increasing levels of inbreeding can result in inbreeding depression, where performance can suffer. Studies in other sheep breeds have demonstrated that as inbreeding increases ewe breeding weights and fertility are reduced and lamb birth and weaning weights are lower.
Relationship Inbreeding coefficient (F)
Father x daughter or mother x son 25.0 % Brother x sister 25.0 % Grandfather x granddaughter or grandmother x grandson 12.5 % Half-brother x half-sister 12.5 % Uncle x niece or aunt x nephew 12.5 % Great-grandfather x great-granddaughter or great-grandmother x great-grandson 6.25 % Half-uncle x niece or half-aunt x nephew 6.25 % First cousins 6.25 %
Understanding the risks associated with inbreeding and knowing how breeding decisions will impact future generations is being made easier with the Society’s new inbreeding decision calculator.
“It can be argued that any animal is only one mating away from being outbred and there are examples of this in iTexel from well-managed outbred matings, such as the ram lamb below from the Incheoch flock (Fig. 1). The lamb’s sire and dam both had F values higher than that determined in the lamb itself. Indeed, two unrelated animals, each with a high F value could be mated to each other to produce outbred offspring with a low inbreeding coefficient,” adds Dr Smith.
Fig.1. Example of an outbred lamb birth-notified in 2020.
Analysis of the average level of inbreeding in birth-notified Texels over the past ten years (Fig. 2) indicates that at the breed level, the level of inbreeding is increasing and was just below 5.5%, on average, for 2020-born animals.
“The overall rate of increase in inbreeding has remained unchanged over the past 10 years. For individual flocks that birth-notified five or more lambs, average flock-level inbreeding coefficients ranged from zero to more than 18%.
“Over the past 10 years the number of flocks that have an average inbreeding coefficient over 7% has risen from 59 (4.2%
of flocks) in 2011 to 229 (16.2 %) in 2020 (Fig 3). Collectively this indicates that inbreeding should be closely monitored both at the breed level and within individual flocks; and is the responsibility of all breeders,” warns Dr Smith.
Fig. 2. Numbers of birth-notified lambs with inbreeding coefficients above and below 7 % each year and the average level of inbreeding in the national pedigree Texel flock
Fig. 3. Number of flocks with an average inbreeding coefficient above and below the 7 % threshold over time
“In addition to levels of inbreeding, the pedigree breed Effective Population Size must also be considered. This is a measure that estimates the minimum number of animals that would be required to produce the lamb crop of a given year while maintaining the same level of genetic diversity; and is calculated from the number of sires and dams that produce offspring.
“This differs from the pedigree Texel census population size of all sires and dams. Over the past 10 years the effective population size of the Texel breed has been reduced by almost 900 animals (Fig. 4) indicating a reduction in genetic diversity in this time. Coupled with the increase in levels of inbreeding, this reduction means there is a greater chance of the risk of inbreeding increasing at a faster rate. A smaller effective population makes it more difficult for breeders to find suitable animals to create outbred crosses,” says Dr Smith.
The number of animals birth notified with an inbreeding value above 7% has also increased in recent years (Fig. 3) causing approximately one in six animals (16%) of all birth notifications in 2020 to have an F value above 7%. This increase appears to be driven by the increase in the use of embryo transfer (ET) technology with one in three ET lambs having an inbreeding coefficient higher than 7% in 2020 compared to one in eight non-ET lambs.
“To help Texel breeders actively manage levels of inbreeding within their flocks the Society has developed tools and resources that can be used to assist in making breeding decisions. As a result of moving to iTexel in 2020, the Society ensured that inbreeding values for individual animals were published on iTexel earlier than in previous seasons, now making this important information available prior to the sales season. This helps to inform any purchasing decisions breeders have to make.
“The Society will also release a new style inbreeding calculator/ predictor through iTexel for this breeding season. This will be simple to use on smartphones / tablets and PCs and will predict the inbreeding coefficient of lambs sired by any sire in the Society pedigree database mated to any ewe within a member’s flock,” he explains.
Members who have logins to iTexel will be able to use this software to export a report of predicted inbreeding values for different matings and make informed breeding decisions about their flocks.
“Keep an eye on your iTexel page and inbox for further information on this software release and how to use it.
“While the current effective population size and levels of inbreeding are acceptable at the pedigree breed level, the trends need to be monitored. Actions of breeders individually and collectively over the coming years will be better informed because of the resources the Society is making available. This will make managing animal, flock and breed levels of inbreeding simpler,” adds Dr Smith.
Fig. 4. Number of lambs with an inbreeding coefficient (F) over 7 % that are birth-notified each year, proportion that are ET lambs, and pedigree Texel effective population size
Glossary
Inbreeding coefficient (F) – a measure, expressed as a percentage, of the level of inbreeding within an animal
Inbreeding depression – a reduction in the level of performance of an individual or population caused by increasing levels of inbreeding
Effective population size – the minimum number of animals required to produce one generation whilst maintaining levels of genetic diversity
Helping members to manage inbreeding
• Inbreeding coefficient values available earlier in the season à make informed purchasing decisions • Inbreeding prediction calculator on iTexel later this year à make informed breeding decisions • Increasing the visibility of the F value across iTexel à be more aware of levels of inbreeding in your flock
Computerised semen analysis aims to boost ET success rates
Amove to Computer Assisted Semen Analysis (CASA) is enabling Shropshire-based embryo transfer specialists Farmgene to increase the accuracy of semen assessment and build a better picture of the reasons for success or failure in ET programmes.
Farmgene founder Ian McDougall says the introduction of CASA was driven by a desire to better serve the company’s customers and achieve better results with ET work across a range of breeds.
“Texels are by far and away the most numerous breed we work with and there are many factors which affect semen quality which we can’t always fully analyse with a standard microscope and the naked eye.
“Using CASA enables us to get a far better picture of semen quality and give much better assessments of likely success,” he explains.
“Essentially CASA, which is used by all the major bovine and porcine semen companies, allows us to make far better assessments of the morphology of motile semen. “Using a standard microscope is great for analysing morphology of non-motile semen, but when it comes to motile semen you simply can’t analyse it well enough with your own eyes. Issues such as proximal droplets are hard to pick out in motile semen, but can have a huge impact on AI and ET success rates, reducing fertilisation efficiency to below 50%.”
Farmgene semen laboratory manager Ana Christensen says the use of CASA has meant that all frozen semen deemed suitable for use have met strict quality criteria and can then be allocated to three groups; Gold, Silver and Bronze. “Gold is the very best combination of high progressive motility and high normal morphology and will be the best choice for ET work, followed by Silver and Bronze.
“Using CASA means we can better inform clients of the chances of success. However, this is only the first step in predicting fertilisation potential.
“The next step is to look into advanced semen analysis and sperm functional tests which will allow us to determine if the sperm is capable of undergoing the changes needed in the uterus and oviduct to allow successful fertilisation and that will further enhance the service we can offer and the chances of success,” says Dr Christensen.
Mr McDougall says the company is driven by a desire to always do better and not simply repeat the same process and hope for better results the next time. “If we do all we can to better understand what has caused success or failure we can hopefully improve the results the next time around.
“There are a huge number of variables in AI and ET programmes and we record every animal we work with in a bespoke database which allows us to interrogate the data and see where we can improve or try a different tweak to the programme.”
CASA also enables Farmgene to offer reassurance when exporting semen due the higher quality of the analysis. “We can provide an accurate analysis of both semen quality and the number of sperm within a dose. For example when exporting to Scandinavia for use in cervical AI programmes we can provide a guarantee that the doses contain the required number of normal progressive sperm per dose that the buyer desires.
“We are also able to freeze semen in a variety of forms and in different extenders which is helping achieve better freezing results than have been previously achieved. In particular we are finding we are now able to freeze semen from some rams whose semen has been difficult to freeze historically.
“Semen is generally frozen in one or two dose pellets or in 0.25ml straws. However, we’re now freezing some in 0.5ml straws in our bespoke extender and that has enabled us to freeze from rams which have previously been problematic.
“There are lots of different reasons why semen will and won’t freeze well and freezing medium and dose concentration are just the tip of the iceberg. Crucially, the 0.5ml straws have a different freezing curve to smaller sizes due to the different surface area:volume ratio and that is one factor which appears to be helping,” adds Mr McDougall.
Study finds recorded genetics offer greatest gains
Increased use of progressive maternal genetics from performance recorded flocks has been shown in a desktop study to have the potential to result in a four-fold increase in monetary gain compared to the status quo.
The study, conducted as part of the Smarter project of which the Society is a partner, investigated whether the Irish sheep population would benefit from elite maternal genetics sourced from Irish or New Zealand flocks and if so how best to use those genetics to maximise gain.
In the study the genetic improvement across future generations of commercial sheep in monetary terms of alternative breeding strategies, was quantified, with a number of subpopulations modelled too, reflecting the current structure of the Irish sheep industry.
The base scenario assumed no change in current breeding strategies, while a progressive Irish scenario looked at the impact of an increased market share for performance recorded genetics.
Meanwhile, a New Zealand scenario investigated the impact of importing New Zealand rams every five years that were elite for maternal genetic merit.
The greatest monetary gain was achieved by the progressive Irish scenario, which had the potential for a four-fold increase in monetary gain compared to the base scenario.
For the strategy that imported elite New Zealand germplasm, the benefit was almost three times greater than the base scenario. The long-term impact of importing elite New Zealand germplasm was hampered by the foreign population having a poor long-term genetic trend and, therefore, benefits quickly plateau.
The researchers say the results demonstrate the potential to accelerate the benefit to the Irish sheep industry without the use of imported genetics, but through the strategic use of progressive genetics.
Society data and technical services manager Ed Smith said the study had yielded similar results to the Society’s own study which was completed by AbacusBio in 2015. “Both of these studies have shown that using performance recorded maternal genetics can have a significant impact on industry output and income.
“The growing influence of Texels as a maternal breed across the UK means there is a significant opportunity to accelerate gains by using higher genetic merit texelplus sires to breed female replacements in commercial flocks, which will be further supported by the adoption of measuring hard to measure traits such as footrot and mastitis as part of the Society’s genomic porgramme.” he added.
