Exploitation of genomic technologies for sustainable intensification of dairy goats
Lead Research Organisation:
Scotland's Rural College
Department Name: Research
Abstract
This project addresses key challenges facing the sustainable intensification of dairy goat milk production by using new genetic and genomic technologies to improve the efficiency of milk production and continuity of supply. A key constraint is the inability of dairy goats to naturally breed out of season, thereby affecting year-round supply of milk. This project therefore will identify sires with daughters that readily breed out of season and to generate genomic predictions of merit for this trait. The exploitation of such ability by the wider commercial goat industry in the UK and abroad will be enabled via genomic predictions for this and a range of other key traits via the development in this project of a low density (LD), lower cost customised single nucleotide polymorphism (SNP) array for UK goats. This will facilitate the imputation from LD to the higher density SNP arrays and allow a greater proportion of the outer herd nucleus to be genotyped, thereby creating greater uptake and impact to the wider UK goat population and beyond. The project will ensure that the balance of breeding objectives for dairy goats is sustainable in the long-term, by including routine collection of conformation scoring and mastitis records as proxy indicators of animal health and longevity into the genomic predictions, thereby helping to translate this and previous TSB-funded research into practice
Technical Summary
This project addresses key challenges facing the sustainable intensification of dairy goat milk production by using new genetic and genomic technologies to improve the efficiency of milk production and continuity of supply.This project will identify sires with daughters that readily breed out of season and generate genomic predictions of merit for this trait. The exploitation of such ability by the wider commercial goat industry in the UK and abroad will be enabled via genomic predictions for this and a range of other key traits via the development of a low density (LD), lower cost customised single nucleotide polymorphism (SNP) array for UK goats. This allows the imputation from LD to the higher density SNP arrays and a greater proportion of the outer herd nucleus to be genotyped, thereby creating greater uptake and impact to a the wider UK goat population and beyond.
Planned Impact
This project offers a unique and innovative approach to prepare the UK goat milk industry to address the challenges it will face. The immediate beneficiaries will be Yorkshire Dairy Goats (YDG) and their customers, who will benefit through having goats that are able to breed out of season, and a more efficient farming enterprise with less wastage of young animals. YDG benefits from this project because the LD array (or 'chip') development requires knowledge from their existing project from the 50K array to produce the required SNPs, and through including out of season breeding as a breeding goal trait, it will become their unique selling point. The LD chip enables the proposed work to be more widely exploited and revenue generated for YDG because a 50k chip plus profit is too expensive for commercial goat producers. Once developed, their value is in enabling other goat producers to improve their animals either by buying YDG animals or in testing their own animals for traits they find difficult to record, such as mastitis.They also benefit through having healthier, longer-living animals, through the inclusion of mastitis, functional fitness and longevity into the genomic breeding programme. YDG benefits through their interaction with applied animal scientists at SRUC, which is reciprocated such that scientists are better able to understand and meet industry needs through their interaction with YDG staff. The UK goat industry as a whole benefits from having access to, and increased knowledge from the results of this project through open days, published articles and shared committees (Goat Veterinary Society). This has already been demonstrated through their (and other) invitations to YDG and SRUC staff to provide advice and deliver presentations (outputs) on goat breeding and health issues. The international scientific community benefits through having colleagues with which to compare results and foster closer collaborations in the pursuit of improving and enhancing methodologies. For instance, using the 50K array in the existing TSB-funded project had not been undertaken for a crossbred goat population in the world, neither had including females as well as males in the genotyped animal pool. The Government will benefit from their investment as this project supports a viable rural business and employer (YDG), whose profits are a source of tax revenue. It also benefits through enhanced food security, lower imports and export of superior genetics. Environmental benefits will be realised in this project through having fewer replacement animals waiting until their progeny are lactating, as the identification of potentially superior males can be done soon after birth with the new technology. Environmental benefits are also apparent as genetic selection is a cumulative and sustainable way to improve performance and reduce the inefficiencies. International governments in poorer countries (where subsistence farming is reliant on small ruminants such as many African countries) will also benefit from this project as they often do not have sufficient research capital available to undertake such a project to benefit their own farmers. The results and experience from this project may enable a step-change to occur in these countries through the generation of the LD arrays because they will be able to leap-frog the large investment required to replicate this project elsewhere and benefit from the lower cost LD technology.
Organisations
Publications
Desire S
(2018)
Pseudopregnancy and aseasonal breeding in dairy goats: genetic basis of fertility and impact on lifetime productivity.
in Animal : an international journal of animal bioscience
Mucha S
(2015)
Estimation of genomic breeding values for milk yield in UK dairy goats.
in Journal of dairy science
Mucha S
(2018)
Genome-wide association study of conformation and milk yield in mixed-breed dairy goats.
in Journal of dairy science
Mucha S
(2022)
Animal Board Invited Review: Meta-analysis of genetic parameters for resilience and efficiency traits in goats and sheep.
in Animal : an international journal of animal bioscience
Rupp R
(2016)
Genomic application in sheep and goat breeding
in Animal Frontiers
Sánchez-Molano E
(2019)
Genetic analysis of novel phenotypes for farm animal resilience to weather variability
in BMC Genetics
Title | MOESM1 of Genetic analysis of novel phenotypes for farm animal resilience to weather variability |
Description | Additional file 1: Figure S1. Monthly average of weather measurements: daily temperature (T) and temperature-humidity index (THI). Standard deviations are shown as bars. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM1_of_Genetic_analysis_of_novel_phenotypes_for_farm... |
Title | MOESM1 of Genetic analysis of novel phenotypes for farm animal resilience to weather variability |
Description | Additional file 1: Figure S1. Monthly average of weather measurements: daily temperature (T) and temperature-humidity index (THI). Standard deviations are shown as bars. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM1_of_Genetic_analysis_of_novel_phenotypes_for_farm... |
Title | MOESM2 of Genetic analysis of novel phenotypes for farm animal resilience to weather variability |
Description | Additional file 2: Figure S2. Manhattan plots and QQ-plots: Total milk yield (A), performance change due to daily temperature change (B), performance change due to temperature-humidity index change (C), absolute value of performance change due to daily temperature change (D), absolute value of performance change due to THI change (E). |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM2_of_Genetic_analysis_of_novel_phenotypes_for_farm... |
Title | MOESM2 of Genetic analysis of novel phenotypes for farm animal resilience to weather variability |
Description | Additional file 2: Figure S2. Manhattan plots and QQ-plots: Total milk yield (A), performance change due to daily temperature change (B), performance change due to temperature-humidity index change (C), absolute value of performance change due to daily temperature change (D), absolute value of performance change due to THI change (E). |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM2_of_Genetic_analysis_of_novel_phenotypes_for_farm... |
Description | The ability of goats to breed out of season is a moderately heritable trait that can be selected for, to extend the breeding season of dairy goats. The application of genomic selection has, for the first time in the UK, been exploited in industry to improve the accuracy of selection, reduce inefficiencies in the breeding programme and enabled 'hard to measure' traits (like resistance to disease, out of season breeding ability and conformation traits) to be selected at a much earlier age compared to conventional breeding . The farmer is now marketing his animals using genomic breeding values. |
Exploitation Route | Animals with good breeding values for out of season breeding will enable the industrial partner to market breeding stock with this information. They can also breed more of their own animals out of season to extend the supply of milk. Using genomic selection has enabled the breeder to only keep breeding females and males with above average merit , right from birth, following the submission of a sample for DNA testing. This can be done with the same level of accuracy as previously obtained from progeny-testing, at a far reduced cost and 4 years sooner. The impact of this for around 1/3 of all UK commercially- managed goats is substantial. |
Sectors | Agriculture Food and Drink |
URL | http://elitegoatgenetics.com |
Description | Yes, the industrial partner in this project is using the information discovered in this project to breed more efficient dairy goats by increasing the rate of genetic gain, selecting animals at an earlier age and without having to wait until daughters have reproduced and are in milk, to obtain genomic breeding values . New knowledge linking the SNP array to phenotypic data from key traits and IP relating to the link between the new technology and the data records has generated a unique selling point (USP). A new company has been set up 'Yorkshire Dairy Goats' , (YDG) to exploit this USP via application of the new breeding programme extending beyond the current farm to new business ventures abroad. Latterly the company has invested in sexed semen which is now being marketed. This both reduces waste and streamlines the reproductive processes, to enable high genetic merit goats to be disseminated worldwide. |
First Year Of Impact | 2016 |
Sector | Agriculture, Food and Drink,Education |
Impact Types | Societal Economic |
Title | Genomic selection pipeline for goats |
Description | The data software pipeline has been created to take large volumes of data directly from the farms into a genomic evaluation data handling, QA and processing pipeline that can be run from the client as frequently as needed. These are combined with lab DNA data using the single nucleotide polymorphism (SNP) 5oK chip to generate pedigree and estimate genomic breeding values. |
Type Of Technology | Software |
Year Produced | 2018 |
Impact | This new system enables the client to be in control of how often results are generated. This means that when new batches of data or animals become available, they are automatically uploaded and processed. |
Description | Conference talk - Review of UK dairy goat genetic improvement |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Three papers presented at the World Congress on Genetics Applied to Livestock Production (WCGALP), Auckland NZ Feb 12-16, 2018. (1) Implementation of genomic selection in UK dairy goats. Mucha, Desire, Geddes, Mrode, Coffey & Conington, Paper no. 511. (2) Deriving genomic breeding values for feed intake and body weight in dairy goats. Desire, Mucha, Coffey, Broadbent, Conington, paper no. 818. (3) Genetic parameters for longevity traits in UK dairy goats. Geddes, Desire, Mucha, Coffey, Mrode, Conington, paper no.547 (poster). |
Year(s) Of Engagement Activity | 2018 |
Description | EAAP President of Sheep and Goat Commission, Belfast 29 Aug-2 September 2016 |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I organised the conference sessions for EAAP's Sheep and Goat Commission and chaired the 'free communications' session as well as the business meeting. |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.eaap2016.org/ |
Description | Farmer workshop |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Presentation(s) were made to showcase the outcomes from the R&D in sheep and goats related to disease resistance and using genomics, from this and related projects. Around 130 attendees were there and lively discussion centred around the lack of investment in the formalisation of genetic improvement in the sheep sector overall. |
Year(s) Of Engagement Activity | 2019 |
Description | Goat Veterinary Society |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Gave a talk about the goat research on genetics and genomics of conformation |
Year(s) Of Engagement Activity | 2015 |
Description | Milking Goat Association |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Delivered a talk on genetics of dairy goat production including longevity and out of season breeding ability |
Year(s) Of Engagement Activity | 2017 |
URL | https://en-gb.facebook.com/pg/MilkingGoatAssociation/photos/?ref=page_internal |