SMAll RuminanTs breeding for Efficiency and Resilience

Deliverables

Documents, reports (5)

Method for identifying environmental challenge events and assessment of their value for selection for resilience

Longitudinal data is so far not used to infer and report unobserved challenges We will describe a method that from repeated phenotypic data milk yield litter size will identify critical points challenging events such as unobserved infections in the lifespan of animals The method will be able to evaluate and identify superior animals for resilience to such events

A report for optimum contribution to manage diversity at critical regions and to assist mating design to maximise heterozygosity and expression of heterosis and evaluation of level inbreeding rate across genomic regions and their impact on performance

Genomic selection requires genomic management of diversity We will describe a method to first assess critical regions possibly carriers of deleterious recessive mutations and second maximize diversity in particular in those regions using optimal contributions and mate allocation

A report of an improved method to calculate genomic relationship across individuals of different purebred and crossbred populations

Joint multiple breed and crossbred genomic evaluations are not fully developed in small ruminants We will create a method to compute joint genomic relationships across individuals within a single breed across multiple breeds and across all possible crosses in a manner that genomic evaluations can generate the most accurate estimates of breeding values within and across populations profiting the information of all populations

Method for assessing potential bias due to design of cross-validation analysis

Crossvalidation studies in small ruminants may underestimate benefit accuracy and genetic progress of genomic selection due to short size of studies and the use of selected animals We will describe a crossvalidation method that generates meaningful estimates of accuracy and expected genetic progress from genomic selection

First batch of practice abstract for end-users

"The resulting innovative knowledge and easy accessible end-user material from this project will feed into the EIP-AGRI (The agricultural European Innovation Partnership) website for broad dissemination. The end-user material to be produced contains a substantial number of summaries for practitioners in the EIP common format (""practice abstracts""), including the characteristics of the project (e.g. contact details of partners, etc). A full package of practice abstracts will be produced by the project, containing all the outcomes/recommendations which are ready for practice. A ""practice abstract"" is a short summary of around 1000-1500 characters (word count – no spaces; see below) which describes the main information/recommendation/practice that can serve the end-users in their daily practice. Guidance and templates for these practice abstracts are available on the EIP-AGRI web site: http://ec.europa.eu/eip/agriculture/en/content/eip-agri-common-format. A total target number of 10 practice abstracts is foreseen for the project. Five ares expected to be delivered in the first batch. "

Websites, patent fillings, videos etc. (1)

Website on line, & communication package

Development and launching of the project website and creation of main communication supports

Publications

Peer reviewed articles (21)

The value of genomic relationship matrices for estimating inbreeding.

Author(s): Villanueva B, Fernández A, Saura M, Caballero A, Fernández J, Morales-González E, Toro MA, Pong-Wong R
Published in: Genetics Selection Evolution, 53, 2021, Page(s) 42, ISSN 0999-193X
Publisher: BioMed Central
DOI: 10.1186/s12711-021-00635-0

Changes in allele frequencies when different genomic coancestry matrices are used for maintaining genetic diversity.

Author(s): Morales-González E, Fernández J, Pong-Wong R, Toro MA and Villanueva B
Published in: Genetic Selection Evolution, 2021, ISSN 0999-193X
Publisher: BioMed Central
DOI: 10.3390/genes12050673

Islands of runs of homozygosity indicate selection signatures in Ovis aries 6 (OAR6) of French dairy sheep

Author(s): Rodríguez-Ramilo S., Reverter A., Legarra A.
Published in: JDS Communications, 2 (3), 2021, Page(s) 132-136, ISSN 2666-9102
Publisher: Elsevier Inc and FASS Inc.
DOI: 10.3168/jdsc.2020-0011

Potentials of using milk performance data and FAMACHA score as indicators for Targeted Selective Treatment in Lacaune dairy sheep in Switzerland

Author(s): K. Schwarz, B, Bapst, M. Holinger, S. Thüer, I. Schleip, S. Werne
Published in: Veterinary Parasitology, 2020, ISSN 0304-4017
Publisher: Elsevier BV
DOI: 10.1016/j.vpoa.2020.100030

Genomic and pedigree estimation of inbreeding depression for semen traits in the Basco-Béarnaise dairy sheep breed.

Author(s): Antonios S., Rodríguez-Ramilo S., Aguilar I., Astruc J., Legarra A., VITEZICA Z.
Published in: Journal of Dairy Science, 104, 2021, Page(s) 3221-3230, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2020-18761

Theoretical and empirical comparisons of expected and realized relationships for the X-chromosome.

Author(s): Druet T., Legarra A.
Published in: Genetics Selection Evolution, 104, 2021, Page(s) 52, ISSN 0999-193X
Publisher: BioMed Central
DOI: 10.1186/s12711-020-00570-6

The levels of artificial insemination and missing sire information make genomic selection not always beneficial in meat sheep

Author(s): J. Raoul, J.M. Elsen
Published in: Animal, 2021, ISSN 1751-7311
Publisher: Cambridge University Press
DOI: 10.1016/j.animal.2020.100040

Livestock disease resilience: From individual to herd level

Author(s): Doeschl-Wilson A, Knap P.W., Opriessnig T. and More S.J.
Published in: Animal, 15, 2021, Page(s) 100286, ISSN 1751-7311
Publisher: Cambridge University Press
DOI: 10.1016/j.animal.2021.100286

Why breed disease-resilient livestock, and how?

Author(s): Knap P.W. and Doeschl-Wilson A
Published in: Genetics Selection Evolution, 52, 2020, Page(s) 60, ISSN 0999-193X
Publisher: BioMed Central
DOI: 10.1186/s12711-020-00580-4

Detection of unrecorded environmental challenges in high-frequency recorded traits, and genetic determinism of resilience to challenge, with an application on feed intake in lambs.

Author(s): Garcia-Baccino C. A., MARIE-ETANCELIN C., Tortereau F., Marcon D., Weisbecker J.-L., Legarra A.
Published in: Genetics Selection Evolution, 53, 2021, ISSN 0999-193X
Publisher: BioMed Central
DOI: 10.1186/s12711-020-00595-x

Exploring the inclusion of genomic information and metafounders in Latxa dairy sheep genetic evaluations

Author(s): I. Granado-Tajada, A. Legarra, E. Ugarte
Published in: Journal of Dairy Science, 103/7, 2020, Page(s) 6346-6353, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2019-18033

Short communication: Methods to compute genomic inbreeding for ungenotyped individuals

Author(s): A. Legarra, I. Aguilar, J.J. Colleau
Published in: Journal of Dairy Science, 103/4, 2020, Page(s) 3363-3367, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2019-17750

Considerable potential exists to improve lambing performance traits in sheep through breeding

Author(s): N. McHugh, T. Pabiou, E. Wall, K. McDermott, D.P. Berry
Published in: Livestock Science, 235, 2020, Page(s) 104007, ISSN 1871-1413
Publisher: Elsevier BV
DOI: 10.1016/j.livsci.2020.104007

Genetic and genomic studies in ovine mastitis

Author(s): C. Oget, G. Tosser-Klopp, R. Rupp
Published in: Small Ruminant Research, 176, 2019, Page(s) 55-64, ISSN 0921-4488
Publisher: Elsevier BV
DOI: 10.1016/j.smallrumres.2019.05.011

Genetic and nongenetic factors associated with the fate of maiden ewe lambs: slaughtered without ever lambing versus retained for breeding1

Author(s): Noirin McHugh, Thierry Pabiou, Kevin McDermott, Eamon Wall, Donagh P Berry
Published in: Translational Animal Science, 4/1, 2020, Page(s) 242-249, ISSN 2573-2102
Publisher: Oxford University Press on behalf of the American Society of Animal Science
DOI: 10.1093/tas/txz156

Behavior of the Linear Regression method to estimate bias and accuracies with correct and incorrect genetic evaluation models

Author(s): F.L. Macedo, A. Reverter, A. Legarra
Published in: Journal of Dairy Science, 103/1, 2020, Page(s) 529-544, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2019-16603

Selection and drift reduce genetic variation for milk yield in Manech Tête Rousse dairy sheep.

Author(s): Macedo F., Christensen O., Legarra A.
Published in: JDS Communications, 2021, Page(s) 31-34, ISSN 2666-9102
Publisher: Elsevier Inc and FASS Inc.
DOI: 10.3168/jdsc.2020-0010

Inbreeding and effective population size in French dairy sheep: Comparison between genomic and pedigree estimates

Author(s): T. Rodríguez-Ramilo, J. M. Elsen, A. Legarra
Published in: Journal of Dairy Science, 2019, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2018-15405

Genetic analyses of live weight and carcass composition traits in purebred Texel, Suffolk and Charollais lambs

Author(s): S. Fitzmaurice, J. Conington, N. Fetherstone, T. Pabiou, K. McDermott, E. Wall, G. Banos, N. McHugh
Published in: Animal, 2020, ISSN 1751-7311
Publisher: Cambridge University Press
DOI: 10.1017/s1751731119002908

The correlation of substitution effects across populations and generations in the presence of non-additive functional gene action.

Author(s): Legarra A., Garcia-Baccino C.A., Wientjes Y.C.J., Vitezica Z.G.
Published in: Genetics, Volume 219, Issue 4, 2021, ISSN 1943-2631
Publisher: Genetics Society of America
DOI: 10.1093/genetics/iyab138

Identification of homozygous haplotypes carrying putative recessive lethal mutations that compromise fertility traits in French Lacaune dairy sheep

Author(s): M. Ben Braiek, S. Fabre, C. Hoze, J.M. Astruc, C. Moreno-Romieux
Published in: Genetics Selection Evolution, 2021, ISSN 0999-193X
Publisher: BioMed Central
DOI: 10.1186/s12711-021-00634-1

Conference proceedings (3)

Repeatability of udder health and welfare traits of semi-extensively reared dairy goats in Greece

Author(s): Sotiria Vouraki, Athanasios I. Gelasakis, Vasileia Fotiadou, Georgios Banos, Georgios Arsenos
Published in: Book of Abstracts of the 72nd Annual Meeting of the European Federation of Animal Science, 2021, Page(s) 272-272, ISSN 1382-6077
Publisher: Wageningen Academic Publishers
DOI: 10.3920/978-90-8686-918-3

Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science

Author(s): Scientific Committee
Published in: 2019, ISBN 978-90-8686-339-6
Publisher: Wageningen Academic Publishers
DOI: 10.3920/978-90-8686-890-2

On the accuracy of estimating resilience

Author(s): Ghaderi-Zefreh M, Riggio V, Matika O, Wilson A, Pong-Wong R
Published in: Proceeding of the 71st Annual Meeting of European Federation of Animal Science, 2020
Publisher: .