Mrode, Raphael A.

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iOnline Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses softwareTraining reportOnline Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses software December 2021The Program thanks all donors and organizations which globally support its work through their contributions to the   CGIAR Trust Fund©2021This publication is copyrighted by the International Livestock Research Institute (ILRI). It is licensed for use under the Creative Commons Attribution 4.0 International Licence. To view this licence, visit https://creativecommons.org/licenses/by/4.0. Unless otherwise noted, you are free to share (copy and redistribute the material in any medium or format), adapt (remix, transform, and build upon the material) for any purpose, even commercially, under the following conditions: ATTRIBUTION. The work must be attributed, but not in any way that suggests endorsement by ILRI or the author(s).NOTICE:For any reuse or distribution, the licence terms of this work must be made clear to others. Any of the above conditions can be waived if permission is obtained from the copyright holder. Nothing in this licence impairs or restricts the author’s moral rights. Fair dealing and other rights are in no way affected by the above. The parts used must not misrepresent the meaning of the publication.  ILRI would appreciate being sent a copy of any materials in which text, photos etc. have been used.Editing, design and layout—ILRI Editorial and Publishing Services, Addis Ababa, Ethiopia.Patron: Professor Peter C. Doherty AC, FAA, FRS Animal scientist, Nobel Prize Laureate for Physiology or Medicine–1996Box 30709, Nairobi 00100 Kenya Phone  +254 20 422 3000 Fax      +254 20 422 3001 Email ilri-kenya@cgiar.orgilri.org better lives through livestock  ILRI is a CGIAR research centreBox 5689, Addis Ababa, Ethiopia Phone +251 11 617 2000 Fax +251 11 667 6923 Email ilri-ethiopia@cgiar.org ILRI has offices in East Africa • South Asia • Southeast and East Asia • Southern Africa • West AfricaContentsAcknowledgements                            ivIntroduction                              1Participants                              2Course instructors                            3 Course facilitators                           4 Outputs and outcomes                          5 Expected outcome                           5Conclusions                              6Other comments                             6vOnline Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses softwareAcknowledgementsThe Bill & Melinda Gates Foundation is gratefully acknowledged for funding the African Dairy Genetic Gains (ADGG) and this training course. 1Online Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses softwareIntroductionCurrently, the African Dairy Genetic Gain (ADGG) program (https://africadgg.wordpress.com/category/adgg/) operates fully in two countries: Ethiopia and Tanzania, and has commenced preliminary activities in Uganda, Rwanda, Kenya and Nigeria. The aim of this course was to develop and strengthen the capacity of the NARS to effectively undertake and manage their respective national dairy and livestock performance recording and genetic evaluation programs using the MiX99 software with the support of the Natural Resources Institute Finland (Luke), and ADGG. The ADGG program recently acquired the license for the use of MiX99 software for genetic evaluation purposes, therefore the specific aim of the course was to provide participants with a working knowledge on Linux computing environment and the use of the software MiX99 for genetic and genomic evaluations. A hands-on approach was adopted using a data set of milk yields and body weight, pedigree and genotypes generated from the ADGG database, thereby providing participants with the necessary practical skills. In addition, participants were equipped with practical skills on post-processing of breeding value solutions to build indices, and rank top bulls and cows.2Online Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses softwareParticipantsA total of 8 females and 17 males participated in the course, with 4 participants from Tanzania, 8 from Ethiopia, 3 from Rwanda , 3 from Nigeria and 6 from Kenya. Chinyere Ekine-Dzivenu, a statistical geneticist in the International Livestock Research Institute (ILRI) Livestock Genetics team also participated in the course on 13-17 December. The participants from each country were either directly associated with current ADGG activities or sources of support to the national Dairy Performance Recording Centres (DPRCs) in each country. 3Online Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses softwareCourse instructorsEnyew NegussieSenior scientistNatural Resources Institute Finland (Luke)FinlandMartin LidauerPrincipal scientistNatural Resources Institute Finland (Luke)FinlandProf. Raphael MrodePrincipal scientist, Quantitative dairy cattle geneticsILRI , Nairobi, Kenya and Professor, Quantitative Genetics and Genomics, SRUC, Scotland4Online Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses softwareCourse facilitatorsEric Anyona from the ILRI Livestock Genetics Team was in charge of all logistics and smooth running of the course with IT support provided by the ILRI ICT team.Brief  outline of  proceedings of  training course• The course commenced at 09:00 hours using Zoom and finished at about 16.30 hrs daily, with a lunch and two coffee breaks. The lecture notes and materials for all practical for each day were stored in Microsoft Teams, which all participants had access to. • The principal investigator (PI) for ADGG, Okeyo Mwai, then welcomed participants in the first day, gave an overview of  ADGG and opened the training course.• The course outline was presented by Enyew Negussie. • The course then commenced. The main areas covered included introduction to Linux computing environment, editors, theoretical basis of  GBLUP and GBLUP and Single step, the use of  MiX99 software for BLUP models: animal, repeatability, multi-trait BLUP models and genomic models such as GBLUP and ssGBLUP. How to set up the instruction file (CLIM file) for MiX99, executing the software and interpretation of  various outputs were covered. Also computation of  reliabilities using the software was also taught in addition to the use of  software Relax2 to compute the relationship matrix and Hginv to compute inverse of  G of  H matrix for ssGBLUP. • The daily schedule was such that the presentation of  lectures was interspersed with practical sessions and then theory sessions. The participants in each country were in one location for most of  the countries, allowing them to work in groups in the practical sessions using Linux installed in their laptops. • The practical sessions were based on an example data set on milk yield, body weight, pedigree and genotypes derived from the ADGG database. • On the last day of  the course, participants were given a lecture and practical sessions to equip them with practical skills on post-processing of  breeding value solutions to build genomic indices, and ranking top bulls and cows for use in practice at their respective institutes.• Finally, in the afternoon of  the final course day a closing remark was given by each of  the course instructors, and Okeyo Mwai, gave the final remarks and officially closed the training course. • All participants received a certificate of  attendance and a link to a repository containing all course materials.5Online Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses softwareOutputs and outcomes• Electronic lectures notes, software and practical examples on the of  linear mixed models and use of  MiX99 software for the prediction of  breeding values and genomic selection.• Procedure for the use of  Linux environment for computing and data analysis.• Lecture notes, steps and programs (R) for post processing GEBV solutions to build indices and rank top bulls and cows Expected outcomeNARS equipped with practical skills in methods for animal quantitative genetics to effectively manage their respective national dairy and livestock performance recording and the use of MiX99 software for genetic evaluation systems.Established network between NARS in Tanzania, Kenya, Nigeria, Uganda and Rwanda and Ethiopia in supporting each other in running of the DPRCs in each country.6Online Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses softwareConclusions• Participants were brought up-to-date on methods in quantitative genetics and the use of  MiX99 software for the practical application of  several genetic evaluation models. We feel the expected outputs and outcomes were achieved.• The practical sessions afforded participants to use of  MiX99 and other software, to work in the Linux environment and undertake breeding value prediction and their reliabilities. In addition, the training equipped them with skills to build indices and rank top bulls and cows.• Basic skills of  programming were also taught and the use of  the Unix system.• Participants felt stretched but also felt it was good training for them.• The course afforded an opportunity for networking and future collaboration among participants and lecturers.Other commentsThe feedback from the participants was very positive and indicated they have learned a lot. Extending the course period by few days and especially dedicating the first one or two days of the course for covering exclusively Linux operating systems, editors and computing environment issues were strongly suggested. 

Online Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses software

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Online Natural Resources Institute Finland (Luke)-African Dairy Genetic Gains (ADGG) training course on Mix99 genetic genomic analyses software

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