Livestock_gene_synthesis

Livestock and Fish genetics flagship synthesis workshop Zen Garden, Nairobi, Kenya 10-11 October 2016

toc
 * Words of welcome by Tom Randolph**

This will help us prepare the report over the entire 5-year program. We need this basis for the next phase. This flagship was well received fro the next phase and we'll always be subject to questions about 'what are you building up', what are you continuing in the second phase. This workshop is critical for establishing that and to make sure that everyone's on the same page. I've been helping synthesise the annual report and it wasn't always clear what the big picture was so I'm eager to hear what stories you have to tell about what was achieved over the past years. We're also preparing a glossy report that will be 20 pages long and capturing highlighting but not capturing the essence of the whole body of work and what the genetics component was able to achieve. I hope to be able to come back some time tomorrow to hear what's been coming out.

We need to get the bigger picture and key achievements. It will help us for the reports Tom talked about. This will be a writing workshop. We'll identify some topics that we'll write synthesis briefs about, on cross-cutting themes and to learn lessons. We have enough time to complete this work and tomorrow we'll have an editor here to help us finalise this. We'll be mapping our projects, looking back at the beginning. Then we'll identify the topics of these briefs we'll be writing and we'll look at the key messages of each brief etc. and organise group feedback. Then we'll have some time for writing. We're very busy here so that's why we keep you from 9 to 5pm here.
 * Introduction by Karen Marshall**


 * **Q**: Are you referring to the scientific audience or other audiences?
 * **A**: Our partners, donors, other parties eager to undertake similar activities. These are not about projects or project outputs but overarching topics where we've learned how we're doing things differently from 5 years ago.

=Individual mapping of projects including genetic activities= This is the list of projects that were mapped:
 * Before 2012** (and continuing over the CRP period)


 * 1) Breeding uniform tilapia
 * 2) Mutual learning of livestock keepers for adapting to climate change
 * 3) Bio repository
 * 4) Reducing impact of infectious diseases on v. chickens in Ethiopia
 * 5) GEF-Asia
 * 6) Genetic improvement of gift tilapia
 * 7) Horro improvement
 * 8) Red massai x Dorper QTL for disease resistance
 * 9) Breeding programs for local breeds
 * 10) Animal genetic training resource
 * 11) Gift correlated responses for selection
 * 12) Angora goat VC
 * 13) Kapiti breeding programs
 * 14) AnGR-AU-IBAR capacity strengthening
 * 15) Reproductive technology platform
 * 16) Dairy Genetics East Africa
 * 17) Progebe
 * 18) (__**All projects following, from 2012**__) Magic cow
 * 19) Senegal dairy genetics
 * 20) Small ruminants improvement Africa-Brazil marketplace
 * 21) Optimization of breeding program for smallholder farmers
 * 22) Small ruminants improvement program ICARDA-Egypt collaoration
 * 23) Genetic improvement of tilapia Abbassa strain
 * 24) Comparative genome sequence analysis to identify disease traits related genes...
 * 25) Genetic characterization of Ethiopian goats
 * 26) Community-based Small Ruminants breeding
 * 27) Sheep genetics in Asia
 * 28) (__**all projects following, from 2013**__) LIVES
 * 29) Uganda pig value chain development
 * 30) Cattle genome characterization (pilot)
 * 31) Carp genetic improvement
 * 32) Mobile recording in CBBP
 * 33) Reducing vulnerability in Somali communities
 * 34) B3Africa ( start in 2015 )
 * 35) (__**all projects following, from 2014**__) Breeding strategies for conservation and sustainable use of livestock genetic resources in Sub-Saharan Africa
 * 36) AGRITT: Tanzania dairy genetics
 * 37) Vietnam pigs (VP)
 * 38) Dual purpose cattle
 * 39) Mola genetics
 * 40) (__**all projects following, from 2015**__) PEARL: developing a framework for decision support tools to optimize dairy in East Africa
 * 41) Ethiopia Small Ruminants value chain SmaRT-Ethiopia
 * 42) African Chicken Genetic Gains (ACGG)
 * 43) Africa Dairy Genetic Gains (ADGG)
 * 44) Small ruminants value chain development
 * 45) Accelerated Value Chain Development (AVCD)-Dairy
 * 46) SPIA molecular tools projects
 * 47) Capacity building in quantitative genetics and genomics
 * 48) Accelerated value chain development program (AVCD)-Livestock
 * 49) (__**all projects following, from 2016**__) Center for Tropical Livestock Genetics and Health (CTLGH)
 * 50) Closing the yield gap
 * 51) Integrated crop-livestock
 * 52) Fish biorepository ( start in 2015 )
 * 53) Genomic tools for Tilapia ( start in 2013 )
 * 54) Feed efficiency in tilapia ( start in 2014 )

=Individual mapping of activities under each project=

Tools

 * Guidelines for CBBPs (26)
 * Harmonized tools for genetic & phenotypic characterization of AnGR developed and promoted in Africa (14)
 * SNP tools developed for Abbassa strain. Importance: Maintain bigour of breeding (productivity). Partnes: James Cook Unit Australia (14)
 * Review of reproductive diversity in Ethiopia sheep breeds (44)
 * Guidelines and on regional AnGR gene banks developed / used promoted (14)
 * New OK tools for performance recording and feedback under smallholder dairy systems developed and promoted (43)
 * Suite of survey tools for assessment of AnGR use (ACGG, DGE, Vietnam pig, Uganda pig, SDG, Somali pastoral)
 * ex determination genes in GIFT identified. Importance: future tools for prod. manipulation (single sex ER). Partners: Stirling Uni (55?)
 * Facilities for tissue preservation protocols for use developed. Collection from breeding programs begun. Importance: valuable research resource (52)
 * Assessment: baseline survey (5000 HHs); asssessment of breed preference and breeding objectives; Value chain analyses for dairy, beef and shoats; rapid appraisal of problems and interventions in value chains of livestock (LIVES)

Genetics

 * Characterization of SR genetic resources in Ethiopia, Egypt, Sudan (12, 20, 25, 26)
 * Demonstrated GxE in red maasai & Dorper sheep (9)
 * Etablishment of FXNAL autonomous CBBP in Ethiopia (25, 26, 41)

Genomics

 * Genetic uniqueness of Asian sheep revealed - Genomic regions for adaptation to challenge environments identified (27)
 * Signature of selection for heat and tolerance and milk production in indigenous African breeds identified (24)
 * Egypt. Identified signature of selection for heat tolerance in Egypt (22, 51)
 * Opened up opportunity to do the same in Sudan (22, 51)
 * Other**
 * Unravelling the contribution of improvement management & genetics in productivity improvement in the Sahel project (Karen- Dairy) (19)
 * Extensive collections made (40 sites, 4 tiems = seasons) in Bangladesh. Partners: ILRI, CCAFS DOF. Importance: highly nutritiuos fish important for women and children assessed as fisheries or aquaculture resource. Baseline info for decision making) tracking response to climate change (39)
 * Correlated responses of survival reproduction to selection for growth in GIFT estimated: No negative response therefore selection ok. No unintended consequences for production + 4 papers published. Partners: Unic. Sains Malaysia, Dept. of Fishery Malaysia (11)

CBBP

 * Development of a data recording management system for CBBP (26)
 * Improvements of livelihoods of CBBP participants (26, 41)
 * Development of mobile recording systems in CBBP (32)
 * Outscaling CBBPs in Afriac (26, 41)
 * Genetic imprvoement of production traits in CBBP (26, 41)

Breeding programs

 * Breeding strategies for profitable use of red maasai sheeep developed and promoted (35)
 * Genetic improvement strategy for Uganda pigs identified (UP)
 * Genetic improvement strategy for smallholder dairy systems in Senegal identified (SDG)
 * Horro breed first susccessful breeding program for indigenous chicken in Ethiopia (7)
 * Outlined strategy for improved breeding of native sheep (9)
 * Breeding program first generation of RoNU produced (31) Brood stock for base populations of catla-silver carp collected. Mol. assessment of all 3 spp done. Importance: Rohu 30% of AQ production in Bangladesh (now 5th country for production worldwide; partners: USAID). Research question: performance (GxE) of RoHu in monoculture vs. polyculture tested (31)

Traits

 * Genetic improvement of fibre quality in tajik angora goats (12)
 * Imrpoved red maasay sheep multiplied and promoted in Kenya (12)

Reports influencing decisions

 * Donors influenced (resources mobilized) to fund ADGG/PAID projects (16)
 * Draft report on the state of Africa's AnGRs: population, trends, users (14)
 * Bio-economic model to assess eftects of selection in __fish__ on management (21)

Improved use

 * Horro breed among tested breeds distrib. in ACGG. One country (7)
 * Production of appropriate genetics for different production systems (a) Boran x Zebu for beef b) HF/J x zebu for dairy, c) selection/breeding for shoats (LIVES)
 * Produced generations support projects: Maria, N. . Dissemination to Egypt to x farms. On farm performance assessed. Production improved some locations. Profitability improved. Partners: James Cook Univ. Australia (23)

Delivery model partnerships etc.

 * Partnerships (PPP) to deliver desired dairy genetics and extension in emerging dairy regions developed and put into practice at scale (45)
 * Delivery of genetics: Bull stations; hormone synchro-beef, dairy, shoats; private/farmer AI tech; community breeding groups-shoats (LIVES)
 * Business models for improved use of AnGR developed and promoted (2, 5)
 * Suitable dairy genetics for SH systems identified - Business models options for delivering the desired genetics described (16)
 * Reproductive package for delivery of improved SR genetics (44)
 * Distribution of improved genotypes (kapiti sheep) for farmers (13)
 * Produced generations. Supported projects: AZAH (II), HLK (!), IM (I). Dissemination to Bangladesh, India, Myanmar, Timor Leste. Major impact study. Partnerships: dept. of Fisheries Malaysia; Investment in program (6)

Use of genomic tools

 * Use of genomic approach to determine breed composition in admixed cattle population (SDG)
 * Genomic tool for determining breed composition/parentage vertification developed for Africa cattle (DGEA/ADGG)
 * Tools for characterizaing indib. AnGR developed and used (5)
 * Markers to identify tilapia strains developed. Partners: DTPs of fisheries Bangladesh & Philippines; Bangladesh Fish Research Institute; Gift Foundation (46)
 * Use of ICT /genomic tools to characterize smallholder herds (16, 3)
 * Genomic tools (SN pvariants) developed for tilapia and carps. Import; Basics for genomic tools input. Partners: James Uni, Australisa; Dart Systems, Stirling Uni, Rolsin, Earlham (53)

Resources for AnGR characterisation

 * Research resource for AnGR characterisation (AZIZI > 500.000)
 * Initiated development of genomics reference resource for African cattle (CTLGH)
 * Establishment of SPF chicken & duck lines with specific NHC haplotypes for disease resistance resaerch (5)

Reproductive technologies

 * New technologies: Cow side hormone assay for estrus detection and pregnancy diagnosis; Pre-tone for pregnancy diagnosis in shoats (LIVES)
 * Field solution of ultra sound based techniques for fertility management in SR (12, 41, 51)
 * Protocols for extended room temp. bull semen developed (16)

New genetic models

 * 1st application of social genetic effects to aquaculture (2 BuT)
 * Combine QG theory on heterogeneity & social interactions __and__ test in aquaculture (1 BuT)
 * Genetics analysis platform (in development)

Phenomics

 * Feed efficiency tools developed. Genetic variance detected. Importance: Ability to directly select in breeding programs and greatly improve prod efficiency. Partners: CIRAD (54)

Capacity development (training)

 * Animal genetic training resources developed and use promoted - AnGR included in university curriculum (10)
 * Capacities of stakeholders (all levels) developed/strengthened on AnGR issues/use/value (5)
 * National partners trained and given relevant software - they are more able to support genetic improvements in their countries (47)
 * Capacities of SSA scientists on AnGR value/use strengthened - Potential for parntership improved/realized (AU-IBAR) (10)
 * Training at different levels, PhD, MSc, national partners, farmers (12, 20, 22, 25, 26, 32, 41, 44, 51)
 * Capacity Development for breeding/genetics: Public sector short term training, MSc; private sector - short term & farmers; gender roles; service providers & input suppliers - short term (LIVES)
 * Knowledge management / docs: Video production, radio programs; seminars; publications - journal, conferences, working papers, briefs; agri knowledge centers; studuy tours/exchange programs
 * Training (5 - GEF Asia)

Policy advocacy / institutions

 * Influencing and funding: Livestock master plan; GTP (growth & transformation plan in Ethiopia); Proposal on Ethiopian animal improvement institute; formulation of paid project; formulation of new MSc program in animal breeding and genetics (BMGF); WB funding for MOLF(150M). (LIVES)
 * CBBP success inlfuenced policy formulation in Ethiopia (26+41)
 * Policies for sustainable use of indigenous breeds RM) developed and promoted (35) (institutional Frome User)
 * Provided useful information for design of ADGG and will provide a framework to practically support farmers (40)
 * Policy briefs (AnGR-related) access & benefit sharing developed (14)
 * Policies for improved use and benefits of ind. AnGR developed and used to inform public on AnGR (5)
 * New institutional frameworks to support pastoralists to breed/market RM (35)

Infrastructures

 * A new center (CTLGH)
 * Establishment of SR reproduction tech lab in Doyogena, Ethiopia (41+44)
 * Joint lab 8 NSFC project
 * Center of excellence for quantitative genetics/livestock genomics for Africa conceptualizaed (47)

Partnerships

 * Network for function capacity (gene/allele towards breeding in sheep (27)
 * Partnerships: ICARDA, NARS, SNV, USAID, MoLF, MoA, MoST (LIVES)
 * New, large, multidisciplinary consortium (B3Africa)
 * 25 national partners trained on breeding programs with course materials on line - more equipped to support improvement programs in their countries ACGG (43)
 * New partnership to understand genomics tropical livestock (CTLGH)
 * New partenrship with private sector (42, 43)
 * Inventory of partners for upscaling - perofrmance recording AI delivery identified and engaged (ADGG/PAID)
 * Opened up new partner opportunities (3)
 * New partnership with colleagues in China - room for future collaboration / Appropriate breed type identified provides more relevant advice to farmers (36)

Recognition

 * CBBP award winning technology from Ethiopian government (26+41)

Gender
=Identifying the key synthesis briefs= These were the 7 briefs identified:
 * First reports on gendered breeding objectives, livestock trait preferences etc. (Somali pastoral)
 * Empowerment of fibre processing women cooperatives in Fergana valley, Tajikistan (12)
 * Pastoral communities esp. women extracting more benefits from the ind. red maasay sheep through milk sales (35)
 * 1) Advances in animal genetic resources (and genomic discoveries). Lead: Olivier. Other members: Joram, Han.
 * 2) Lessons on breeding programs around institutions, capacities, policies for sustaining breeding programs. Lead: Aynalem. Other members: Tadelle, John, Azage, Hans, Okeyo.
 * 3) Development, evaluation, application of novel tools for informing breeding programs. Lead: Raphael. Other members: Julie, DJ, Han Makdy, Joram.
 * 4) Field phenotyping & incentives for farmer recording. Lead: Karen. Other members: Okeyo, Joram.
 * 5) Use of value chain framework for genetics R4D (including livelihoods). Lead: Azage. Other members: John, Julie, Aynalem.
 * 6) Delivery of improved genetics. Lead: Jasmine. Other members: Okeyo, Mourad, Makdy.
 * 7) Relative role of livestock genetics. Lead: Steve. Other members:.

=Final words=
 * From the flagship leaders**

__**Okeyo**__ For me the most exciting part has been to. There's been a lot of changes. Every month we were bombarded with ideas for how to do it this way or that way. There was a lot of evolution in the management of the CRP and hwo we managed ourselves but at least we managed to achieve this far. We now have networks that go beyond the CRP and that is beautiful. There is nothing that you can bank on like (professional) networks and I commend you on being very professional, even when you disagreed. You didn't say nasty words to one another. Getting the reports done and the info in was tough. We were in the wilderness, we discovered the trees, and now we know that trees, however big the trees they will never be a forest.

__**John**__ Having not been part of the CRP at its onset it's been very interesting working with this bunch of people. There are few times when we all got together. I can only think of Naivasha. The interactions on scientist-to-scientist basis were great. The disappointment is that the grand plan was not met with a grand dollar. The transactional costs of working from a distance of each other were... We could have accomplished a lot of things. We weren't able to engage more scientifically and largelly because of the difficulty with dollars. I reiterate that the pulling together of information at the end of the year has been difficult. We can see that this work is beginning to focus.

__**Karen**__ It's the last time that I speak to this group. The CRP has facilitated interactions among all of us and it's been a very valuable thing. For the genetics component, this work has made us think about what we do and our strategy is much much stronger than it was before. The CRP has facilitated that. What we did well was to set the vision and strategy as a team in the Naivasha, and it really captured the experience of many people. We have embraced the challenge of finding solutions to difficult problems. We have some models on the ground (and we are evaluating them) and we are technical geneticists but we've also worked on value chains, partnerships etc. And th other thing we've done well is to advocate strongly for the conjunction of feeds, health and genetics. Feeds haven't been funded through Window 1 & 2 so this cooperation will be even more important. To me it's been a fantastic experience also leaning on John and Okeyo. The people are really starting to see this as sthg that supports overhead but as sthg that brings value. Out of these 2 days, it's remarkable we get 6 briefs nearly finished.


 * Outputs**

Hereby the 6 draft briefs (as of 13 October 2016) - Lead: Karen Marshall - Lead: Raphael Mrode - Lead: Aynalem Haile (still to be split in 2). Lead 1: Azage Tegegne. Lead 2: Julie Ojango - Lead: Jasmine Bruno

Mapping of projects (visuals)