Current status of the evaluation of genetic diversity in livestock breeds

Transcription

1 1st Globaldiv Workshop, Bydgoszcz Current status of the evaluation of genetic diversity in livestock breeds Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S and the Globaldiv Consortium Introduction Domestication of animals: YBP Today: enormous diversity of local populations High-output breeds replacing local lower output breeds Erosion of genetic resources 20% of breeds are at risk of extinction 62 breeds went extinct from

2 Introduction Genetic diversity essential for maintaining future breeding options Management of animal genetic resources (AnGR) is mandatory Effective management of AnGR requires data on: Population size & structure Geographical distribution Production environment Within- and among-breed genetic diversity Demographic characterization Needed to assess risk status Risk status depends on: Population size and structure (N e ) Current and predicted future population trends Geographical distribution Data across political borders essential Available global data stored in FAOs Domestic Animal Diversity Information System (DAD-IS) 2

3 Demographic characterization: DAD-IS In 2008 DAD-IS contained: 7040 local breeds 500 regional transboundary breeds 551 international transboundary breeds Data needed to assess risk status unavailable for: 47% of avian breeds 52% of mammalian breeds More data needed Production Environment Recording Breeds are exposed to varying environmental conditions: Climate Pathogens Feed resources Assumption: adaptation to environmental conditions occurs production environment descriptors (PEDs) needed as a surrogate measure for adaptation and putative functional diversity 3

4 Production Environment Recording Set of PEDs proposed by FAO: Management environment Natural environment Disease and parasite prevalence Climate - available on high resolution maps georeferencing breed distributions is a priority Breed description databases Breed societies Advertise their breeds Often no facts/figures Useful overview 4

5 Breed description databases National websites Contain breeds considered national heritage Often few hard facts National languages problematic for wide audience Breed description databases International websites Contain wide range of breeds/species E.g. Breeds of Livestock - University of Oklahoma Usually in English -> wide audience 5

6 Breed description databases FABISnet: Worldwide network of national and regional databases Factual info stored in dedicated fields Multiple language capability EFABIS: Network of 13 European national databases Breed description databases DAD-IS: FAO node of FABISnet Data from 198 countries More than populations from 37 species Degree of endangerment calculated automatically Completeness of data needs improvement 6

7 Genetic characterization - cattle 2 domestication events: Bos taurus & Bos indicus MtDNA, microsatellite, Y-chromosomal data reveal migration/introgression events Breeds: histories & level of genetic diversity assessed Bos primigenius Introgression Bos taurus Bos taurus Bos indicus Bos javanicus Introgression Genetic characterization - yak Single domestication event MtDNA: min. 3 maternal yak lineages in ancestral gene pool Microsatellite data: high genetic diversity in Mongolian and Russian yak Bos grunniens 7

8 Genetic characterization - water buffalo mtdna: 2 domestication events Microsatellites: Most genetic diversity within breeds Bubalus arnee, 2n=50 River type Some defined breeds Bubalus arnee, 2n=48 Swamp type No recognized breeds Bubalus bubalis Genetic characterization - sheep No correlation geography and mtdna haplogroups Predomestic population: mutiple maternal lineages C B D C C D E Ovis orientalis C Little Y- chromosomal variation A B A Ovis aries 8

9 Genetic characterization - goats mtdna: shows little geographical structure Y-chromosomal & microsatellite data show clear geographical structure C F A 90% of goats worldwide Capra aegagrus G G D B B Capra hircus Genetic characterization - camelids In total 4 domesticated species with same karyotype Camelus bactrianus Vicugna pacos Camelus dromedarius Lama glama 9

10 Genetic characterization - camelids In total 4 domesticated species with same karyotype MtDNA and microsatellite data reveal domestication events: Lama guanicoe cacsilensis Vicugna vigugna mensalis Vicugna pacos Lama glama Genetic characterization - camelids MtDNA and microsatellite data: independent domestication events for Domedary and Camel Microsatellite data: Genetic differentiation between populations/ breeds assessed Camelus dromedarius Camelus bactrianus 10

11 Genetic characterization - pigs mtdna: multiple domestication events Y-chromosome highly variable Microsatellite data: Chinese breeds more variable than European breeds Sus scrofa Genetic characterization - horses MtDNA multiple domestication events Y chromosomal data: only few stallions contributed Microsatellite data: geographically restricted studies on genetic diversity of breeds Equus caballus 11

12 Genetic characterization - chickens MtDNA: multiple domestication events and migrations Polynesian/Pacific migration only to Easter Island Microsatellite data: jungle fowl & traditional unselected populations harbor large portion of total genetic diversity Broiler lines more polymorphic than layers Gallus gallus Gallus sonneratii Gallus lafayettii Gallus gallus Molecular databases 3 major databases (dbs): GenBank (NCBI) EMBL-Bank DDBJ-DNA Databank of Japan Smaller project-specific dbs, e.g: AVIANDIV PigDBase CaDBase Numerous dbs on livestock genomics Valuable resource for development of markers 12

13 Conclusion Characterization efforts: Growing amount of systematically collected info on breeds and their environment Molecular studies of many livestock species/breeds Data should be stored in dbs to guarantee: Longterm availablility Searchability Public accessability New technologies will enhance our insight and ultimately uncover molecular basis of functional diversity Thanks to you for your attention! 13

14 Molecular databases Molecular data stored to guarantee: Longterm accessability Public availability Searchability 3 major databases: GenBank, EMBL-Bank, DDBJ 14