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Common-use Data System for Food
     Animal Genetics in Taiwan



                                  Ming-Che Wu
             Taiwan Livestock Research Institute
A reservoir of genetic adaptability acts a buffer
against potentially harmful environmental and
economic change.




     Food security and mileage (Sustainability)
System for Food Animal Genetics
               in Taiwan
                                  Phase I (1987~1992):
    Conservation farms
●

                                      Conservation farms
                                  Phase II(1993~1998):
● Web site www.angrin.tlri.gov.tw

                                      Web site
                                Phase III(1999~2004):
    Cryopreservation Bank
●


                                 Conservation center
                                Phase IV(2005~2008):
    Molecular techniques
●


                                    Research and Utilization
    Genetic resources           Phase V(2009~2012):
●


    exchange                        Global Bioidentification System
Common-use
• DNA in food chain
• Biogenetic banks in
  supporting scientific
  research
• Genomic selection on
  farm level
• Web-based barcode
  system with food mileage
乳 Milk




DNA in food chain
                    Meat 肉



           Egg 蛋
Origin
assurance
- market to farm
Web site: www.angrin.tlri.gov.tw
Common Use Data System For Food Animal Genetics In Taiwan
Common Use Data System For Food Animal Genetics In Taiwan
Common Use Data System For Food Animal Genetics In Taiwan
BioUtilization

    Conservation           Biodiversity
                 Species
                                          Species
                                          verification
                            Value add
    Selection    Demand
                                          New
                                          breed/line
                            Tracking
                  Export
                                          Genetic
                                          improvement
Genomic breeding
(source:FAO, 2007)

                   Global Movement of AnGR
     (milk)
 (pork)
(pork)
    (pork)
   (milk)
   (milk)

             (chicken meat)
        (chicken egg)
       (fur sheep)
Biogenetic resources are parts of our life.
          Genetic diversity is threatened by
          - genetic erosion
          - habitat loss
          - social value sinking
          - economic setback
          - food print mileage




From Farm to DNA Bank
Genetic
  Banking
   Living form
    Cell/tissue
DNA/RNA/mRNA/
  cDNA/protein
Development of miniature pig for biomedical research in Taiwan
                                                      Ming-Che Wu, PhD
                                                      Taiwan Livestock Research Institute
                                                      www.angrin.tlri.gov.tw
                                                      mcwu@mail.tlri.gov.tw




                                              Taiwan




                                                 Lanyu
Common Use Data System For Food Animal Genetics In Taiwan
Development of miniature pig for biomedical research in Taiwan
                                                             Ming-Che Wu, PhD
                                                             Taiwan Livestock Research Institute
                                                             www.angrin.tlri.gov.tw
                                                             mcwu@mail.tlri.gov.tw




            Lanyu 200




                                                         Hybrid
                                                         Hybrid
                     Inbreeding            Duroc




GPI-CRC-PGD Genotyped                         Mitsae (Lanyu 50)
                           Spotty Lanyu
Line (Lanyu 300)            (Lanyu 100)       (50% Lanyu + 50% Duroc)
Mitasi minipig was developed from sib-mating on hybrid of Duroc
and Lanyu breed.

                                                        1989
                                                        1990

                                                        1991

                                                        1992


                                                        1993


                                                        1994

                                                        1995
                                                        (Lanyu 50)
                                                               50
Fullsib Mating on
coat color selection




                 19
Development of miniature pig for biomedical research in Taiwan
                                                         Ming-Che Wu, PhD
                                                         Taiwan Livestock Research Institute
                                        Lanyu 300        www.angrin.tlri.gov.tw
                                                         mcwu@mail.tlri.gov.tw
                                        Lanyu 50
                                        Lanyu 100
                    Lanyu 200




Conservation to Bio-
utilization (1987-2008)                                             Lanyu 300
                                                                    Lanyu 100
                                        Lanyu
                           Lanyu 100                                Lanyu 400
                           Lanyu 50
                                        Black
                                        1980




                                                       Lanyu White
                                       Spotty Lanyu
                                                             2005
                                       1993
Semen collection and storage
Ex situ conservation of minipig
• Cell Bank
   - Sperm bank, Oocyte bank, Embryo bank
• DNA Bank

    Taiwan Animal Germplasm Center
        http://www.angrin.tlri.gov.tw/
Taiwan Animal Germplasm Center
  http://www.angrin.tlri.gov.tw/
CryoArk for Taiwan




 Cryotanks: 24K*5 + 38K*17 + 80K*2 = 926K
(CryoArk for Taiwan: 46,000 sp. in total)
Oocyte
          Sperm


Embryo



Cell Bank
•K Series - Liquid nitrogen storage with controllable
                      temperatures between (-100°C to -196°C)
  Small LN Tank




                                                -185℃ Vapor
                                                storage

                  •designed for large
                  vial capacities up
                  to 6000 vials (2 ml
                  vial) in box type
                  racks.




-80℃ Freezer
Bio-security
          -185℃ Vapor
          storage
                •designed for large
                vial capacities up to
                6000 vials (2 ml vial) in
                box type racks.
Gene Banking
DNA Banking
2007                                 Living form/Cell/Tissue
                                  DNA/RNA/mRNA/cDNA/Protein
Cattle          6180
Water Buffalo     58
Goat           3127
                         Oocyte
Sheep             14
Horse             14
Rabbit            88
Swine         25129
Chicken       11650
Muscovy         151
                       Embryo
Duck             689
Hybrid Duck      128
Goose            431
Turkey            14
Black Swan       135
Quail             50
Total         47858
Common Use Data System For Food Animal Genetics In Taiwan
Landrace          Lanyu            Duroc             Taoyuan

            Lee-Sung Inbreeding Mitsae           TLRI Black

                      Spotty

                                                        Meishing

Yorkshire
                                         Hampshire     Berkshire
    LY

                   Pig Breeding
LYD Hog
Impact of common-use breeding data on production efficiency
    2.20

                    Duroc          Landrace       Yorkshire
    2.15          Feed efficiency(Feed/Gain) from 40 to 110 kg of body weight



    2.10



    2.05



    2.00
           2000     2001    2002    2003   2004   2005   2006    2007

                                           Birth year of boar
Common Use Data System For Food Animal Genetics In Taiwan
Growth performance test for breeding pig
Auction
Elite animal labeled with the breeder name
prior to auction
Performance data of individual pig with its own pedigree along with genotype
information




         Auction price of each pig and buyer soon after sold
On-line Statistics for Auction Data of Elite Pig




Auction                                                 Price (NT$)
                      No. of Breeder and Buyer
Year
Cow Milk Production in Dairy Herd Improvement System
Regional Statistics on Dairy Farming Sector




                          Cow Milking Performance
         No. of Farmers
County
Profiles of daily milk yield per cow in average and number of DHI farms
(1990 ~ 2008)
                                                                                                                                                                                                                                               400
25
                               Daily Milk Yield (kg)
24
                               DHI Farm (N)
                                                                                                                                                                                                                                               350
23

22
                                                                                                                                                                                                                                               300
21

                                                                                                                                                                                                                                               250
20

19                                                                                                                                                                                                        4.6
                                                                                                     4
                                                                                                    3.8
                                                                                                                                                                                                          4.4
                                                                                                                                                                                                                                               200
                                                                                                    3.6
                                                                                                                                                                                                          4.2
                                                                                                    3.4
18                                                                                                  3.2
                                                                                                                                                                                                          4
                                                                                                     3
                                                                                                                                                                                                          3.8
                                                                                                    2.8
                                                                                                                                                                                                                 Profile on milk quality in
                                                                                                                                             Protein %             Protein % (milk yield adjusted)
                                                                                                    2.6
                                                                                                                                                                                                          3.6
                                                                                                    2.4
17                                                                                                                                                                                                               protein percentage from
                                                                                                    2.2                                                                                                   3.4

                                                                                                                                                                                                                                       150
                                                                                                                                                                                                                 those farms having more
                                                                                                     2
                                                                                                                                                                                                          3.2
                                                                                                    1.8
                                                                                                                                                                                                                 than 22 kg of milk yield
                                                                                                    1.6                                                                                                   3

16                                                                                                  1.4
                                                                                                                                                                                                                 recorded in 2007.
                                                                                                                                                                                                          2.8
                                                                                                    1.2
                                                                                                     1                                                                                                    2.6
                                                                                                                                          .1




                                                                                                                                          .2
                                                                                                      .07
                                                                                                            .14
                                                                                                                  .32
                                                                                                                        .37
                                                                                                                        .39
                                                                                                                               .59
                                                                                                                                        .77
                                                                                                                                        .86


                                                                                                                                        .15
                                                                                                                                        .39
                                                                                                                                        .45
                                                                                                                                        .52
                                                                                                                                        .55
                                                                                                                                        .76
                                                                                                                                        .81
                                                                                                                                        .04
                                                                                                                                        .11
                                                                                                                                        .24
                                                                                                                                        .36
                                                                                                                                        .62
                                                                                                                                        .69
                                                                                                                                        .79
                                                                                                                                        .92
                                                                                                                                        .07
                                                                                                                                        .17
                                                                                                                                        .24
                                                                                                                                        .52
                                                                                                                                        .97
                                                                                                                                        .28
                                                                                                                                        .51
                                                                                                                                        .57
                                                                                                                                        .28
                                                                                                                                        .42
                                                                                                                                        .71
                                                                                                                                        .74
                                                                                                                                        .05


                                                                                                                                        .16
                                                                                                                                        .51
                                                                                                                                      23




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15                                                                                                                                                                                                                                             100
     07

           11

                    03

                          07

                                   11

                                         03

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                                                                                                                                                                                                     07

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                                                                                                                                                                                                                                          03
 99

          99

                00

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                               00

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Regulation for genomic breeding - Animal Industry Act Article 17
The competent authority may dispatch inspector to examine or test the breeding
flock, breeding stock, facilities, pedigree registry and related records of breeders, and
the breeders shall not evade, interfere with or object to such examination or testing.
Breeding flock or breeding stock found to have contracted notified disease or have
hereditary disease during the aforesaid examination or testing shall be banned from
breeding. The aforesaid inspectors shall present their identification when carrying out
their duty.

            Pig        Cow     Goat Chicken          Duck     Goose     Deer     Rabbit
        Hal-1843      BLAD     G6S     HSP70        PRL      PRL       IGF2      GPI
        ESR           DUMP     IGF2    PRLR         ESR      ESR       XY        PGD
Gene
        HFABP-H       CITR     mtDN    PRL          ZW       ZW        D5FAD     XY
                               A
        HFABP-ad      CVM              ESR          mtDNA    mtDNA     mtDNA     IGF2
        IGF2-In3      XY               mtDNA                                     mtDNA
        IGF2-In7      GH               ZW
        D5FAD         mtDNA
        D-Loop
        SW18
        SW1943
        SW2588
        PRLR
DNA barcoding for pigs
                                                          DNA
Hal-1843 gene for stress (AB), ESR gene for prolificacy
(MN) and 16,613bp mtDNA for maternal origin,
especially on D-loop region (1,175bp) of 29 SNPs and
UTRn (tacacgtgcg 10bp)17~27 in various breeds of pigs.




              AB+MN+18SNP+UTR+11SNP
                                mtDNA D-Loop
                     AAMNcaattgctcgtttctcag24tgctcgaaacc
  A0021-02 Lanyu
  T0596-01 Taoyuan AAMMcaattgcttgttttccag24tgctcgaaact
  L0074-10 Landrace AAMNttgccattcaccctccaa27tgcttaaaatt
  Y0150-03 Yorkshire AAMNcaattgcctgttttccag25tccccgaaacc
                      AANNttgccattcaccctccaa26tgcttaaaatc
  D0167-05 Duroc
Native Chicken Barcode
 MMFFAARR
   2-3-5-Z                                       (Red feather)
 PRL-ESR-HSP70-PRLR
  NNEEBBPP

                      Chicken genome
                                                 (Black feather)



                                                  (Silky feather/Black meat)




2-3-5-Z-mtDNA
PRL-ESR-HSP70-PRLR-CoI

MMEEAAPP CCGGTCC                       Broiler
Common-use
• DNA in food chain
• Biogenetic banks in
  supporting scientific
  research
• Genomic selection on
  farm level
• Web-based barcode
  system with food mileage
Acknowledgements        •   Wu Lab
                             –   Mr. Yun-Yu Lai
                             –   Dr. Ren-Bao Liaw
 •                           –
     Funding Sponsors            Dr. Yuchia Huang
                             –
     – COA                       Dr. Ter-Yu Lin
                             –
     – TLRI                      Ms. Hsiu-Rong Tsai
                             –   Mr. Hsenn-Ben Chu
     – NAIF
                        •   Collaborators
                             –   Prof. Hsiu-Luan Chang
                             –   Dr. Lih-Ren Chen
                             –   Prof. Feng-Pang Cheng
                             –   Prof. Larry Schook, UIUC
                             –   Prof. Harris Lewin, UIUC
                             –   Dr. Le Thi Thuy, Vietnam
                             –   Prof. Rangsun Parnpai, Thailand
                             –   Dr. Libertado C. Cruz, Philippines
                             –   Prof. Chis Maxwell, Australia
                             –   Prof. Locksley E. McGann, Canada
                             –   Prof. Hoon Taek Lee, Korea

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Common Use Data System For Food Animal Genetics In Taiwan

  • 1. Common-use Data System for Food Animal Genetics in Taiwan Ming-Che Wu Taiwan Livestock Research Institute
  • 2. A reservoir of genetic adaptability acts a buffer against potentially harmful environmental and economic change. Food security and mileage (Sustainability)
  • 3. System for Food Animal Genetics in Taiwan Phase I (1987~1992): Conservation farms ● Conservation farms Phase II(1993~1998): ● Web site www.angrin.tlri.gov.tw Web site Phase III(1999~2004): Cryopreservation Bank ● Conservation center Phase IV(2005~2008): Molecular techniques ● Research and Utilization Genetic resources Phase V(2009~2012): ● exchange Global Bioidentification System
  • 4. Common-use • DNA in food chain • Biogenetic banks in supporting scientific research • Genomic selection on farm level • Web-based barcode system with food mileage
  • 5. 乳 Milk DNA in food chain Meat 肉 Egg 蛋
  • 11. BioUtilization Conservation Biodiversity Species Species verification Value add Selection Demand New breed/line Tracking Export Genetic improvement Genomic breeding
  • 12. (source:FAO, 2007) Global Movement of AnGR (milk) (pork) (pork) (pork) (milk) (milk) (chicken meat) (chicken egg) (fur sheep)
  • 13. Biogenetic resources are parts of our life. Genetic diversity is threatened by - genetic erosion - habitat loss - social value sinking - economic setback - food print mileage From Farm to DNA Bank
  • 14. Genetic Banking Living form Cell/tissue DNA/RNA/mRNA/ cDNA/protein
  • 15. Development of miniature pig for biomedical research in Taiwan Ming-Che Wu, PhD Taiwan Livestock Research Institute www.angrin.tlri.gov.tw mcwu@mail.tlri.gov.tw Taiwan Lanyu
  • 17. Development of miniature pig for biomedical research in Taiwan Ming-Che Wu, PhD Taiwan Livestock Research Institute www.angrin.tlri.gov.tw mcwu@mail.tlri.gov.tw Lanyu 200 Hybrid Hybrid Inbreeding Duroc GPI-CRC-PGD Genotyped Mitsae (Lanyu 50) Spotty Lanyu Line (Lanyu 300) (Lanyu 100) (50% Lanyu + 50% Duroc)
  • 18. Mitasi minipig was developed from sib-mating on hybrid of Duroc and Lanyu breed. 1989 1990 1991 1992 1993 1994 1995 (Lanyu 50) 50
  • 19. Fullsib Mating on coat color selection 19
  • 20. Development of miniature pig for biomedical research in Taiwan Ming-Che Wu, PhD Taiwan Livestock Research Institute Lanyu 300 www.angrin.tlri.gov.tw mcwu@mail.tlri.gov.tw Lanyu 50 Lanyu 100 Lanyu 200 Conservation to Bio- utilization (1987-2008) Lanyu 300 Lanyu 100 Lanyu Lanyu 100 Lanyu 400 Lanyu 50 Black 1980 Lanyu White Spotty Lanyu 2005 1993
  • 21. Semen collection and storage Ex situ conservation of minipig
  • 22. • Cell Bank - Sperm bank, Oocyte bank, Embryo bank • DNA Bank Taiwan Animal Germplasm Center http://www.angrin.tlri.gov.tw/
  • 23. Taiwan Animal Germplasm Center http://www.angrin.tlri.gov.tw/
  • 24. CryoArk for Taiwan Cryotanks: 24K*5 + 38K*17 + 80K*2 = 926K (CryoArk for Taiwan: 46,000 sp. in total)
  • 25. Oocyte Sperm Embryo Cell Bank
  • 26. •K Series - Liquid nitrogen storage with controllable temperatures between (-100°C to -196°C) Small LN Tank -185℃ Vapor storage •designed for large vial capacities up to 6000 vials (2 ml vial) in box type racks. -80℃ Freezer
  • 27. Bio-security -185℃ Vapor storage •designed for large vial capacities up to 6000 vials (2 ml vial) in box type racks.
  • 28. Gene Banking DNA Banking 2007 Living form/Cell/Tissue DNA/RNA/mRNA/cDNA/Protein Cattle 6180 Water Buffalo 58 Goat 3127 Oocyte Sheep 14 Horse 14 Rabbit 88 Swine 25129 Chicken 11650 Muscovy 151 Embryo Duck 689 Hybrid Duck 128 Goose 431 Turkey 14 Black Swan 135 Quail 50 Total 47858
  • 30. Landrace Lanyu Duroc Taoyuan Lee-Sung Inbreeding Mitsae TLRI Black Spotty Meishing Yorkshire Hampshire Berkshire LY Pig Breeding LYD Hog
  • 31. Impact of common-use breeding data on production efficiency 2.20 Duroc Landrace Yorkshire 2.15 Feed efficiency(Feed/Gain) from 40 to 110 kg of body weight 2.10 2.05 2.00 2000 2001 2002 2003 2004 2005 2006 2007 Birth year of boar
  • 33. Growth performance test for breeding pig
  • 35. Elite animal labeled with the breeder name prior to auction
  • 36. Performance data of individual pig with its own pedigree along with genotype information Auction price of each pig and buyer soon after sold
  • 37. On-line Statistics for Auction Data of Elite Pig Auction Price (NT$) No. of Breeder and Buyer Year
  • 38. Cow Milk Production in Dairy Herd Improvement System
  • 39. Regional Statistics on Dairy Farming Sector Cow Milking Performance No. of Farmers County
  • 40. Profiles of daily milk yield per cow in average and number of DHI farms (1990 ~ 2008) 400 25 Daily Milk Yield (kg) 24 DHI Farm (N) 350 23 22 300 21 250 20 19 4.6 4 3.8 4.4 200 3.6 4.2 3.4 18 3.2 4 3 3.8 2.8 Profile on milk quality in Protein % Protein % (milk yield adjusted) 2.6 3.6 2.4 17 protein percentage from 2.2 3.4 150 those farms having more 2 3.2 1.8 than 22 kg of milk yield 1.6 3 16 1.4 recorded in 2007. 2.8 1.2 1 2.6 .1 .2 .07 .14 .32 .37 .39 .59 .77 .86 .15 .39 .45 .52 .55 .76 .81 .04 .11 .24 .36 .62 .69 .79 .92 .07 .17 .24 .52 .97 .28 .51 .57 .28 .42 .71 .74 .05 .16 .51 23 29 22 22 22 22 22 22 22 22 23 23 23 23 23 23 23 24 24 24 24 24 24 24 24 25 25 25 25 25 26 26 26 27 27 27 27 28 30 34 15 100 07 11 03 07 11 03 07 11 03 07 11 03 07 11 03 07 11 03 07 11 03 07 11 03 07 11 03 99 99 00 00 00 01 01 01 02 02 02 03 03 03 04 04 04 05 05 05 06 06 06 07 07 07 08 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
  • 41. Regulation for genomic breeding - Animal Industry Act Article 17 The competent authority may dispatch inspector to examine or test the breeding flock, breeding stock, facilities, pedigree registry and related records of breeders, and the breeders shall not evade, interfere with or object to such examination or testing. Breeding flock or breeding stock found to have contracted notified disease or have hereditary disease during the aforesaid examination or testing shall be banned from breeding. The aforesaid inspectors shall present their identification when carrying out their duty. Pig Cow Goat Chicken Duck Goose Deer Rabbit Hal-1843 BLAD G6S HSP70 PRL PRL IGF2 GPI ESR DUMP IGF2 PRLR ESR ESR XY PGD Gene HFABP-H CITR mtDN PRL ZW ZW D5FAD XY A HFABP-ad CVM ESR mtDNA mtDNA mtDNA IGF2 IGF2-In3 XY mtDNA mtDNA IGF2-In7 GH ZW D5FAD mtDNA D-Loop SW18 SW1943 SW2588 PRLR
  • 42. DNA barcoding for pigs DNA Hal-1843 gene for stress (AB), ESR gene for prolificacy (MN) and 16,613bp mtDNA for maternal origin, especially on D-loop region (1,175bp) of 29 SNPs and UTRn (tacacgtgcg 10bp)17~27 in various breeds of pigs. AB+MN+18SNP+UTR+11SNP mtDNA D-Loop AAMNcaattgctcgtttctcag24tgctcgaaacc A0021-02 Lanyu T0596-01 Taoyuan AAMMcaattgcttgttttccag24tgctcgaaact L0074-10 Landrace AAMNttgccattcaccctccaa27tgcttaaaatt Y0150-03 Yorkshire AAMNcaattgcctgttttccag25tccccgaaacc AANNttgccattcaccctccaa26tgcttaaaatc D0167-05 Duroc
  • 43. Native Chicken Barcode MMFFAARR 2-3-5-Z (Red feather) PRL-ESR-HSP70-PRLR NNEEBBPP Chicken genome (Black feather) (Silky feather/Black meat) 2-3-5-Z-mtDNA PRL-ESR-HSP70-PRLR-CoI MMEEAAPP CCGGTCC Broiler
  • 44. Common-use • DNA in food chain • Biogenetic banks in supporting scientific research • Genomic selection on farm level • Web-based barcode system with food mileage
  • 45. Acknowledgements • Wu Lab – Mr. Yun-Yu Lai – Dr. Ren-Bao Liaw • – Funding Sponsors Dr. Yuchia Huang – – COA Dr. Ter-Yu Lin – – TLRI Ms. Hsiu-Rong Tsai – Mr. Hsenn-Ben Chu – NAIF • Collaborators – Prof. Hsiu-Luan Chang – Dr. Lih-Ren Chen – Prof. Feng-Pang Cheng – Prof. Larry Schook, UIUC – Prof. Harris Lewin, UIUC – Dr. Le Thi Thuy, Vietnam – Prof. Rangsun Parnpai, Thailand – Dr. Libertado C. Cruz, Philippines – Prof. Chis Maxwell, Australia – Prof. Locksley E. McGann, Canada – Prof. Hoon Taek Lee, Korea