RABBIT SELECTION BEFORE THE GENOMICS ERA

Transcription

1 RABBIT SELECTION BEFORE THE GENOMICS ERA Agustín Blasco Institute for Animal Science and Technology Universidad Politécnica de Valencia Valencia. Spain

2 ICTA INSTITUTE OF ANIMAL SCIENCE AND TECHNOLOGY GENETICS NUTRITION REPRODUCTION

3 FARMS

4 FARMS

5 Why rabbits?

6 Why Rabbits? We eat them 122,000 Ton/year of LAMB carcass 65,000 Ton/year of RABBIT carcass

7 Why Rabbits? RABBIT IS A GOOD ANIMAL MODEL 1. Rabbit is cheap 2. Rabbit has short generation interval (6 months) 3. Rabbit has physiological peculiarities: - OVULATION INDUCED BY COITUS - NO FETAL MIGRATION BETWEEN UTERINE HORNS - LAPAROSCOPY TECHNIQUES ARE FEASIBLE 4. Meat quality studies are feasible (not with mice!)

8 1.The fascinating new technologies Cloning Transgenesis GWAS Gene editing 2. Genomic selection in perspective Dairy cattle Everyting else 3. Rabbits Commercial rabbits Rabbit as a model

9 GENETICS EVOLUTION MENDELIAN ANCIENT AGE WRONG PARADIGM DARK AGE (Infinitesimal model heresy)

10 GENETICS EVOLUTION GENOMICS RENAISSANCE MODERN EDITING GENES AGE

11 BIOTECHNOLOGY Cloning EXPECTATIONS Transgenics

12 CLONING EXPECTATIONS

13 CLONING EXPECTATIONS

14 COMPLETE LIST OF CURRENT CLONED PRODUCTS

15 TRANSGENIC EXPECTATIONS Detecting MAJOR GENES Transferring genes to the same or other specie Comercialise transgenic animals or products

16 COMPLETE LIST OF TRANSGENIC PRODUCTS In Europe, before the approval of the TTIP

17 GWAS Let us find a gene Most economic traits (INCLUDING DISEASE RESISTANCE) do not have major genes Most major genes can be easily captured by selection or introgression GWAS + Biology systems improves our knowledge about genetic determination (architecture?) of traits

18 GENE EDITING Feasible in many genes of an individual! Which genes? How we edit?

19 Two successes GENE EDITING

20 GENOMIC SELECTION Genomic selection is useful for: Shortening generation intervals (dairy cattle) Traits that have low h 2 like fertility or LS Traits difficult or expensive to measure like meat quality etc.

21 etc. GENOMIC SELECTION Genomic selection is less useful: When it is too expensive to be applied (rabbits) When generation interval is not shortened When h 2 is too low or too high When training population should be reevaluated often

22 GENOMIC SELECTION Why GS is so succesful in Dairy Cattle? Large generation intervals Selection is mainly in males but males do not express the traits of interest Dairy Cattle is a big bussiness. Expensive sires Whole World Selection Nucleus for Holstein Farmers changed their behaviour buying semen

23 GENOMIC SELECTION BEEF CATTLE Large training populations needed Continuous phenotyping needed Genotyping is expensive Traits are often recorded in the male Not possible with exceptions (e.g. American Angus) Need A.I. No large recording structures (mainly for new traits) Too much for many breeds Generation interval is not halved RESPONSE TO SELECTION IS NOT GOING TO BE DOUBLED

24 GENOMIC SELECTION Traits with moderate-high h 2 Measured in the animal Precision (proportional to the response to selection) Weight at some age h 2 ~ 0.4 r ~ 0.7 same precision as genomics Weight + Genomics =

25 Accuracy GENOMIC SELECTION Selection on a Associations break each generation Accuracy decreases New equations should be made New records are needed Generation a, b, k: parameters of a growth curve From: Ibáñez and Blasco, JAS 2011 MEAT QUALITY: Frequent re-estimation Large training populations

26 GENOMIC SELECTION NUCLEUS PIGS 100 genomics Multiplication 1 Grand Parents 500 Genetics 100 Production 600 Commercial 15 Sows 750 Pigs for slaughter

27 GENOMIC SELECTION NUCLEUS RABBITS 100 genomics Multiplication 1 Grand Parents 25 Genetics 2 Production 27 Commercial 15 Does 750 Rabbits for slaughter

28 GENOMIC SELECTION Reduce costs by imputation Percentage of correct imputation

29 GENOMIC SELECTION Challenge: NEW traits Carcass quality Meat quality Health Feed efficiency etc.

30 Commercial farm performance GENOMIC SELECTION Some technical problems with NEW TRAITS An example from pigs Daily gain Backfat Food intake Residual food intake Purebreed nucleus performance Provided by Peter Knap (Genus-PIC, 2015) New trait!

31 GENOMIC SELECTION Relationships with other TRAITS An example from poultry Correlation between predicted and observed phenotype for FCR: Food conversion ratio no genomics genomics From: González Recio et al. GSE, 2009 Great genomics advantage!...but r g (FCR,Growth) = and you will weigh the chicken!

32 GENOMIC SELECTION First, calculate h 2 and r g - see how large the training population should be - see the effect in other traits - see how much information come from other traits Second, calculate, taking into account - you need a large phenotyped training population - you should phenotype again time to time Third, pay attention to GxE interactions

33 RABBITS V Maternal LS A Maternal LS R Terminal sire Growth V x A C

34 RABBITS LINE V LINE A NUCLEUS SIRE LINE R Multipliyer V x A VxA Commercial X R

35 RABBITS NUCLEUS LINE LINE SIRE LINEA V A R V x A VxA x R

36 RABBITS H:Hyperprolific LS LP: Longevity LS R Terminal sire Growth V x A C

37 P G P E RABBITS Litter size at weaning P G E

38 RABBITS RABBIT IS A GOOD ANIMAL MODEL 1. Rabbit is cheap 2. Rabbit has short generation interval (6 months) 3. Rabbit has physiological peculiarities: - OVULATION INDUCED BY COITUS - NO FETAL MIGRATION BETWEEN UTERINE HORNS - LAPAROSCOPY TECHNIQUES ARE FEASIBLE 4. Meat quality studies are feasible (not with mice!)

39 RABBITS SELECTION FOR OVULATION RATE OR LS NBA

40 RABBITS SELECTION FOR OVULATION RATE + LITTER SIZE OR LS NBA

41 G enet ic averages RABBITS SELECTION FOR UTERINE CAPACITY 1. 6 High line Low line

42 RABBITS SELECTION FOR UTERINE CAPACITY High line Low line

43 RABBITS SELECTION FOR UTERINE CAPACITY HIGH - LOW Day of Gestation Implantation No differences in Fecundation rate N=

44 INTRAMUSCULAR FAT

45 RABBITS SELECTION FOR INTRAMUSCULAR FAT

46 RABBITS SELECTION FOR ENVIRONMENTAL SENSITIVITY Base G1 G2 G3 G4.

47 RABBITS SELECTION FOR ENVIRONMENTAL SENSITIVITY

48 GENOMICS METABOLOMICS

49 GENOMICS Full sequence

50 GENOMICS You cannot be against genomics, as you cannot be against NIRS, GENOMICS IS A TOOL Genomic selection is clearly useful in Dairy cattle Genomic selection is less obviously useful in other species, - Define objectives and scenarios - Careful genetic and economic studies before application USE GENOMIC SELECTION WITH THE BLACK BOX GENOMICS is much more tan Genomic Selection

51 OPTIMISTIC: Someone who thinks we live in the best possible World PESIMISTIC: Someone who thinks that the Optimistic is right