RABBIT SELECTION BEFORE THE GENOMICS ERA

Agustín Blasco

Institute for Animal Science and Technology

Universidad Politécnica de Valencia

Valencia. Spain

ICTA

INSTITUTE OF ANIMAL SCIENCE AND TECHNOLOGY

• GENETICS

• NUTRITION

• REPRODUCTION

FARMS

FARMS

Why rabbits?

Why Rabbits?

We eat them

122,000 Ton/year of LAMB carcass

65,000 Ton/year of RABBIT carcass

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 !)

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

GENETICS EVOLUTION

MENDELIAN ANCIENT AGE

WRONG PARADIGM

DARK AGE

(Infinitesimal model heresy)

GENETICS EVOLUTION

GENOMICS

RENAISSANCE

MODERN EDITING

GENES AGE

BIOTECHNOLOGY

Cloning

Transgenics

EXPECTATIONS

CLONING EXPECTATIONS

CLONING EXPECTATIONS

COMPLETE LIST OF CURRENT CLONED PRODUCTS

Detecting MAJOR GENES

Transferring genes to the same

or other specie

Comercialise transgenic

animals or products

TRANSGENIC EXPECTATIONS

COMPLETE LIST OF TRANSGENIC PRODUCTS

In Europe, before the approval

of the TTIP

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

GWAS

Let us find a gene

GENE EDITING

Which genes?

How we edit?

Feasible in many genes

of an individual !

GENE EDITING Two successes

GENOMIC SELECTION

Genomic selection is useful for:

• Shortening generation intervals (dairy cattle)

• Traits that have low h2 like fertility or LS

• Traits difficult or expensive to measure like meat quality

•…etc.

GENOMIC SELECTION

Genomic selection is less useful:

• When it is too expensive to be applied (rabbits)

• When generation interval is not shortened

• When h2 is too low or too high

• When training population should be reevaluated often

•…etc.

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

GENOMIC SELECTION

• Large training populations needed

• Continuous phenotyping needed

• Genotyping is expensive

• Traits are often recorded in the male

BEEF CATTLE

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

GENOMIC SELECTION

Weight at some age

Traits with moderate-high h2

h2 ~ 0.4 r ~ 0.7

Precision (proportional to the

response to selection)

same precision as genomics

Weight + Genomics € €€ = €€€

Measured in the animal

GENOMIC SELECTION

• Associations break each generation

• Accuracy decreases

• New equations should be made

• New records are needed

Generation

Accura

cy

a, b, k: parameters of a growth curve

Selection on a

MEAT QUALITY:

· Frequent re-estimation

· Large training populations From: Ibáñez and Blasco, JAS 2011

GENOMIC SELECTION

NUCLEUS

Multiplication 1 ♀ Grand Parents

Commercial 15 ♀ Sows

750 Pigs for slaughter

500 € Genetics

100 € Production

600 €

100 € genomics

PIGS

GENOMIC SELECTION

NUCLEUS

Multiplication 1 ♀ Grand Parents

Commercial 15 ♀ Does

750 Rabbits for slaughter

25 € Genetics

2 € Production

27 €

100 € genomics

RABBITS

Reduce costs by imputation

Percentage of correct imputation

GENOMIC SELECTION

GENOMIC SELECTION

• Challenge: NEW traits

Carcass quality

Meat quality

Health

Feed efficiency

… etc.

GENOMIC SELECTION

Some technical problems with NEW TRAITS

Purebreed nucleus performance

Com

merc

ial fa

rm p

erf

orm

ance

Daily gain Backfat Food intake Residual food intake

New trait ! Provided by Peter Knap

(Genus-PIC, 2015)

An example from pigs

Correlation between predicted and observed phenotype for

FCR: Food conversion ratio

Great genomics advantage! ...but rg (FCR,Growth) = −0.7

...and you will weigh the chicken!

GENOMIC SELECTION

An example from poultry

no genomics

genomics

From: González Recio et al. GSE, 2009

Relationships with other TRAITS

GENOMIC SELECTION

• First, calculate h2 and rg

- 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

V

Maternal

A

Maternal

R

Terminal sire

♀ V x A

♂ C

LS LS Growth

RABBITS

LINE

V

♀ VxA ♂ R

LINE

A

SIRE LINE

R

NUCLEUS

Multipliyer

♂ V x ♀A

♂ ♀

Commercial

X

RABBITS

♀ VxA ♂ R ♂ V x ♀A

♂ ♀

x

♂

LINE

V

LINE

A

SIRE LINEA

R

NUCLEUS

RABBITS

H:Hyperprolific

LP: Longevity R

Terminal sire

♀ V x A

♂ C

LS LS Growth

RABBITS

RABBITS

Litter size at weaning

P G P E

P

G

E

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 !)

RABBITS

SELECTION FOR OVULATION RATE

RABBITS

NBA

OR

LS

SELECTION FOR OVULATION RATE + LITTER SIZE

RABBITS

NBA

OR

LS

1 2 3 4 5 6 7 8 9 10

G enerat ion

-1.6

-1.2

-0.8

-0.4

0.0

0.4

0.8

1.2

1.6

Ge

ne

tic

a

ve

ra

ge

s

High line

Low line

SELECTION FOR UTERINE CAPACITY

RABBITS

High line

Low line

SELECTION FOR UTERINE CAPACITY

RABBITS

0

12

Day of Gestation

1 1 0 1 2 3 3 6

30

No differences in

Fecundation rate 2.4 1.8

1.8 1.0 0.4

0.4

1.0 2.5 Implantation

SELECTION FOR UTERINE CAPACITY

RABBITS

HIGH - LOW

N= 251 ♀

INTRAMUSCULAR FAT

SELECTION FOR INTRAMUSCULAR FAT

RABBITS

.

Base G1 G2 G3 G4

SELECTION FOR ENVIRONMENTAL SENSITIVITY

RABBITS

SELECTION FOR ENVIRONMENTAL SENSITIVITY

RABBITS

GENOMICS

METABOLOMICS

GENOMICS

Full sequence

• 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

GENOMICS

Someone who thinks that the Optimistic is right

OPTIMISTIC:

PESIMISTIC:

Someone who thinks we live in the best possible World