Is the porcine RN locus a pleiotropic QTL? A Bayesian marker assisted segregation analysis

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Is the porcine RN locus a pleiotropic QTL? A Bayesian

marker assisted segregation analysis

Norbert Reinsch, Christian Looft, Iris Rudat, Ernst Kalm

To cite this version:

Original

article

Is the

_porcine

RN

locus

a

pleiotropic

QTL?

A

_Bayesian

marker assisted

segregation analysis

Norbert Reinsch*

Christian Looft Iris

_Rudat,

Ernst Kalm

Institut für Tierzucht und

_Tierhaltung

der Christian-Albrechts-Universität

zu

Kiel,

Olshausenstraße

40,

24098

Kiel, Germany

(Received

5 March

1997; accepted

18 March

₁₉₉₈₎

Abstract - The

_question

of

possible pleiotropic

effects of the

_porcine

RN locus on

production

traits was addressed. Chromosome 15 microsatellite

_{data, mapping}

results and

performance

data from the Kiel RN

_{mapping experiment}

were used to compare

heterozygous

RN-/rn

+

carrier animals and

_rn

₊

_/rn

₊

non-carriers.

_Progenies

from 14

_Hampshire

x Piétrain

_sires,

all of which were

_heterozygous

at both the RN and RYR1

_loci,

were recorded for 24 traits. Dams were either Landrace

_Large

White

crossbreds or Landrace or

_Large

White

purebreds.

The number of _progeny with valid

records

_ranged

from 323 to

418, depending

on the trait. A mixed

_{polygenic-major}

gene inheritance model was

applied, using

a

Bayesian approach.

Reflectance and

terminal

pH

were lowered in carriers.

Additionally,

a 2.42 mm increase in muscle

depth

in the

_loin,

an

_enlargement

of loin _eye area

_by

1.39

cm

2

and a 0.46 % increase in estimated lean meat content due to the RN- allele were observed. It was shown that the increased lean meat content was not

_{high enough}

to

_outweigh

the economic loss from poor

technological yield.

The proportion of

_genetic

variance in progeny which could be attributed to the RN locus

_ranged

from 5 to 55 %. More than 40 %

of the total

_genetic

variance in eye muscle

depth

was

generated by

the

_joint

action of RN and RYR1. This is discussed with respect to

_uniformity

of end

products

in a

crossbreeding

scheme. The results suggest that not

only

loci which are involved in

glycogen metabolism,

but also those which are related to muscular

development,

may be

_regarded

as

_possible

candidate _genes for the RN locus.

_©

Inra/Elsevier,

Paris

major genes

/

pig meat _quality

_/

chromosome substitution effects

_/

Gibbs sampler

*

Résumé - Analyse Bayésienne de ségrégation, assistée par marqueurs, pour savoir si le locus RN chez le Porc a des effets _{pléïotropiques.} On a abordé la

question

de la

possibilité

d’effets

_{pléïotropiques}

du locus RN chez le Porc. Des données

concernant des microsatellites au chromosome _15, des résultats de

_cartographie

et

des données de

_performances

issus de

_{l’expérience}

de localisation du

_gène

RN à Kiel ont été utilisés pour comparer des porteurs

hétérozygotes

RN

-

/rn

+

et des non _porteurs

rn

+

/rn

+

.

Les descendances de 14 verrats

_Hampshire

x

_Piétrain,

tous

doubles

_{hétérozygotes}

aux locus RN et RYRI ont été

_analysés

pour 24 caractères.

Les mères ont été soit des croisées Landrace x

_Large-White

soit des pures Landrace

ou

Large-White.

Le nombre de descendants avec données valides a varié de 323 à 418 suivant le caractère. Un modèle à hérédité mixte

_{polygénique-gène majeur}

a été

appliqué.

On en a

_inféré,

suivant la méthode

_Bayésienne,

aux distributions

_marginales

a

_{posteriori, grâce}

à

_{l’échantillonnage}

de Gibbs. Les résultats ont montré que la

réflectance est diminuée d’environ une unité chez les _porteurs et que le

_pH

ultime a été abaissé _pour le filet et pour le

jambon.

Les résultats les

_plus

importants ont été

que l’allèle RN- a entraîné un accroissement de

_2,42

mm de

_{l’épaisseur}

du

_filet,

un

accroissement de la surface du filet de 1,39

cm

2

et

un accroissement de

0,46

% de la

teneur en viande

_maigre.

Il a été montré que l’accroissement de la teneur en viande

maigre

n’est pas assez

_grand

_pour contrebalancer la perte

économique

provenant

du mauvais rendement

technologique.

La

proportion

de variance

génétique

chez la descendance croisée attribuable au locus RN a varié de 5 à 55 %. Plus de 40 % de la variance

génétique

de

l’épaisseur

de noix a été

expliqué conjointement

par les

génotypes

RN et RYR1. Ce résultat est discuté par rapport à l’uniformité

_qui

est

souhaitée chez les

_produits

terminaux. La conclusion est _que les différents allèles au

QTL

devraient être assemblés dans différentes

_lignées

de manière à

_fabriquer

des

hétérozygotes

chez les

produits terminaux, quand

les

homozygotes

sont défavorables ou

_quand

les

hétérozygotes

sont difficiles à obtenir par sélection. Les résultats

suggèrent

que d’autres loci que ceux

_impliqués

dans le métabolisme du

_glycogène,

peuvent être considérés comme candidats pour le locus

RN,

par

exemple

ceux

concernés par le

développement

musculaire.

©

Inra/Elsevier,

Paris

gène majeur

/

qualité de viande

_/

porc

/

effet de gène

/

échantillonnage de Gibbs

1. INTRODUCTION

Two alleles

_(RN-

and

_rn

₊

₎

have been found to

_segregate

at the

_porcine

RN locus in

_{purebred Hampshires}

and in

_Hampshire

crossbreds. This _gene was

dis-covered

_by

Naveau

_[19]

_by

its effect on the Rendement

_{Technologique}

NAPOLE

(RTN

!20!).

’Hampshire-type’

meat

_[18]

from carriers of the unfavourable RN-allele is known to exhibit an increased muscle

_glycogen

content,

lowered termi-nal

_pH

and an increased

_cooking

loss. The

_ability

of muscle

_glycogen

to bind

water is similar to

_protein

in fresh muscle

tissue,

but this water is set free

dur-ing

the

_cooking

process and

generates

the increased loss

_[17].

Measurements of

_{technological yield}

in cured cooked ham

_processing

as well as the

glycolytic

potential

in muscle tissue

_(weighted

sum of concentrations of lactate and its

preliminary

stages

in muscle energy metabolism:

glucose, glucose-6-phosphate

and

_glycogen)

showed a bimodal distribution in

_{pig populations}

with both

alleles

_segregating

_[4,

_19!.

This observation is

_{explained by}

the dominant mode of inheritance

_{[8, 19!.}

All these facts were the foundation for the

_mapping

of the

RN locus to chromosome 15 in the

_{neighbourhood}

of the microsatellite markers

The financial loss as a _consequence of _any kind of heat

processing

was

estimated to reach 5.29 DM per carcass

(50

%

lean meat

_content)

of a carrier

animal

_(3!.

This

penalty

from the

_primary

_gene effects _may be reason

enough

to select

_against

the unfavourable dominant RN- allele.

However,

breeders would like to know if there are additional costs or benefits from such a selection

because of the existence of

_pleiotropic

effects on other traits such as lean meat content.

_Moreover,

_knowledge

of

_pleiotropic

effects may be

helpful

to make a more educated _guess on

possible

candidate _{genes in}

positional cloning

studies.

In a

_preliminary

_report

[9]

_{marginally significant}

effects of the RN

_genotype

on

body

_composition

characteristics and

growth

traits were found in animals

from a

_synthetic

line. An examination of _{sensory traits}

[10]

showed additive

and favourable effects of RN- on flavour as well as an undesired dominant

impact

on

tenderness, juiciness

and

mellowness,

whereas

aspect

was affected

only

in

_{heterozygotes.}

In

_Hampshire

_(Swedish

Landrace x Swedish

Yorkshire)

crossbreds

_[13]

a

_stronger

taste and smell was found in

heterozygous

carrier

animals as well as a

_greater

acidity

and a beneficial effect on Warner-Bratzler

shear force.

_Recently

Le

_Roy

et al.

_!11)

presented

new results from the Laconie

synthetic

line. The

_weight

of ham and loin was

_{significantly}

increased in carriers

and backfat thickness was

_{significantly}

reduced when measured at back and rump. The RN effect on carcass lean content as measured

during

grading

failed to be

_significant,

while the error

_probability

for RN effects on an estimate of lean

content,

made from the

_weight

of several

_cuts,

almost reached the

_significance

threshold

_{(5.3 %).}

In order to contribute more information on

pleiotropic

RN- effects this

investigation

makes use of the chromosome 15 microsatellite

data, mapping

results and

_performance

data from the Kiel RN

mapping experiment

[22].

Carriers and non-carriers of the RN- allele from litters of 14

boars,

which

were

_heterozygous

at the RN locus and at the

_{RYRI locus,}

were

_compared.

A

Bayesian

approach

was

_developed

to combine

_phenotypic

and

genetic

marker information for

_genotype

assignment

of _progeny and to

_analyse

24 traits

related to

_growth,

carcass

_quality

and meat

_{quality. Additionally,}

results on

the

_proportion

of

genetic

variance attributable to the RN and RYR1 loci are

given.

2. MATERIALS AND METHODS

2.1. Animals and

_genotypes

Performance data were recorded from _progeny of the Kiel RN

mapping

ex-periment.

Fourteen

_{Hampshire-Pi6train}

crossbred sires known to be

heterozy-gous both at the RN locus and the RYRI

(Ryanodine receptor)

locus

con-tributed female and male castrated

_offspring

to the

_experimental

families. These boars were mated to

_homozygous

_rn

₊

_/rn

₊

Landrace x

_{Large White,}

Landrace and

_Large

White sows to

_produce

progeny with

expected proportions

of 50

%

RN-/rn

+

and 50

%

_rn

₊

_/rn

₊

genotypes.

The

_assumption

of

homozygosity

of all sows is based on the fact that Feddern

[3]

could not find _any animals with

high glycolytic potential

within both dam lines.

Furthermore,

there is no

in other breeds than

_Hampshires

or

_Hampshire

crossbreds. Terminal

muscu-lus

_longissimus

dorsi

_glycogen

content of all

_offspring

was determined from a

meat

_sample

drawn 24 h after

_slaughter

between the 13th and 14th ribs. All

14 boars had two

_types

of extreme

_offspring,

with either low or

_high

muscle

glycogen

content,

and were therefore classified as

_{heterozygous. Genotypes}

at

the RYRI locus were determined with a DNA

_probe.

Since most of the sows were

homozygous

stress resistant NN at the RYR1

locus,

the

proportions

of

Nn and NN

_genotypes

among

offspring

were both about 50

%.

The number of

observations from _progeny

_{being homozygous}

stress sensitive nn was below 10

for all traits. Unbalancedness with

_respect

to sires within the two

_generation

family

structure of the

_experiment

can be seen in

_figure

1. Sires and dams

orig-inated from a commercial

_{crossbreeding}

_programme. All progeny were fattened

under usual

production

conditions at the Hohenschulen

experimental piggery

of the Kiel

_University

until

_finishing

_groups reached an _average

_liveweight

of

approximately

110

_kg.

More details on the Kiel RN

_experiment,

especially

on

glycogen

measurement,

marker

_genotypes

and _map

_{construction,}

can be found

in Reinsch et al.

_!22!.

2.2. Traits

A set of 24 traits was

_{investigated,}

_concerning

_growth,

carcass

_quality

and meat

_quality.

Growth is described

_by

carcass

length

and a series of

weights:

birthweight, weight

at

_weaning,

_weight

at

_beginning

of the

_fattening

period,

endweight

and

_{slaughterweight. Dressing}

was

_computed

as the ratio

of

_{slaughterweight}

and

_endweight.

Six different fatness traits were available:

backfat thickness measured at three different

_positions

of the carcass

(neck,

middle and end of the

_back),

_{the average} of these three

values,

loin fat area and

backfat thickness measured with an

_{optical probe}

after

_slaughter

for commercial

grading.

Carcass meatiness is described

_by

eye muscle thickness and lean meat

content,

both commercial

_grading

_results,

loin _{eye area,} and

_{additionally by}

a score

_(1-5)

of

_belly

meat content. The

_pH

of the musculus

_longissimus

dorsi

(m.

l.

_dorsi)

between the 13th and 14th ribs was measured

_{approximately}

1 h

after

_slaughter

_(single

_measurement)

and 24 h after

_slaughter

_(average

of three

measurements).

Conductivity

was measured in the same muscle 1 and 24 h

after

_slaughter.

Terminal

_pH

₍₂₄

h

_post

_mortem)

in the ham was measured in

the musculus semimembranosus and is an _average of two values. Reflectance

(m.

l.

_dorsi)

was measured

_{during grading}

with a Fat-O-Meater

_probe.

Meat

brightness

(average

of two

_{measurements)}

of the m. l. dorsi was taken 24 h

post

mortem at a cross section of the carcass between the 13th and 14th ribs. For

_measuring

meat

_brightness,

_pH

values and

_conductivity

an

_Opto-Star

apparatus,

a

_pH-Star

and a LF-Star device

_(Mathaus,

_P6ttmes,

_Germany)

were

used,

respectively.

For each trait _{the number of progeny with valid observations}

is

_given

in table II.

2.3.

_Competing

_hypotheses

The contrast between

_RN-/rn

₊

and

_rn-/rn

₊

_genotypes

is

_equivalent

to

the sum

_a+d,

where a is half the difference between the

_genotypic

values of the

mean of both

_homozygotes

_!2!.

Thus we

_expect

a zero contrast if there are no

pleiotropic

effects at all _or,

_{alternatively,}

if a

_equals

minus d. There is

_only

one

genetic

situation with a

_equal

to minus

_d,

that is

_complete

dominance of

rn

+

over

rn

+

.

_However,

this case is

_only

of interest when selection is aimed at a

population

where all three

_genotypes

are

_present,

such as

_{purebred Hampshires.}

In the German

_pig

_{industry Hampshires}

are

_usually

used to

_{produce Hampshire}

Pi6train crossbreds as terminal sires which are mated to either Landrace or

Landrace x

_Large

White sows.

_Consequently

_only

RN-/rn

+

and

_rn+/rn+

genotypes

are observed in the

_{target genotypes}

of such a

_{crossbreeding}

scheme.

Though

all three

_possible

_genotypes

are of scientific

_interest,

the contrast under

investigation

is

_currently

the most

_important

_aspect

of RN

_pleiotropy

from a

short term commercial

_point

of view under these circumstances. Hence two

competing

hypotheses

are to be

_judged:

H

l

:

either no effect at all of the RN- allele or

_complete

dominance of

_rn

₊

_;

and

H

2

:

all other modes of inheritance with a + d different from zero.

2.4. Statistical

_analysis

A mixed

_{polygenic-major}

_gene inheritance model was

_applied.

_Using

a

Bayesian approach, marginal

posterior

distributions of the contrast mentioned above and other

_important

model

_components

were

_generated

via a Gibbs

sampling

scheme

_{[5, 6!.}

This scheme _may

_briefly

be summarized as follows.

At the

_beginning

of each

_cycle

a

_genotype

was drawn for each _progeny from a discrete distribution conditional on

_phenotypic

or

_genetic

marker information

for that

_animal,

its

_performance

in a

_{particular trait,}

and values for all fixed and random effects from the

_previous

round of the Gibbs

_cycle.

Since sires were

known to be

_heterozygous

carriers and dams were known to be

_homozygous

non-carriers it was not _{necessary to} draw

genotypes

for

_parent

animals or gene

frequencies.

Fixed and random effects were then drawn from _proper

conditionals,

and the effects of both

_genotypes

were treated like any other

fixed effect in this

_step.

_Finally,

new values for the residual

_variance,

_polygenic

variance and variances for other random effects were

_generated

from inverted

Chi-square

distributions.

In order to execute the first

_step

of the Gibbs

_cycle

it was _necessary to

assign

a

_prior

_probability

r for

being

a RN- carrier to each _progeny. Musculus

longissimus

dorsi

_glycogen

content

_(its

distribution is shown in

_figure

₂₎

was

used as a

_phenotypic

marker:

_offspring

with low

_glycogen

content _up to the 30

%

percentile

of the

_glycogen

distribution

₍₇

_!tmol-g-1)

were classified as

rn+/rn+

and those with

_glycogen

content above the 70

%

_percentile

₍₁₀₀

_!tmol-g-1)

as

RN-/rn

+

,

with values of 0 and 1 for r,

respectively.

The

genotype

of all other

_offspring

with

_glycogen

content within a medium

_region

of

_uncertainty

(7 !mol!g-1

<

_glycogen

content < 100

_!mol!g-1)

was treated as unknown. So far the

_assignment

of

_genotypes

was identical to the

procedure

we used to _map

the

_{RN gene}

_!22!.

The bounds of the

_{uncertainty region}

are of course somewhat

arbitrary.

However,

it has been shown that

_mapping

results

obtained

_by

_using

these bounds were in

_good

_agreement

with the

_findings

of other researchers and

insensitive to variation of these bounds

_!22!.

For further treatment of all animals within the

_{uncertainty region}

we made use of our male _map of chromosome 15

(see

figure 3

for marker loci and male

multipoint

map

distances).

For each

of those _progeny the smallest informative marker interval

_bracketing

the RN locus was used to derive the risk r of

_having

received a RN- allele from its

sire. In most cases r was

fairly

close to 0 or 1. In those cases where either a

recombination had occurred within the interval SW120-SW906

_(RNis

_mapped

exactly

in the middle of this

_interval)

or where no marker information was

available at all an r-value of 0.5 was used since all _progeny

_analysed

are

descendants of a

_mating

between an

RN-/rn

+

and an

rn

+

/rn

+

_genotype.

All models

_applied

to the different traits

_comprised

an effect for RN

geno-type,

various fixed

_effects,

one uncorrelated random common environmental

effect and one

polygenic

effect. The

corresponding design

matrices and param-eter vectors are denoted

_by

_X

_l

_,

_X

₂

_,

_Z

₁

_,

_Z

₂

and

b

l

, b

2

,

ui and u2,

respectively.

In contrast to the other

_design

matrices

_X

_l

is unknown

_prior

to

_analysis.

The

current realizations of

_b

_l

_,

_b

₂

_,

ui and u2

during

iteration are

_{symbolized by}

b

l

,

b

2

,

ul and U2- Variance

components

for common

_environment,

_polygenic

component

and

_residuals,

_{(T c 2, 6}

_a

_and

_u

₂

have transient values

_{s!, S2}

_and

₈₂

_e

During

the first

step

of the Gibbs

_cycle

from each

_single

observation

_y

_*

the difference

_{y = y}

_*

_-

_x2b

₂

_-

_{ziul - z2}

_u2 was

_computed,

where

x2, z’

_and

z2

_are rows of the

_design

matrices

_X

₂

_,

_Z

_l

and

Z

2

for a

particular

observation. Then two

_{probabilities}

pi and p2 = 1 &mdash;

Here !1 and p2 are the

_components

of

_b

_l

_,

i.e. the effects of both

geno-types

which were

_{generated during}

the

_previous

iteration and

_0(yl

_/

_,t

_l

_,S

₂

₎

and

ø(yl

f

..tZ,

se)

are

_probability

densities from normal distributions at the location

y with variance

se and

means _!,1 and P2,

respectively.

A

genotype

was drawn

for each progeny in each round of the Gibbs

_cycle

from a discrete distribution

with

_{probabilities}

_PI and _p2 = 1 - p i

. In those cases, where r has an extreme

value of 0 or 1

_(equivalent

to an extreme

_glycogen

_measurement)

_pi is identical

to r and remains constant from iteration to iteration for a

_particular

observa-tion;

in all other cases _PI is a data

_dependent

modification of r

_changing

from

cycle

to

_cycle.

The

_prior

_probability

r itself

_is,

of _course,

_independent

of the

trait

_analysed.

The values for r were not recalculated at the

_beginning

of each Gibbs

_cycle,

since the

_paternal

_linkage

_phases

between markers and also

be-tween markers and RN were known to almost

_certainty,

based on 300 _progeny

informative for RN and _{496 progeny with} marker data available

_(22!.

Sampling

of

_genotypes

is

_equivalent

to

_sampling

one of all

possible

_X

_l

ma-trices. Therefore the

_computations

_proceeded

_by

an

_update

of the mixed model

equations using

the last

_sampled

version of

_X

₁

_.

_Finally

new vectors

_b

_l

_,

_b

₂

_,

UI

and u2for fixed and random effects were

_sampled

from normal conditionals and

components

_{s!, s2 and se}

from

inverted

_Chi-square

distributions as described

for

_{Bayesian analysis}

of mixed models with flat

_priors

_by,

_e.g.

_Wang

et al.

_!2?!,

Jensen et al.

_[7]

and Janss et al.

_!6!.

Fixed effects in all cases

_comprised

RYRI

_genotype,

_sex, line of dam and a

seasonal

_effect,

which was defined as month of birth for

_birthweight,

month at

weaning

day

for

_weaning

_weight

and as month of

_slaughter

for all other traits. A

_parity

of dam effect

_{(1, > 2)}

as well as a linear

_regression

on litter size was

fitted to

_{early growth}

traits. Growth traits were corrected for _age

(linear

and

quadratic)

and carcass traits for

_{slaughterweight.}

_{Litter, day}

of

_slaughter

and

pen were used as random uncorrelated common environmental effects for

_early

growth

traits,

meat

_quality

traits and all other

_traits,

_{respectively.}

For exact

Computation

of

_{probabilities}

for alternative

_{coupling phases}

for marker loci in sires and of risk values r for

_progenies

were

performed

with our own

FORTRAN _program. RISKOFIT

_software,

a derivative of LMMG

[21]

was used

for the Gibbs

_sampler.

The UNIVARIATE and AUTOREG

_procedures

of the SAS

_package

_[25]

were used to

_compute

the mean and the standard deviation

of the

_marginal

_posterior

distribution of the contrast between RN- carriers and non-carriers and to check for serial correlations and other

_properties.

Non-parametric

estimates of the

_marginal

_{posterior probability density}

functions

as well as 95

%

confidence intervals for these functions were calculated with

the lifetable method as

_implemented

in the LIFETEST

_procedure

_[25].

One

long

Gibbs chain with one million

_cycles

was run for each trait. From each

50th

_cycle

the _{contrast !,1 - p2} was written to a

file,

along

with other model

parameters

of

_interest,

and saved for

_post

Gibbs

_analysis.

Since the first 20 000

iterations were discarded

_(burn-in

_plus

a wide

_safety

margin),

results

_originate

from 19 600

_single

values per trait. CPU time varied somewhat from trait to

trait and was

roughly

16 h when a 100 MH Pentium PC was used and 5 h on a SUN

_ultra-sparc

workstation. For all estimated means the

_probability

mass of a

_{highest posterior}

content

_region

bounded

_by

zero on either side was

determined from a normal distribution _curve, which was used to

_approximate

the

_{posterior distribution,}

with mean and variance estimated from the Gibbs

sample.

A contrast is

_reported

as

_significant

if this

_probability

mass exceeded

95 %.

Finally

for all traits with a

_significant

result another

_long

chain was

gener-ated. A total of 80 000 values was

sampled

for each of three

_parameters

from

four million

_post

Gibbs

_cycles

_per trait: the difference between RN

_genotypes,

the difference between RYR1

genotypes,

and the

_polygenic

variance. From these

data, samples

for six

_population

_parameters

were

_generated:

_samples

of the

QTL

variance due to the RN

locus,

of the

QTL

variance due to the RYRI

lo-cus, of the total

genetic variance,

of the ratio of RN variance and total

_genetic

variance,

of the ratio of RYR1 variance and total

_{genetic variance,}

and of the

polygenic heritability

h

P

2

.

In order to obtain a realization of the total

_genetic

variance _{vg both}

_QTL

variances and the

_polygenic

variance from one

_cycle

were

summed:

By analogy, samples

for the

_{polygenic heritability}

were

_generated

as ratios

of the

_polygenic

variance and the sum of

polygenic,

common environmental

(table !,

and residual variances:

From each

sampled

contrast between RN

_genotypes

an observation for the

RN variance _VRN was

_computed

as

Observations for the RYR1 variance VRYR were

_computed

in

_exactly

the

between NN and Nn

genotypes.

This

_corresponds

to a situation where all boars are

_{doubly heterozygous}

(Nn,

RN-Irn

+

),

all sows are

_doubly

_homozygous

(NN, rn

+

/rn

+

)

and the RN- and n alleles in final crossbred progeny are

found

_exclusively

in

_heterozygous

_genotypes

with a

_frequency

of 0.5. Since the

standard Pi6train boar used

_by

the

_industry

is

_homozygous

stress

_sensitive,

the

n allele at the RYR1 locus has been eradicated to a

large

extent in dam

lines,

and the RN-

_frequency

in the sire

lines,

from where our animals

_originate,

seems to be

_high

_[22],

such a

_genetic

situation can be

regarded

as close to

reality.

3. RESULTS AND DISCUSSION

Examination of serial correlations showed that uncorrelated values for the difference between

_genotypes

were obtained

by

the

sampling

of each 50th

realization from the Gibbs chain. Posterior means and

posterior

standard

deviations are shown in table IL Because of

uncorrelatedness,

the

corresponding

Monte Carlo errors are

_just

the ratio of standard deviation and _{square root} of

the size of the Gibbs

sample.

All

_posterior

distributions turned out to be

_highly

symmetric

and could be very well

approximated

by

a normal distribution. In

figure

/!

a typical non-parametric

estimate of the distribution curve is shown as an

example,

together

with its 95

%

confidence limits. These confidence limits

show the

_good

determination of the distribution curve,

especially

in the tails. A

joint plot

of this curve and its normal

_{approximation}

show them to be almost identical

_{(figure 4).}

Small but

_significant

effects were found for

_pH

values measured 24 h after

slaughter

(table

77).

Reflectance was

significantly

lowered in RN- carriers with a difference of

nearly

one unit. The most

_{important results, however,}

are a

highly significant

2.4 mm increase in _eye muscle

thickness,

an

_enlargement

of

loin _eye area of 1.39

cm

2

and

a 0.46

%

increase in estimated lean meat content.

Neither

_conductivity

nor _any

growth

trait was affected

_by

RN

_genotype.

An

_impact

of RN on

_optical

meat

_properties

was also found

_by

Le

_Roy

et al.

[11]

and Lundstr6m et al.

_[13],

who

reported

an increase in several surface

reflectance

measurements,

taken 1

_day

and 4

_days

after

_{slaughter. Although}

these traits are not

_{important economically,}

_knowledge

of RN effects may

lead to the

_development

of

_{optical procedures}

for RN- detection and

_quality

control,

e.g. at the

_{slaughterhouse.}

For all traits with a

_significant

RN effect the

estimated difference between

_{heterozygotes}

at the 7!7! locus and

homozygous

stress resistant animals is shown in table IV.

The entire _range of fatness traits showed no _response at all to RN-. Le

Roy

et al.

_(11!

found evidence for the reverse: backfat thickness was reduced in

carriers. It should be noted here that it is not

possible

to

_distinguish

between

pleiotropic

effects of the RN locus itself and the

_pleiotropic

effects of the RN

region,

i.e. all

_coupled

loci close to RN. Thus the RN

_region

in one

_experiment

may show other characteristics than in another

experiment.

In the

_experiment

described

_by

Le

_Roy

et al.

_[11]

the

_genotypes

of all

recorded progeny were

fully

determined

by

the

homozygosity

of their

parents.

misclassified RN

_genotypes,

when RTN was used for classification instead of

glycolytic

potential.

A

_region

of

_uncertainty,

where the observed

_phenotype

generates

more or less

equal

likelihoods for carriers and

non-carriers,

is a

problem

of every

phenotypic

measure which _may be used as a classification

criterion. This

_study

is an

_attempt

to overcome this

_{problem by combining}

phenotypic

measures,

genetic

markers and a _proper statistical

procedure,

which takes account of uncertain

_genotypes.

_Despite

many

genotypes

being

fixed or known with

_{high probability,}

there was still room for

_changes

in the

number of carriers from iteration to iteration. In the

_analysis

of lean meat

content,

for

_example,

the minimum and maximum number of carriers were

142 and

_201,

_{respectively,}

with an _average value of 160. This variation is due

to animals with uncertain

_genotypes

because of a recombination within the

flanking

marker interval or because of low marker informativeness. For these

progeny the choice of their

genotype

completely

rests on their

_performance

in

a

specific

trait. Another _way to

_exploit

_glycogen

content as a

_major

source for

genotype

discrimination would have been a multivariate

_{analysis, combining}

glycogen

and other traits.

_{However, incorporating}

_glycogen

as a

_phenotypic

marker is easier to

_implement

without

_ignoring

_important

information. The

close normal

approximation

of the

posterior

probability

curve for the contrast

between

_{genotypes suggests}

that a

_{regression analysis}

would have

_provided

similar results with

_regard

to differences between

_genotypes.

A

_Bayesian

or a

maximum likelihood

_{approach, however,}

is also well suited for an examination

of variance

_components.

When

_{considering figure 2}

the

_{within-genotype}

variance of

_glycogen

content

seems to be affected

_by

RN. This

_phenomenon

_may be

_{explained by}

two

_specific

features of

glycogen

measurements:

_first,

the

_large

difference between low

is considered instead of

_glycogen

content

_[3].

This is the reason

why

variance

effects of RN were

_regarded

as

_{glycogen specific}

and have not been further

investigated

in this

study.

Benefits from increased lean meat content are not

_{high enough}

to

_outweigh

financial losses from decreased

_{technological}

_yield

and to

_justify

the use of the

RN- allele in future

_pig

_breeding.

_Figure

5 illustrates a calculation

revealing

this fact: 1.47

_kg

of fresh lean meat from a carrier animal is _{necessary in} order

to obtain 1

_kg

of

_processed

lean

_meat,

_compared

to 1.41

_kg

of fresh lean meat

from a non-carrier

_(conversion

factors of 0.68 and 0.71 are from Feddern

[3]).

If we assume a carrier with 55

%

lean meat

_content,

then a

_non-carrier,

which is

_genetically

identical

_except

at the RN

_locus,

has 54.5

%

lean meat

_content,

according

to our results. Therefore there are 2.67

kg of slaughterweight

needed

to

_produce

the same amount of 1

_kg

_processed

lean

_meat,

_compared

to 2.59

_kg

from a non-carrier. This translates to costs of 12.60 DM and 12.22 DM _per

_kg

processed

lean meat,

using

carcasses from carriers or

_{non-carriers,}

respectively

(4.72

DM _per

_kg

carcass

weight).

The cost difference of 0.38 DM is still

_positive

though

somewhat lower than in a situation where both

_genotypes

have an

equal

lean meat content of 55

%

_{(0.52 DM).}

The

weight

of bones and fat per

kg

processed

lean meat is reduced

_by

0.02

_kg

in

_{non-carriers,}

a side effect which is

neglected

in these calculations as well as the increased

drip

loss in carriers

[13].

The

_proportion

of the total

_genetic

variance

_{explained by}

the RN locus

the loin. The

_proportion

of the

_genetic

variance which can be attributed to

RYRI as the second

_QTL

known to be

_segregating

in this

population

also reaches considerable levels up to 20

%

for eye muscle

depth.

Thus the

joint

action of both

_C!TLs

_generates

more than 40

%

of the total

_genetic

variance

in eye muscle

depth,

though

only

those two

_genotypes

which are of

practical

importance

are assumed to occur at each locus. The estimate of the

_polygenic

heritability

for _eye muscle

_depth

is rather low at 16.5

%

_{(table IT!}

compared

to the estimates for loin eye area and lean meat content

_(62.9

and 36.0

_%).

In the

_four-way

_{crossbreeding}

scheme that is considered

_here,

the RN and RYRI alleles are combined in such a _way that terminal sires are almost

exclu-sively doubly heterozygous

for these two loci. Since eye muscle

depth

can be

regarded

as a

_type

trait it can be

_expected

that Pi6train x

_Hampshire

crossbred

boars will exhibit a

high

degree

of

uniformity,

not

_only

with

respect

to muscle

depth

measurements,

but also when

_they

are

_visually

scored.

_However,

this

uniformity

is

_obviously

lost in the

_{target genotype}

of the

_{crossbreeding}

scheme.

The RN-RYRI

_{example clearly}

demonstrates that

_commercially

selected

_pig

populations

exist,

where

_knowledge

on

_QTLs

_may be used to increase

Furthermore,

it throws some fundamental

_light

on the

_potential

_impact

of

_QTL

detection on

_{crossbreeding}

schemes in livestock

_species:

the

_crossing

of

_highly

inbred lines as a means for variance reduction is not feasible in animal

_breeding

because of

_inbreeding

_depression.

An alternative

_approach

towards

_uniformity

may

exploit

knowledge

on

_{existing QTLs}

_by

_crossing

lines which are

homozy-gous at a number of known

QTLs. Homozygosity

_may be for the same or for

alternative alleles in different

_lines,

_depending

on

pleiotropic

effects on the

en-tire set of

_{breeding goal}

traits. Alleles to be fixed in sire lines are, of course,

those with favourable effects on

_production

but unfavourable effects on

repro-duction. Alternative

QTL

alleles should be assembled in different lines in such

a _way that 100

%

_{heterozygosity}

is achieved in end

_products

in cases where

homozygosity

is not desired or cannot be reached

_by

selection within a short

time.

An

_interesting

fact is that the chromosomal

_region

of the bovine MH locus

(muscular hypertrophy)

and also the

_{neighbourhood}

of the RN locus were

shown to be

_homologous

to the human chromosome 2

_[1,

_23,

_26].

Therefore

the bovine

_MH,

if

identified,

is

_probably

a candidate for the

_porcine

RN.

_Apart

from

_this,

the results from this

_study

_along

with the

_findings

of Le

_Roy

et al.

[11],

who found an increased

weight

of ham and

loin,

both

_suggest

that all

loci,

which are involved in muscle tissue

_development,

_may be

_regarded

as new

members in the

_assembly

of candidate _genes for the RN locus.

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