Phenotypic and genetic characterization of local chicken ecotypes in Ethiopia

Tadelle Dessie

Phenotypic and genetic characterization of local chicken

ecotypes in Ethiopia

Tadelle Dessie

Development of Genomic Characterization Protocols for Rational Conservation and Utilization of Avian Genetic Resources

South Korea, October 2011

Tadelle Dessie

Contents

• Introduction• Objectives• Material and Methods• Results and Discussion• Conclusion and Recommendations

Contents

Introduction

Objectives

Materials & Methods

Results & Discussion

Conclusion & Recommendations

Tadelle Dessie

Poultry

• Fulfilling different purposes in different times

• Transformed to big industry

• Forms of production systems in LDC’s

• Large in number and wider in distribution

Contents

Introduction

Objectives

Materials & Methods



Introduction

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Production systems in Ethiopia

• Village production system• Commercial production system• Small scale production system

⇒ Based on:

• Objectives of the producer• Type and number of animals• Management system followed

Contents

Introduction

Objectives

Materials & Methods



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Village production system

• 90% of meat and egg• 95% of chicken population

• Source of protein and small cash

⇒ Little attention to the system and animals

Contents

Introduction

Objectives

Materials & Methods



⇒ Predominant production system

• Continuous predominance of markets

Even though local chicken have:-a number of fitness treats-Good mothers-Requires low input etc

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Main objective

To advance a system oriented identification, characterisation and

evaluation of local chicken ecotypes of Ethiopia

Contents

Introduction

Objectives

Materials & Methods



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Specific objectives

• Asses functions and importance of chicken production systems Contents

Introduction

Objectives

Materials & Methods



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Specific objectives

• Asses functions and importance of chicken production systems

• Understand production objectives and purposes

Contents

Introduction

Objectives

Materials & Methods



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Specific objectives



• Valuate performance traits

Contents

Introduction

Objectives

Materials & Methods



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Specific objectives



• Valuate performance traits • Identify and analyse constraints and

opportunities

Contents

Introduction

Objectives

Materials & Methods



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Specific objectives




opportunities • Evaluate the phenotypic performance

(both intake and output traits)

Contents

Introduction

Objectives

Materials & Methods



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Specific objectives




opportunities • Evaluate the phenotypic performance

(both intake and output traits) • Estimate the genetic distance between

and within the ecotypes

Contents

Introduction

Objectives

Materials & Methods



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Materials & Methods

• Module I: On-farm investigation of poultry systems and ecotypes

Three program modules:Contents

Introduction

Objectives

Materials & Methods



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Materials & Methods


• Module II: On-station growth perfomance evaluation of the different chicken ecotypes


Introduction

Objectives

Materials & Methods



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Materials & Methods


• Module II: On-station perfomance evaluation of the different ecotypes of local chicken

• Module III: Measuring the genetic distance between and within the different chicken ecotypes


Introduction

Objectives

Materials & Methods



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Module IOn-farm investigation

Structure of the study

• 5 agro-ecological zones

• 2 market sheds from each agro-ecological zone (one village / market shed)

• 25 households from each village

∑ 5 x 2 x 25 = 250 households

Contents

Introduction

Objectives

Materials & Methods



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Study regions and market sheds

Contents

Introduction

Objectives

Materials & Methods



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Module IOn-farm investigation

Structure of the study sites• 5 agro-ecological zones• 2 market sheds from each agro- ecological zone • 25 households from each village ∑ 5 x 2 x 25 = 250 households

Methods of data collection

• Structured questionnaire integrated With Participatory Rural Appraisal (PRA)• Transect walk and recall survey

Contents

Introduction

Objectives

Materials & Methods



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Materials

• Five chicken ecotypes (Eggs from Households)• Reference breed (Fayoumi)

Module IIOn-station investigation

Contents

Introduction

Objectives

Materials & Methods



Management chicks• Debre Zeit Agricultural Research Centre• Deep litter system• Feed on starter and grower rations• Vaccinated for NCD

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Data collected• Body weight - every two weeks

• Feed intake -daily

• Mortality -when it occurs

• Carcass and related traits -at 12 weeks

Module IIOn-station investigation

Contents

Introduction

Objectives

Materials & Methods



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DNA Isolation

Genomic DNA

Wholeblood

3 … n=251 2Ecotype 1

Ecotype 6

.

.

.

Module IIIMeasuring the genetic distance

Contents

Introduction

Objectives

Materials & Methods



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Genetic markers• Microsatellite markers

Module IIIMeasuring the genetic distance

Contents

Introduction

Objectives

Materials & Methods



- 10 primers

Polymerase Chain Reaction (PCR)

– Automated thermocycler• About 30 cycles -until 1 mil. Amplification• Huge number of copies and enough starting

template

– Specific program for each primer

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Program used for MCW222

Gel electrophoresis -verification PCR product

1X4 Min2 Min2 Min

29X1 Min1 Min1 Min

1X1 Min1 Min4 Min

72 °C55 °C94 °C

Number of cycles

TemperatureContents

Introduction

Objectives

Materials & Methods



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Module III Measuring the genetic distance

Fragment analysis

– A.L.F. TM DNA Sequencer

• automated electrophoresis and analysis of sequencing

• fluorescently levelled DNA molecules and primers

– Signals detected by photodetector -serial data

– A.L.F. manager version 2.5 / OS/2 operating system

Contents

Introduction

Objectives

Materials & Methods



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Data analysis

Parameter/ data type Type of test Software used

Qualitative data SPSS 10.0

Quantitative data Analysis of variance SAS 6.12

Intake and growth data Analysis of variance SAS 6.12

Hetrozygosity and PIC Hetrozygosity andpolymorpihcity

Genepop

Allele frequenciesand mantel matrix

Mantel test Cervus 2.0

AMOVAUnbiased standardgenetic distance

Genetic distanceBootstrap analysis

Arlequin 2,000Microsat and Mega2.1

Poylogenetic consensustree

Neighbour-joiningmethod (NJ) andUPGMA-tree

Arlequin 2,000

Contents

Introduction

Objectives

Materials & Methods



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Results

Contents

Introduction

Objectives

Materials & Methods



a aabb

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Hen performance history

Contents

Introduction

Objectives

Materials & Methods



a aabb

50% of chicks died

Non -stimulated46 eggs/year

-Disease-Predation-Feed-Information

• Constraints

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Hen performance history and measures to improve laying

Contents

Introduction

Objectives

Materials & Methods



a aabb

Stimulated76 eggs/year

50% of chicks died

Non -stimulated46 eggs/year

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Measures to improve laying performance

Contents

Introduction

Objectives

Materials & Methods



• Set eggs under two broody hens

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Input-output relationships

Contents

Introduction

Objectives

Materials & Methods



ReproductionSaleConsumptionManure

Output

Market value

Non-market value

-Cleaning the environment

-Socio-religious function-Tick control

Foundation stock Replacement stock Grain supplements

-SFRB

Market value

Non-market value

Input

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Mean use pattern of chicken (%) (250 HH)

Contents

Introduction

Objectives

Materials & Methods



Regions Repla Sale Consumption -cement

Tilili 36.4a 47.4a 16.2c

Horro 27.1bc 44.9b 28.0b

Chefe 32.3ab48.0a 19.8c

Jarso 31.3ab46.1a 22.6b

Tepi 23.8c 33.4c 42.8a

Mean 31 44 25+SE 1.2 1.1 1.4

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Mean live body weight (+SE) of chicken ecotypes

0

200

400

600

800

1000

1200

1400

Tilili

Horro

Chefe

Jars

oTep

i

Fayuam

i

Ecotypes

Liv

e b

od

y w

eig

ht

(g)

Day old 42 d 84 d 126 dContents

Introduction

Objectives

Materials & Methods



a d c b

e e

a

c b b

c c

a

c b b

c c

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Mean live body weight (+ SE)

Contents

Introduction

Objectives

Materials & Methods



0

200

400

600

800

1000

1200

1400

8 weeks 10 weeks 12 weeks 18 weeks

Ages

Mea

n liv

e bo

dy w

eigh

t (g)

Male Female

∆ = 36%

∆ = 35%

∆ = 39%

∆ = 36%

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0

2

4

6

8

10

Tilili

Horro

Chefe

Jars

oTep

i

Fayou

mi

Ecotype

AD

G (

g)

0

2

4

6

8

10

FC

R

Average Daily Gain (ADG)

Feed Conversion Ratio (FCR) Contents

Introduction

Objectives

Materials & Methods



Mean daily body weight gain and Feed Conversion Ratio

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0

2

4

6

8

10

Tilili

Horro

Chefe

Jars

oTep

i

Fayou

mi

Ecotype

AD

G (

g)

0

2

4

6

8

10

FC

R


Feed Conversion Ratio (FCR) Contents

Introduction

Objectives

Materials & Methods



a

c b bc

d d


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0

2

4

6

8

10

Tilili

Horro

Chefe

Jars

oTep

i

Fayou

mi

Ecotype

AD

G (

g)

0

2

4

6

8

10

FC

R


Feed Conversion Ratio (FCR)


Contents

Introduction

Objectives

Materials & Methods



a a

b b

a a

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Coefficients of variation (%) of live body weight (Animal-level)

Contents

Introduction

Objectives

Materials & Methods



0

5

10

15

20

25

30

35

40

45

50

Tilili

Horro

Chefe

Jars

oTep

i

Fayou

mi

Ecotype

Co

eff

icie

nt

of

va

ria

tio

n (

%)

Male Female

22-37 %

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Mean Heterozygosity levels (gene diversity level)

Ecotypes Het. %

Tilili 63Horro 57Chefe 63Jarso 55Tepi 61Fayoumi 60

- 4% (MCW78 in Jarso) to 92%(ADL268 in Tilili)- Desplys high within ecotype genetic variation

Contents

Introduction

Objectives

Materials & Methods



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Unbiased standard genetic distance

(pairwise ecotype comparisons)

Contents

Introduction

Objectives

Materials & Methods



-Retrieved using 100 permutations and 100 bootstrap replicates

Ecotypes Tilili Horro Chefe Jarso Tepi Fay.Tilili ***Horro 0.047 ***Chefe 0.095 0.089 ***Jarso 0.102 0.108 0.089 ***Tepi 0.094 0.094 0.193 0.188 ***Fayoumi 0.251 0.254 0.336 0.351 0.307 ***

- Moderate genetic divergence among ecotypes

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Neighbour Joining tree (unbiased standard genetic distance)

Contents

Introduction

Objectives

Materials & Methods



-Assorted the ecotypes according their origin-Bootstrapping values were between 53 to 100 % in NJ trees-Local ecotypes formed two distinct groups-cluster

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Correlation between genetic and geographic distances

Contents

Introduction

Objectives

Materials & Methods



r=0.62

-Isolation by distance based on normalised mantel statistic

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Conclusion and recommendations

• The production system:– Indigenous and integral part of the farming

system– Form the basis for transforming from

subsistence to more economically productive system based on:

⇒ Semi-scavenging model that combined technical improvement with institutional

and organisational support aiming at increasing flock productivity

Contents

Introduction

Objectives

Materials & Methods


Conclusion & Recommendation

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• The ecotypes: Large variation between ecotypes (higher

performance leveles-Tilili and Chefe ecotypes) and presence of reasonable genetic divergence

⇒ Thus, it is recommended that testing the combing ablity by crossing Tilili and Chefe ecotypes

Contents

Introduction

Objectives

Materials & Methods



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• The ecotypes:

The existance of large between bird variation within ecotypes for most traits and the presence of high hetrozygosity values as a gene diversity level

⇒ It is therefore, important to use this variability for rapid improvement of local ecotypes through selection

Contents

Introduction

Objectives

Materials & Methods



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• The ecotypes:

High genetic variation manfested: ...moderate genetic divergence among ecotypes...unique alleles in most of tested loci…high microsatellite polymorphism...large number of alleles…high heterozygosity values

⇒ Sustainable utilisation and conservation.However more detailed stdy using more microsatllite loci and QTL analysis for traits

of interest is recommended

Contents

Introduction

Objectives

Materials & Methods



Technology

Phenotypic and genetic characterization of local chicken ecotypes in Ethiopia