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
Results & Discussion
Conclusion & Recommendations
Introduction
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
⇒ Predominant production system
• Continuous predominance of markets
Even though local chicken have:-a number of fitness treats-Good mothers-Requires low input etc
Tadelle Dessie
Main objective
To advance a system oriented identification, characterisation and
evaluation of local chicken ecotypes of Ethiopia
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Specific objectives
• Asses functions and importance of chicken production systems Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Specific objectives
• Asses functions and importance of chicken production systems
• Understand production objectives and purposes
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Specific objectives
• Asses functions and importance of chicken production systems
• Understand production objectives and purposes
• Valuate performance traits
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Specific objectives
• Asses functions and importance of chicken production systems
• Understand production objectives and purposes
• Valuate performance traits • Identify and analyse constraints and
opportunities
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Specific objectives
• Asses functions and importance of chicken production systems
• Understand production objectives and purposes
• Valuate performance traits • Identify and analyse constraints and
opportunities • Evaluate the phenotypic performance
(both intake and output traits)
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Specific objectives
• Asses functions and importance of chicken production systems
• Understand production objectives and purposes
• Valuate performance traits • Identify and analyse constraints and
opportunities • Evaluate the phenotypic performance
(both intake and output traits) • Estimate the genetic distance between
and within the ecotypes
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Materials & Methods
• Module I: On-farm investigation of poultry systems and ecotypes
Three program modules:Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Materials & Methods
• Module I: On-farm investigation of poultry systems and ecotypes
• Module II: On-station growth perfomance evaluation of the different chicken ecotypes
Three program modules:Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Materials & Methods
• Module I: On-farm investigation of poultry systems and ecotypes
• 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
Three program modules:Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Study regions and market sheds
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Materials
• Five chicken ecotypes (Eggs from Households)• Reference breed (Fayoumi)
Module IIOn-station investigation
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Management chicks• Debre Zeit Agricultural Research Centre• Deep litter system• Feed on starter and grower rations• Vaccinated for NCD
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
DNA Isolation
Genomic DNA
Wholeblood
3 … n=251 2Ecotype 1
Ecotype 6
.
.
.
Module IIIMeasuring the genetic distance
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Genetic markers• Microsatellite markers
Module IIIMeasuring the genetic distance
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
- 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
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Results
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
a aabb
Tadelle Dessie
Hen performance history
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
a aabb
50% of chicks died
Non -stimulated46 eggs/year
-Disease-Predation-Feed-Information
• Constraints
Tadelle Dessie
Hen performance history and measures to improve laying
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
a aabb
Stimulated76 eggs/year
50% of chicks died
Non -stimulated46 eggs/year
Tadelle Dessie
Measures to improve laying performance
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
• Set eggs under two broody hens
Tadelle Dessie
Input-output relationships
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
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
Tadelle Dessie
Mean use pattern of chicken (%) (250 HH)
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
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
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
a d c b
e e
a
c b b
c c
a
c b b
c c
Tadelle Dessie
Mean live body weight (+ SE)
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
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%
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
Mean daily body weight gain and Feed Conversion Ratio
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
a
c b bc
d d
Mean daily body weight gain and Feed Conversion Ratio
Tadelle Dessie
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)
Mean daily body weight gain and Feed Conversion Ratio
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
a a
b b
a a
Tadelle Dessie
Coefficients of variation (%) of live body weight (Animal-level)
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
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 %
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendations
Tadelle Dessie
Unbiased standard genetic distance
(pairwise ecotype comparisons)
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
-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
Tadelle Dessie
Neighbour Joining tree (unbiased standard genetic distance)
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
-Assorted the ecotypes according their origin-Bootstrapping values were between 53 to 100 % in NJ trees-Local ecotypes formed two distinct groups-cluster
Tadelle Dessie
Correlation between genetic and geographic distances
Contents
Introduction
Objectives
Materials & Methods
Results & Discussion
Conclusion & Recommendations
r=0.62
-Isolation by distance based on normalised mantel statistic
Tadelle Dessie
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
Results & Discussion
Conclusion & Recommendation
Tadelle Dessie
Conclusion and recommendations
• 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
Results & Discussion
Conclusion & Recommendation
Tadelle Dessie
Conclusion and recommendations
• 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
Results & Discussion
Conclusion & Recommendation
Tadelle Dessie
Conclusion and recommendations
• 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
Results & Discussion
Conclusion & Recommendation