Practical application of advanced molecular techniques in the improvement of animal agriculture: The cases of camel, cattle, sheep, goat, donkeys and chicken in Ethiopia

Practical Application of Advanced Molecular Techniques
in the Improvement of Animal Agriculture: The Cases of
Camel, Cattle, Sheep, Goat, Donkeys and Chicken in
Ethiopia
Tadelle Dessie, Mengistie Taye,
Adebabay Kebede, Kefena Effa,
Zewdu Edea and Wondmeneh Esatu
27 Annual Conference of Ethiopian Society of Animal Production (ESAP)
EIAR, Addis Ababa, 29–31 August 2019

I Introduction
Ⅱ What are molecular techniques?
Ⅲ
Ⅳ
Conclusion and implicationsV
Advantages of molecular techniques
Application of Molecular genetic techniques in Ethiopian livestock

Introduction:
Why do we
bother while
Selection is doing
so well?
• Selection of best performing strains have been
practiced for several years now
• Immense achievements were possible through
selection
• The need for more production, efficiency and
robustness remains critical
• Decision making tools are therefore required

Changes mainly due to selection

Additional tool in
identifying the right
animal
• The information can be used in
selection programs that aimed at
increasing productivity,
enhancing environmental
suitability/ adaptation and
thereby maintaining genetic
diversity.
• The first step is to understand the
genetic control of the trait of
interest and then to identify the
genes involved.
• The choice of breeds for such
studies should be informed by a
knowledge of inbreeding, genetic
diversity, and population
structure.

What are molecular techniques in general?
Molecular genetics
• investigates the genetic makeup of living things at the molecular (DNA, RNA,
and Protein) level.
• It involves the identification and mapping of genes and genetic
polymorphisms associated with adaptation and productive traits.
• involves the manipulation and analysis of DNA, RNA, protein, and lipid.
• Molecular techniques are commonly used in molecular biology, biochemistry,
genetics, and biophysics disciplines.

Advantages of molecular techniques
• Conventional animal breeding is related to the
phenotypic selection where traits are measured
directly, animals with superior performance in the traits
are used as parents of the next generation.
• Selection based on phenotypic traits have limitations
associated with data collection and precision of
measurement unless proper measures are taken.
• Can only be applied for traits measured easily and
moderately to highly heritable, and it is costly as it
demands the maintenance of the breeding stock during
measurement.
Nevertheless, to date, most genetic progress
for quantitative traits in livestock has been
made by selection on phenotype or
Estimated Breeding Values (EBV) derived
from the phenotype without knowledge of
the number of genes that affect the trait or
the effects of each gene.

Advantages contd…
1
Genetic progress may be enhanced with the
knowledge of the genetic architecture of
quantitative traits: the underlying genetic basis
of a phenotypic trait and its variational
properties.
2
Molecular genetic information can result in greater
genetic gain than phenotypic information is with
no genotyping error, the molecular genetic
information is free from environmental effects
resulting in highest heritability.

Advantages contd…
Molecular genetic information can be obtained at an early age
that selection decision can be made earlier and generations
intervals are quite short.
Molecular genetic information can be obtained on all selected
candidates, which is especially beneficial for sex-limited traits,
traits that are expensive or difficult to record, or traits that
require the slaughter of the animal (carcass traits).
With molecular genetic techniques, it is possible to unravel
many genetic polymorphisms at the DNA level.

Application of molecular genetic techniques in various livestock
species in Ethiopia

Camel
• Camel is an important animal in arid
areas of the country
• The pressure due to shortages of
feed causing movement
• DNA sequences from mitochondrial
cytochrome-b gene and genotyping
of 6 nuclear microsatellite loci were
examined to assess genetic diversity
and phylogenetic relationship of
Ethiopian camels (Yoseph et al 2018).

Cattle
• There have been some attempts to characterize populations
at the genome level (Taye et al., 2018; Edea et al., 2017;
Zerabruk et al., 2011).
• African cattle are believed to have developed a wide range of
adaptations to tropical environments
• Hailu et al. (2008), evaluated the genetic diversity, population
structure and degree of admixture of 10 Ethiopian cattle
populations using 30 microsatellite markers.
• The main target was to find out if the current uncontrolled
mating practices resulted a high risk of becoming genetically
homogeneous.
• The study revealed that the various levels of admixture and
high genetic diversity make Ethiopian cattle populations
suitable for future genetic improvement, and utilization under
a wide range of agro-ecologies in Ethiopia.
• The genetic variability and extent of population substructures
in five indigenous cattle breeds of North-Western Ethiopia
were also studied using 22 microsatellite markers.

Genetic diversity, with-in
variability and putative gens
• Controlling gene flow between breeds by
adopting effective breeding and management
practices to maintain variability and overcome
within-breed substructures is suggested to
facilitate the conservation and utilization of
each breed (Zewdu et.al., 2010).
• Zerabruk et al. (2011), considered
microsatellite variation to determine genetic
diversity, population structure and admixture
of seven North Ethiopian cattle breeds by
combining multiple microsatellite data sets
from other cattle populations abroad.
• Overall, North Ethiopian cattle showed a high
level of within‐population genetic variation
and indicated their potential for future
breeding applications.
• Results of the analysis identified important
putative genes and gene regions that are
involved in different biological processes and
pathways associated with different tropical
environment adaptation traits including
thermotolerance, disease and parasite
resistance and feed utilization.

Chicken
• Genetic improvement of indigenous chicken exercises in Ethiopia, as
in other developing countries, have been towards the use of exotic
chicken strains to improve the local chicken.
• Extensive crossbreeding has been common over the 5 decades of
poultry research in Ethiopia. An exception is a single selective
breeding program in indigenous chicken in Ethiopia with the
application of quantitative genetics approaches
• The earlier research on the genetic characterization was by Tadelle
(2003) who have characterized five chicken ecotypes of Ethiopia using
microsatellite markers. The result has led to the discovery of some
unique alleles that are believed to be involved in production traits.
• Later, Halima (2007) has characterized some indigenous ecotypes
from Northwestern parts of Ethiopia using microsatellite markers to
reveal the between- and within-population genetic variations.

• A genome-wide association study (GWAS)
conducted by Psifidi et al (2016) using single
nucleotide polymorphism (SNP) markers to
reveal the association of markers with
phenotypic traits.
• SNPs significantly associated with immune
system, disease resistance, and production
traits in indigenous village chickens were
identified. Adebabay (2019), studied the
genetic diversity and population structure of
Ethiopian chicken strains.
• The study further investigated the signature
of artificial selection with a whole-genome
analysis that showed positive genetic
selection through a short-term selective
breeding program.

Evaluation of changes using genomic approach
• Selective breeding for genetic improvement
is expected to leave distinctive selection
signatures within genomes.’
• PCA was performed using all SNPs from 27
populations (n = 20,867,451 SNPs)
(Adebabay, 2019)
• PC1 (25.95%) separates Improved Horro
from the rest of non-improved chicken
populations.

Donkeys
• Genetic diversity and matrilineal genetic signature of
native Ethiopian donkeys (Equus asinus) inferred from
mitochondrial DNA (mtDNA) sequence polymorphism
was conducted (Kefena et al., 2014).
• In the study, mtDNA sequence polymorphisms of six
morphologically diverse domestic donkeys (Equus
asinus) populations in Ethiopia was investigated.
• The result suggested that Ethiopia could be one of the
centers of diversities for domestic donkeys in the Horn
of Africa.
• The present study also overrides some previous reports
that claimed donkeys were solely an Egyptian
domesticate.

Goats
• The genetic diversity within and among 11
indigenous Ethiopian goat populations/types was
investigated using microsatellite markers (Tesfaye,
2004).
• Solomon (2014) studied the molecular genetic
diversity and homozygous segments of two goat
breeds of Ethiopia using 47K genome-wide SNPs
markers to understand the within and between
breed diversity for future breed improvement and
conservation planning.
• Getnet et al. (2017) also used mtDNA markers to
characterize the genetic diversity and population
structure of Ethiopian goats.
• Another study by Getnet et al. (2017), identified
genetic variants associated with fecundity traits in
some Ethiopian goat populations, and this could be
used in Marker Assisted Selection.

Sheep
• The genetic and morphological diversity and
population structure of 14 traditional sheep
populations originating from four ecological zones in
Ethiopia (sub‐alpine, wet highland, sub‐humid
lowland, and arid lowland) were studied by Gizaw et
al., (2007).
• The study showed a strong indication of adaptive
divergence in morphological characters, patterns of
morphological variation being highly associated with
ecology.
• The genetic diversity and population structure of
Ethiopian sheep populations were characterized
using high-density SNP markers to reveal their
genetic diversity for improving breeding strategies
and mapping quantitative trait loci associated with
productivity (Zewdu et al. 2017).
• The high-density SNP data generated in the study
can be used to identify genes and pathways relevant
for physiological adaptation to extreme
environments and variation in phenotypic traits
(Zewdu et al. 2017).

Practical examples from ILRI
Cryopreservation!
• A response to conservation
plea!!
• Methodology proven,
collection and
cryopreservation started

Proof of concept
finalized; the
first gene
edited chick
@ Edinburgh
sensitive and
engagement
to follow

AfriChickSNP
In molecular biology, SNP array is
a type of DNA microarray which
is used to detect polymorphisms
within a population.
A DNA microarray is a collection
of microscopic DNA spots
attached to a solid surface.
Being developed, once released
it will be used for screening and
genetic improvement

Conclusion and implications
• Advanced molecular techniques being used to some extent
in various species, mainly focusing on the characterization
of genetic diversity and population structure.
• They all are academic efforts and not supported by
phenotypic information.
• Conventional breeding approaches which would have
provided an opportunity to make use of the pieces of
knowledge and information generated from the molecular
technique exercises seemed to be given less attention.
• Very poor commitment from researchers is also hampering
the application of the knowledge in the design of the
breeding programs. Researchers were not committed
enough to further peruse the avenue of breeding programs
that are to be set up in villages.
• The lesson can be learned from community-based breeding
program for Menze sheep and Horro chicken breeding
programs.
• Among the molecular technique studies, some of the
efforts help in better understanding of the domestication
but practically less important.
• Donkeys being hardy animals, are most appreciated by
villagers for their ability to thrive and perform under harsh
environments.
• Breeding programs to improve their traction ability might
be more relevant but needs to be based on farmers
interests.

Take home message
• The use of molecular genetic technologies offers
• a way to identify and select breeding animal at an early age,
• to select for a wide range of traits, and
• to enhance reliability in predicting the phenotype on the mature individual.
• The broad categories of existing gene-based options include
• molecular analysis of genetic diversity,
• animal identification and traceability production,
• reproductive enhancement, transgenic livestock,
• germ line manipulation, and
• gene-based trait selection.

Take home message
• The eventual application of molecular
genetics in breeding programs depends
on developments in the following four
key areas:
• Molecular genetics: identification
and mapping of genes and genetic
polymorphisms
• QTL detection: detection and
estimation of associations of
identified genes and genetic
markers with economic traits
• Genetic evaluation: integration of
phenotypic and genotypic data in
statistical methods to estimate
breeding values of individual
animals in a breeding population
• Marker-assisted selection:
development of breeding strategies
and programs for the use of
molecular genetic information in
selection and mating program

Practical application of advanced molecular techniques in the improvement of animal agriculture: The cases of camel, cattle, sheep, goat, donkeys and chicken in Ethiopia

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Practical application of advanced molecular techniques in the improvement of animal agriculture: The cases of camel, cattle, sheep, goat, donkeys and chicken in Ethiopia