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Practical Application of Advanced Molecular Techniques
in the Improvement of Animal Agriculture: The Cases of
Camel, Cattl...
I Introduction
Ⅱ What are molecular techniques?
Ⅲ
Ⅳ
Conclusion and implicationsV
Advantages of molecular techniques
Applic...
Introduction:
Why do we
bother while
Selection is doing
so well?
• Selection of best performing strains have been
practice...
Changes mainly due to selection
Additional tool in
identifying the right
animal
• The information can be used in
selection programs that aimed at
increasi...
What are molecular techniques in general?
Molecular genetics
• investigates the genetic makeup of living things at the mol...
Advantages of molecular techniques
• Conventional animal breeding is related to the
phenotypic selection where traits are ...
Advantages contd…
1
Genetic progress may be enhanced with the
knowledge of the genetic architecture of
quantitative traits...
Advantages contd…
Molecular genetic information can be obtained at an early age
that selection decision can be made earlie...
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...
Cattle
• There have been some attempts to characterize populations
at the genome level (Taye et al., 2018; Edea et al., 20...
Genetic diversity, with-in
variability and putative gens
• Controlling gene flow between breeds by
adopting effective bree...
Chicken
• Genetic improvement of indigenous chicken exercises in Ethiopia, as
in other developing countries, have been tow...
• A genome-wide association study (GWAS)
conducted by Psifidi et al (2016) using single
nucleotide polymorphism (SNP) mark...
Evaluation of changes using genomic approach
• Selective breeding for genetic improvement
is expected to leave distinctive...
Donkeys
• Genetic diversity and matrilineal genetic signature of
native Ethiopian donkeys (Equus asinus) inferred from
mit...
Goats
• The genetic diversity within and among 11
indigenous Ethiopian goat populations/types was
investigated using micro...
Sheep
• The genetic and morphological diversity and
population structure of 14 traditional sheep
populations originating f...
Practical examples from ILRI
Cryopreservation!
• A response to conservation
plea!!
• Methodology proven,
collection and
cr...
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 po...
Conclusion and implications
• Advanced molecular techniques being used to some extent
in various species, mainly focusing ...
Take home message
• The use of molecular genetic technologies offers
• a way to identify and select breeding animal at an ...
Take home message
• The eventual application of molecular
genetics in breeding programs depends
on developments in the fol...
Practical application of advanced molecular techniques in the improvement of animal agriculture: The cases of camel, cattl...
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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

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Presented by Tadelle Dessie, Mengistie Taye, Adebabay Kebede, Kefena Effa, Zewdu Edea and Wondmeneh Esatu at the 27 Annual Conference of the Ethiopian Society of Animal Production (ESAP), EIAR, Addis Ababa, 29–31 August 2019


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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

  1. 1. 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
  2. 2. I Introduction Ⅱ What are molecular techniques? Ⅲ Ⅳ Conclusion and implicationsV Advantages of molecular techniques Application of Molecular genetic techniques in Ethiopian livestock
  3. 3. 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
  4. 4. Changes mainly due to selection
  5. 5. 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.
  6. 6. 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.
  7. 7. 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.
  8. 8. 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.
  9. 9. 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.
  10. 10. Application of molecular genetic techniques in various livestock species in Ethiopia
  11. 11. 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).
  12. 12. 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.
  13. 13. 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.
  14. 14. 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.
  15. 15. • 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.
  16. 16. 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.
  17. 17. 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.
  18. 18. 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.
  19. 19. 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).
  20. 20. Practical examples from ILRI Cryopreservation! • A response to conservation plea!! • Methodology proven, collection and cryopreservation started
  21. 21. Proof of concept finalized; the first gene edited chick @ Edinburgh sensitive and engagement to follow
  22. 22. 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
  23. 23. 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.
  24. 24. 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.
  25. 25. 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

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