12/10/2017

Breeding use of molecular

technologies

Sigit Prastowo

The breeding concept

•P=G+E
• P is the phenotype which is visually observed. For example growth
rate, feed eficiency, reproduction, meat quality.
• G is the blue print information in term of DNA sequence. It‘s carry
potential trait that inheritance from parent to offspring.
• E is supporting factor to express the potential of G. For example feed,
housing and health management.
• In the breeding strategy, G is need to be selected and supported with
E to maximize the expected P.

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Breeding in marbling (example)

Marbling :
Intramuscular fat deposition within the muscle of
beef.
Marbling correlated with more tender beef.

In term of breeding :
• Marbling heritability is considered 0.35-0.4
• mean 35-40% is inheritance from its parent
• There are 60-65% of environmental factor which
determine the expression of gene potential for
marbling trait
• Breed specific for marbling trait
Figure source :
http://www.exoticmeatmarkets.com/wabefraumasc8.html

The marbling trait

Controlled by protein that reponsible for
1. Fat deposition
2. Fat composition

Lines of evidence shows that beef with high marbling express more SCD, TG, DGAT1 gene.
Those genes control the sintesis of fatty acids and it‘s compostion which deposit intra
muscularly.

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Another example
• Double muscle in Belgian
Blue cattle
• Muscling gene controlled
by mutation in Myostatin
GDF8

Another example
• Egg colour
• Controlled by GMS1 gene

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Another example

Discussion....
• Selected gene in Lab Work
• Gene information
• Associated trait

Lets talk about it

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The influence of genetic value

Genome Genetic Value Environment Phenotype

A -2 +4 +2 +1 +1 +10 +16 -10 +6

B -2 0 -2 +1 +1 +3 +1 +9 +10

C -2 0 -2 -1 -1 -4 -10 +20 +10

Warp up
• Gene screening by using molecular technologies
• having possibility to shorten breeding time (generation
interval : l)
• in the aim to enhance the profit
• Followed with mating system

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Genetic screening methods

Marker selection

SNP screening method

Marker selection

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SNP screening method

Production trait SNP

Gene Whole blood and Gene expression

Marbling tissue sample
Growth trait

DNA & RNA PCR setup Association study

Gene >< candidate trait

Insilico study Primer design

Strategic breeding
(insilico)

The mating system

Male
A A Elite stock
Female

a Aa Aa F1 (commercial
a Aa Aa stock)

Mating arranged to ensure Embryos stock

the trait is inheritance carry genes for
marbling trait

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Steps in Genomic Selection

http://nationalhogfarmer.com/genetics-
reproduction/evaluation-selection/genomic-
selection-tools-0426

Recalling about DNA

concept

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The stucture of DNA and RNA

•DNA
• Double helix
• Nucleotide A, G, T, C

•RNA
• Single helix
• Nucleotide, T = U

Transcription > mRNA > Ribosome > translation > protein

Protein is the end product of many genes, are polymer made up

of amino acids commonly found in proteins

The information encoded in mRNA called genetic code cosist of a

Linear series of nucleotide triplet (codon). This information stored
In DNA.

DNA makes RNA, which most oftem makes protein.

The central dogma of genetic

Using and alphabet of only four letters (A, T, C, and G), genes direct
The synthesis of highly specific proteins that collectively serve as the
Basic fo all biological function.

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Doors for genetic selection

• Bioinformatic
• DNA and RNA sequence
• PCR (Polimerase Chain Reaction)

DNA sequence
>gi|258513349:14757332-14759082 Bos taurus breed Hereford chromosome 18, Bos_taurus_UMD_3.1.1, whole genome
shotgun sequence. MCR1 gene 1751bp.
CTACCGCGGCCCGGTAAGGCAGGAGGTCCCCACAGGACAGGAGGAGGCAAGCGGCCCAGAAATGTCTGCCTGTGGGCAACCGCACATCCA
GGGAAGAGGTGGGGAGGCGGACTGAGAACAGAAGAGCGAAGCCGCGCCCAGAGGGCTGGCCCCATAAGCTTGGGGCCATGCCTGGGCC
GACATTTGTCCAGCCAGGGAGGGGAGGTGTGAGGCCCCTCCCAGGGGAGCCATGAGTTGAGCAGGACCCTGAGAGCAAGCACCCCTTCCT
GCTCCCTGCGGGACGATGCCTGCACTTGGCTCCCAGAGGCGGCTGCTGGGTTCCCTTAACTGCACGCCCCCAGCCACCCTCCCCTTCACCCT
GGCCCCCAACCGGACGGGGCCCCAGTGCCTGGAGGTGTCCATCCCTGACGGGCTCTTTCTCAGCCTGGGGCTGGTGAGTCTCGTGGAGAA
CGTGCTGGTAGTGGCTGCCATTGCCAAGAACCGCAACCTGCACTCCCCCATGTACTACTTTATCTGCTGCCTGGCTGTGTCTGACTTGCTGGTG
AGCGTCAGCAACGTGCTGGAGACGGCAGTCATGCTGCTGCTGGAGGCCGGTGTCCTGGCCACCCAGGCGGCCGTGGTGCAGCAGCTGGAC
AATGTCATCGACGTGCTCATCTGCGGATCCATGGTGTCCAGCCTCTGCTTCCTGGGTGCCATTGCTGTGGACCGCTACATCTCCATCTTCTACGC
CCTGCGGTACCACAGTGTTGTGACACTGCCCCGAGCGTGGAGGATCATTGCGGCCATCTGGGTGGCCAGCATCCTCACCAGCCTGCTCTTCAT
CACCTACTACAACCACAAGGTCATCCTGCTGTGCCTCGTTGGCCTCTTCATAGCTATGCTGGCCCTGATGGCCGTCCTCTACGTCCACATGCTGG
CCCGGGCCTGCCAGCATGCCCGGGGCATTGCCCGGCTCCAGAAGAGGCAGCGCCCCATTCATCAGGGCTTTGGCCTCAAGGGCGCTGCCAC
CCTCACCATCCTGCTGGGCGTCTTCTTCCTCTGCTGGGGCCCCTTCTTCCTGCACCTCTCGCTCATCGTCCTCTGCCCCCAGCACCCCACCTGTG
GCTGCATCTTCAAGAACTTCAACCTCTTCCTGGCCCTCATCATTTGCAACGCCATTGTGGACCCCCTCATCTATGCCTTCCGCAGCCAGGAGCT
CCGGAAGACGCTCCAAGAGGTGCTGCAGTGCTCCTGGTGAGGGTGGCAGTGCCGTCGTGTGCCCCAGGCCTGTGAGGCCAGGGCAGTCCC
TTGACAAAGAGGATCGGCTAGACCATCCCTGAAGGTGAGGGTGCACAGGCCTTTGGGGCCTGAGAGGGGAATCTCAGGACTCTCCAGGAG
GCTGTGCAGAATGAGGAGGCTGGGGAGATGGTGGGGCATGGCCTCCCACACCTAGAAAGGAGGGCCCCCACCCCTCCATCTGGGGCCCCA
CTCTGGGGCCGGTGCCCACACCCCACCCCACCCAAAGCTGTGGGAAGTCCCGCTCCAAGGACTTCATGACCAGCACAGGAGGAGGTGGGG
CCCACAGTGGGGGGCTTTTCTCTTCTAACGCTCTGTGGTGACTGGGAGCCGGGCTCAGCCCGTCTGCCAGCAGCACATGCATTCGGCAGAC
ACCCCAGCCAGGCCTGCTCTGGGGAACCAGCAGCCAATATGCAGGCTCCAGGGCCAGGAAGCAGTGCAGCAGTATTAATAAACGTGATGCT
TGGTGCAACCTC

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Bioinformatic database
• NCBI • Ensembel

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