MarkerAssisted Selection and consequences on breeding programs

1
Marker-Assisted Selection and consequences on
breeding programs

• Sylvie GARREAU,
• France

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Presentation

• Introduction
• SAM1 2001 - 2007
• SAM2 2008
• Consequences on breeding programs and genetic
  organization

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Introduction

• Beetween 1996 and 1999,a large QTL (chromosomic
  regions with a significant effect on a
  quantitative trait) detection experiment was
  carried out in France
• Based on the results obtained, a Marker-Assisted
  Selection (MAS) program was implemented.
• What are the results?
• How to use the results in program breeding ?

Source S Fritz, UNCEIA
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SAM1 2001-2007
Source S Fritz, UNCEIA
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What is a QTL

• QTL chromosomic regions with a significant
  effect on a quantitative trait

Source S Fritz, UNCEIA
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SAM1 2001 - 2007

• the markers are too far from genes to know
  directly the value of these genes ? SAM1 (intra
  family)

Source S Fritz, UNCEIA
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Assessment of QTL program

• More than a hundred of QTL detected in 2000
• 3 to 5 QTL per trait of interest
• The chromosomic regions (QTL) have big size and
  contain beetween 50 and more of 300 genes

Source S Fritz, UNCEIA
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Gain of reliabilities due to SAM1

• 2074 bulls born in en 2006. EBV July 2007

Breeding companies can expect higher genetic
progress by using SAM1. At a same genetic
progress, it means that you can reduce the size
of progeny bulls program of 10
Source S Fritz, UNCEIA
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Assessment SAM1

• 60 000 animals typed in 7 years on 45 markers
• 8 traits of interest evaluated
• Small but real gains for SAM1 to improve the
  results of breeding programs
• SAM1 allows data, experience and development of
  software that are useful for QTL fine mapping

Source S Fritz, UNCEIA
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Implementing SAM22008
Source S Fritz, UNCEIA
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QTL fine mapping results
Some families are added and a lot of markers are
used in order to precise the QTL position and to
allow studies on first genes candidates !
Source S Fritz, UNCEIA
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QTL fine mapping results
The results on fine mapping are used to implement
a SAM2.

• A same markers sequence is generally associated
  to a onely one allele of gene ? SAM2

Source S Fritz, UNCEIA
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Principle of SAM2
GPM

SAM 2 is more simple and more efficient,
especially in uncommon families.
Sire
Dam
-

Sire 2
Dam 2

-
-

Heifer
Source S Fritz, UNCEIA
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And Genomic Selection ?
Source S Fritz, UNCEIA
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Principles of SG
All the genome can be studied by SNP
Source S Fritz, UNCEIA
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Principles of SG
Source S Fritz, UNCEIA
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Principles of SG
Genotypes and performances are enough to estimate
breeding values of animals !
Source S Fritz, UNCEIA
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Consequences of SG
Two animals with the same genotyping will have
the same EBV
Source S Fritz, UNCEIA
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Consequences de la SG
The reliability of EBV will be the same for both
male and female !
Source S Fritz, UNCEIA
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Consequences of SG
The cow performance will not have influence on
the EBV reliability, and also on the EBV itself
The EBV reliability will be the same for a cow
and a heifer
Source S Fritz, UNCEIA
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The French Way
Source S Fritz, UNCEIA
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The French Way
A mixed method using SNP markers but also QTL
effects !
Source S Fritz, UNCEIA
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Conclusion
Source S Fritz, UNCEIA
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SAM2 or SG what we could expect

• Reliability around 0.50 for all traits for all
  animals !
• It needs to update links beetween markers SNP and
  effects.
• Milk recording at a large scale is always useful
• Reliabilities are only 0.50
• A complementary program of progeny tested bulls
  is necessary

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SAM and SG

• State of the art
• En France
• Since 2001 SAM1
• Each month, EBV are delivered to the breeding
  companies for young bulls.
• In 2008 implementing of SAM2
• New EBVs are expected soon
• Bulls semen could be sold and used without
  progeny results ?
• Less bulls tested on progeny ?