MOLECULAR MARKERS AND MARKER ASSISTED SELECTION

SHAKIL BHATP.G. SCHOLAR

ANIMAL BIOTECHNOLOGY

Introduction

In developed countries animal breeding is based on quantitative genetics

Nicolas,(1996)

Quantitative genetics is multifactorial, influenced both by gene and environmental factors and their interaction

(Beuzen et al., 2000)

Improvement of livestock focuses on the selective breeding of

individuals with superior phenotypes Williams,(2005)MAS is a powerful tool in animal breeding, improves the whole range of desirable traits

MARKERS

MORPHOLOGICAL

CHROMOSOMAL

BIOCHEMICAL

GENETIC

MORPHOLOGICAL MARKERS

BIOCHEMICAL MARKERS

CHROMOSOMAL MARKERS

Molecular markers

Molecular marker are specific fragments of DNA that can be identified within the whole genome

They are used to 'flag' the position of a particular gene

Molecular markers are used in molecular biology to identify a particular sequence of DNA

(Chauhan and Rajiv, 2010)

Features of Molecular Markers

Characteristics:Co-dominant expression

Early onset of phenotypic expression

High polymorphism Random distribution throughout

the genome Assay can be automated

Hybridization- based DNA markers

RFLP, oligonucleotide fingerprinting

PCR based DNA markers

RAPD, AFLP, SSR

Sequencing based DNA markers and DNA Chip

SNP

Classes of Molecular Markers

Vogel et al.,(1998)

Restriction Fragment Length Polymorphism (RFLP) Principles

RFLP analysis is a standard, well-tested procedure for estimation of genetic diversity Tanksley, (1993)

RFLP analysis is based on the ability of restriction enzymes to cleave DNA at specific target nucleotide sequences

Fairbanks, (1995)

• Simple sequence repeats are present in the genomes of all eukaryotes and consists of several to over a hundred repeats of a 1-4 nucleotide motif.

SNP

• The most common genetic polymorphism

• Distribute throughout genome with high density

• More stable and easy to assay

• Facilitates large scale genetic association studies as genetic markers.

MARKER ASSISTED SELECTION

THEORY AND PRACTICE

ADVANTAGES

MAS vs PHENOTYPIC SELECTION

The process of using the results of DNA-marker testing to predict the genetic merit of the animal being tested and assist in the selection of individuals to become parents in the next generation.

• Marker assisted selection (MAS) is an indirect selection process where a trait of interest is selected not based on the outward appearance of the trait itself but on a genetic marker near the trait (gene) on the DNA.

• MAS - Use of information from genetic markers to help make selection decisions of animals for genetic Improvement.

• This is done in a manner that exploits both known major genes and all unknown genes.

CONVENTIONAL BREEDING

P1 P2

MARKER-ASSISTED BREEDING

P1 X P2

MAXIMIZE GENETIC GAIN

TO REDUCE POPULATION

SIZE FOR TRAITS

LEVEL OF RECOMBINATION

BETWEEN MARKER AND QTL

Combined approaches

ADVANTAGES

TIME COST RECESSIVE GENES

LOW HERTIBILITYSEASONAL

CONSIDERATIONSGEOGRAPHICAL

CONSIDERATIONS

GENE STACKING EARLY DETECTION MULTIPLE GENES

QTL DETECTION

GENE MAPPING

MARKER GENOTYPING

GENETIC EVALUATION

REQUIREMENTS

Potential benefits from MAS are greatest for traits that

Have low heritability

Are difficult or expensive to measure (disease resistance)

Are currently not selected for as they are not routinely measured (tenderness)

•Time consuming

•Difficult

•Costly

•Performed off season

•Gene pyramiding

•Early stages of development

•Several selections simultaneously

•Low heritability traits

MAS Vs. PS

MAS in selection programming

BETWEEN BREED

SELECTION

INTROGRESSION

IMPROVEMENT OF SYNTHETIC LINES

WITHIN BREED

SELECTION

CURRENT STATUS OF MAS

OBSTACLES

CHALLENGES

Low impact of MAS

Resources not availableMarkers may not be cost-effectiveQTL mappingQTL effects may depend on genetic background or be influenced by environmental conditionsPoor integration of molecular genetic and conventional breeding

Cost - a major obstacle

Future challenges