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[SANET-MG] marker assisted selection
25 July 2005
Prof. Joe Cummins
“Marker assisted selection: breeding using molecules as markers but not
transgenes”
Currently crop biotechnology is based on the use of bacterial transgenes
to impart herbicide tolerance or insect resistance on the crops. In this
process an array of genes area added to the crops to make the primary
bacterial transgenes work. This technology provides little hope of
providing major advances in yield , stress tolerance or long term
resistance to microbes or nematodes. Traditional breeding of crops and
animals has been based on the use of markers that are usually inherited
following Mendelian patterns. The main agricultural traits governing
yield (or size), stress resistance or long term disease protection are
the quantitative trait loci (QTL). One of the founders of the study of
population genetics ,R.A. Fisher, described QTL as many independent
loci that added together to provide traits such as size(1). QTL are
seldom tightly linked on a chromosome and the loci are dispersed about
many chromosomes in the genome. Selection of QTL traits has been
inherently slow and meticulous but because the traits have fundamental
importance the results have provided the main crop and animal
enhancements. Fisher believed that QTL were made up very many loci each
adding small increments to the selection for a trait such as size. How
ever, QTL may be made up of a relatively small ,say twenty or so, loci
that could be easily managed provided that the loci could be identified.
Fisher’s idea of QTL is probably best served by the slow and meticulous
selection strategies used in traditional genetics while QTL with
relatively few loci can be readily selected using molecular markers.
Currently, it appears that many QTL may have relatively few loci but
some important QTL may be closer to the very large number of loci
envisioned by Fisher, in which case the molecular markers are unlikely
to be cost effective.
In contrast to the added transgenes used in genetic modification there
is a growing arsenal of molecular markers (polymorphisms) that aid in
identifying QTL and selecting them for crop and animal enhancement. The
process employing such markers is called marker assisted selection
(MAS), that technology differs from genetic modification because the
genes being selected for crop or animal improvement are not altered in
any way. The molecular markers used in selection are probed using
sequences from a gene bank but the genes in the crop or animal are not
altered, only identified. The markers used to probe the progeny of a
cross are not the QTL loci themselves but they are close to the QTL on
the genetic map. Of course the markers can be used to determine the
molecular identity of the QTL, but the molecular marker is used even
when the QTL is identified because the marker is cheaper and quicker to
use to identify a large number of progeny. Of course recombination may
separate the marker from a QTL allele but the closer the marker is to
the QTL the more remote is the chance of separation by recombination.
The more polymorphic markers available for a breeding program the more
effective will be that program.
There are several types of molecular markers used in MAS these include
restriction length polymorphism (RFLP),random amplification of
polymorphic DNA (RAPD), amplified length polymorphism(AFLP) single
sequence repeats (SSR) as the main marker strategies and single
nucleotide polymorphisms SNPs(2) RFLP is the use of restriction enzymes
to cut chromosomal DNA at short restriction sites, polymorphisms result
from duplications or deletions between the sites or mutations at the
restriction sites. RFLP provided the basis for most early work but
requires a relatively large amount of DNA and is rather expensive in a
large screening program (2). RAPD utilizes low stringency polymerase
chain reaction (PCR) amplification with single primers of arbitrary
sequence to generate strain-specific arrays of anonymous DNA fragments
(3). The method requires tiny DNA samples and analyses a large number
of polymorphic loci (2). AFLP requires digestion of cellular DNA with a
restriction enzyme , ligating adapters to each restriction fragment and
a subset of such fragments are amplified using primers with 16 adapter
defined sequences with one arbitrary nucleotide (4). The method measures
up to 100 polymorphic loci and requires a relatively small DNA sample
for each test (4). SSR are based on DNA microsattelites that are widely
dispersed through out the genome of eukaryotes. Microsattelites are
selectively amplified to provide simple sequence repeat markers (5).SSR
requires tiny DNA samples and has a low cost per analysis (2). SNPs are
detected using PCR extension assays that efficiently pick up point
mutations (6). The procedure requires little DNA per sample and costs
little per sample once the method is established (2). One or two of
methods described above are employed in a typical MAS breeding program.
MAS has been employed in cereals. It was extensively deployed in maize
breeding Corporations including Monsanto and Syngenta have invested
heavily in the program. SNP appear to be the dominant marker for
selection. Wheat has seen less progress in MAS than maize but there
is good success in the area of quantitative disease resistance. Rice has
also seen extensive activity in MAS centering on pyramiding disease
resistance genes. SNPs appear to be identified for all the major cereals
(7). MAS is being used to improve forage crops through QTL for nitrogen
use efficiency. There was a strong response to marker selection on
nitrogen use efficiency (8). The pome fruits, apple and pear, have
extensive MAS , mainly based on RFLP,RAPD,SSR and AFLP. The traits being
selected include fruit production, storage and disease resistance (9). A
global strategy using MAS for livestock genetic improvement in the
developing world was proposed . QTL mapping would be used in genetic
improvement and to bring together desirable traits from around the world
(10). It has been proposed that conservation of allelic richness in wild
crop relatives is greatly enhanced by assessment of genetic markers
(11). The information from wild crop relatives could be directly
employed in MAS of the crop plant.
A recent review by William Hill of Edinburgh University focused on the
QTLs for oil production in maize and for body size in chickens. In
neither case could individual QTL with substantive quality be detected.
Instead , Identified QTLs created small additive increments which could
be selected , but with patience (12). Hill’s report suggested that the
Fisher view of QTLs prevailed and that the use of MAS might not be cost
effective in such selections. It may be that MAS may be effective in
areas such as disease resistance and some agronomic traits but that
important traits such as oil production in maize or body size in
chickens are dealt with most effectively using traditional selection
methods.
Farmers in developing countries and even some farmers in the developed
world face the growing control of seed production by a few multinational
corporations. One solution has been to educate farmers in the art of
plant breeding to provide varieties tuned to the local environment and
free of the greedy demands of seed corporations. It is highly unlikely
that indigenous farmers will take to MAS and molecular genomics.
However, those who advise indigenous farmers would gain valuable
insights in recognizing markers linked to valuable agronomic traits and
pass on those insights to the indigenous plant breeders to assist them
in making selections with immediate benefits.
In the long run it seems likely that MAS will play an important role in
plant breeding, even though it may not be as large as is being claimed
by promoters. MAS should not effect organic certification because
transgenes are not introduced into the crop. Molecular genetics is only
used in analyzing the crosses. It may be best to tentatively accept MAS
and to point out that the technique is far more effective in crop and
animal improvement than is the use of transgenes.
References
1. Fisher,R The Genetics of Natural Selection, Oxford University
Press,Oxford 1930
2. Korzun,V. Molecular markers and their application in cereal breeding
Marker Assisted selection: A fast track to increase genetic gain in
plant and animal breeding? 2003 http://www.fao.org/biotech/Conf10.htm
3. Wang,G,Whittam,T,Berg,C. and Berg,D. RAPD (arbitrary primer)PCR is
more sensitive than multilocus enzyme electrophoresis for distinquishing
related bacterial strains Nucleic Acid Research 1993,21,5930-3
4. Lin,J,Kuo,J. and Ma,J. A PCR based DNA fingerprinting technique:AFLP
for molecular typing of bacteria Nucleic Acid Research 1996, 24,3649-50
5. Hayden,M. and Sharp,J. Targeted development of informative
microsatellite (SSR) markers Nucleic Acid Research 2001,29, E44-4
6. Torjek O, Berger D, Meyer RC, Mussig C, Schmid KJ, Rosleff Sorensen
T, Weisshaar B, Mitchell-Olds T. and Altmann T. Establishment of a
high-efficiency SNP-based framework marker set for Arabidopsis. Plant J.
2003,36(1):122-4
7. Koebner,R. MAS in cereals: Green for maize, amber for rice , still
red for wheat and barley Marker Assisted selection: A fast track to
increase genetic gain in plant and animal breeding? 2003
http://www.fao.org/biotech/Conf10.htm
8. Dolstra,O,Denneboom,C,deVos,A. and vanLoo,E. Marker assisted
selection in improvement of quantitative traits for forage crops Marker
Assisted selection: A fast track to increase genetic gain in plant and
animal breeding? 2003 http://www.fao.org/biotech/Conf10.htm
9. Tartarini,S. Marker-assisted selection in pome fruit breeding Marker
Assisted selection: A fast track to increase genetic gain in plant and
animal breeding? 2003 http://www.fao.org/biotech/Conf10.htm
10. Gibson,J. Strategies for utilizing molecular marker data for
livestock genetic improvement in the developing world Marker Assisted
selection: A fast track to increase genetic gain in plant and animal
breeding? 2003 http://www.fao.org/biotech/Conf10.htm
11. Schoen,D. and Brown,A. Conservation of allelic richness in wild crop
relatives is aided by assessment of genetic markers Proc. Natnl. Acad.
Sci. USA 1993,90,10623,27
12. Hill,W. A century of corn selelction Science , 2005,307,683-4
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