Agriculture Reference
In-Depth Information
fragment length polymorphism (RFLP), ampli-
fi ed fragment length polymorphism (AFLP),
microsatellites or simple sequence repeats (SSRs),
and single nucleotide polymorphisms (SNPs). All
of these types of markers and derived variations
have been used in wheat genetic mapping. Today,
SSRs prevail as the dominant marker system
(Bryan et al., 1997; Roder et al., 1998; Somers et
al., 2004), though SNPs are quickly maturing as
a robust DNA marker system. In addition, a novel
type of marker platform that merges RFLP and
microarray technology (diversity array tech-
nology, DArT) was developed in Australia that is
particularly useful in biparental crosses and
quick assembly of a genetic map (http://www.
diversityarrays.com/; Semagn et al., 2006). The
method is microarray-based (hybridization-
based), fast, and relatively inexpensive. Gener-
ally, the primary attributes of a good DNA marker
are that it (i) is PCR-based, (ii) has low cost per
data point, (iii) has codominant allele detection,
and (iv) has high throughput. The SSR and SNP
markers satisfy all of these requirements (Table
14.2).
Genetic maps are routinely developed from
biparental crosses. Typically, the parents of the
cross are inbred to limit heterogeneity of alleles
of progeny, and it is common to develop either
F
2
, BC
1
, doubled haploid (DH), or recombinant
inbred line (RIL) populations, depending on the
fi nal application, time, and budget. The RIL
population passes through several meiotic events
in development, thus creating more breakpoints
along the chromosomes. The other three popula-
tion types feature only one meiotic event in the
F
1
generation, which is used to develop the fi nal
mapping population. Table 14.3 summarizes a
RIL versus DH population to exemplify this idea.
Consistent with theoretical expectation, the RIL
population has very near twice the number of
breakpoints per chromosome as the DH popula-
tion. The progeny in the population segregate
at many points in the genome, and this can
be detected by DNA markers such as SSRs.
Genetic maps are then constructed by collecting
the genotype data over many progeny and calcu-
lating recombination distances between the
segregating loci (Perretant et al., 2000; Somers
et al., 2004).
Finally, QTL analysis is the merger between
the genetic map information and phenotypic
data collected on progeny from the same biparen-
tal cross that was mapped. Quantitative trait
locus analysis is essentially a regression analysis
to determine associations between loci along
Table 14.3
Comparison of recombinant inbred line (RIL)
versus doubled haploid (DH) populations for chromosome
breakpoints on chromosome 1A.
Chromosome 1A
Breakpoints
Total
Population
Type
Cross
Range
Mean
Synthetic
×
Opata
RIL
59
0-7
3.0
SC2180V2
×
AC Karma
DH
30
0-4
1.5
Note:
Based on random selection of 20 individuals per
population.
Table 14.2
A comparison of molecular marker technology and application to marker-assisted selection.
Marker Type
a
Application Cost
b
Inheritance
Abundance
Polymorphism
Development Cost
RFLP
Codominant
Low
Medium
Medium
High
RAPD
Present/absent
Medium
Low
Low
Low
AFLP
Present/absent
Medium
Medium
Low
Medium
SSR
Codominant
Medium
High
High
Medium
SNP
Codominant
High
Low
High
Low
DArT
Present/absent
Medium
Medium
Medium
Low
a
RFLP, restriction fragment length polymorphism; RAPD, random amplifi ed polymorphic DNA; AFLP, amplifi ed fragment
length polymorphism; SSR, simple sequence repeat (microsatellites); SNP, single nucleotide polymorphism; DArT, diversity
array technology.
b
Includes time and labor costs and is based on current detection platforms.
