Marker-Assisted Breeding for Cassava Mosaic Disease Resistance - Translational Genomics for Crop Breeding: Biotic Stress - page 303

Fig. 15.4. Ethidium bromide stained agarose gel of individuals from the recombinant bulks, evaluated with the RAPD
marker RME-1. A fragment around 800bp (arrow) can be observed in the resistant parent (RP) and resistant bulks (RB), and it is
absent in the susceptible parent (SP) and susceptible bulk (SB). For a color version of this figure, please refer to the color plate.

CMD resistance. Given its near immunity-level
resistance to CMD, two levels of molecular anal-
ysis were conducted. The first was to test the
cultivar for the CMD2 gene and to use a cross
of this parent to do a BSA test to identify fur-
ther genes or QTLs that may be involved in the
high CMD resistance observed in this cultivar.
Initial molecular analysis of TMS97/2205 with
CMD2 markers identified the presence of the
CMD2 gene in this cultivar, showing that the
CMD2 gene was involved in the CMD resistance
of this cultivar. Further genetic analysis of this
cultivar as a source of high resistance to CMD
using a segregating F 1 population derived from
a TMS97/2205 x NR8083 cross was initiated
involving 530 SSR markers to identify QTLs for
CMD resistance.
The F 1 population from the cross between
TMS97/2205 and NR8083 was analyzed to iden-
tify markers linked to gene(s) associated with
resistance to CMD via bulked segregant anal-
ysis (BSA) as described by Michelmore and
colleagues (1991). Two bulked (pooled) DNA
samples corresponding to the extreme groups of
resistant and susceptible individuals, based on
the phenotypic data from a two-year evaluation,
were prepared. Markers that are polymorphic
between the two pools are expected to be genet-
ically linked to the trait used to construct the
pools (Michelmore et al. 1991). The bulks were
made by mixing equal volumes of DNA solution

from each of the genotypes in each bulk (resistant
vs. susceptible). The composition of the resistant
bulk was 24 individuals and 12 individuals were
used for the susceptible bulk. DNA extraction
and genotyping was as described above. For the
BSA, a total of 530 SSR markers, with wide
coverage of the cassava genome, were used for
genotyping. The parents of the selected cross
were screened for polymorphic markers. The
polymorphic markers between the two parents
were then used to analyze the contrasting bulks
to identify SSR markers with possible associa-
tion with genes (QTLs) for resistance. Results of
BSA analysis identified a marker (NS198) asso-
ciated to a QTL for CMD resistance explaining
11% of the phenotypic variance observed. This
QTL was designated CMD3 .
The combined effect of this QTL ( CMD3 )
and CMD2 may account for the high resistance
of TMS97/2205. The SSR marker is located on
the same linkage group as the CMD2 gene but
is at least 36cM away from the CMD2 marker
loci (SSRY28, SSRY158, NS169) (Whankaew
et al. 2011). The SSR marker SSRY106 in the
genomic region with NS198 and in the inter-
val with CMD2 markers was not significantly
linked to the CMD2 gene, indicating that NS198
is associated with a different QTL. The syner-
gistic effect of the CMD2 gene and this QTL
( CMD3 ) may have accounted for the high resis-
tance to CMD observed in TMS97/2205.