See discussions, stats, and author profiles for this publication at: https://www.researchgate.

net/publication/257942035

Identification of QTL for Fusarium Root Rot Resistance in

Common Bean

Article  in  Journal of Crop Improvement · June 2013

DOI: 10.1080/15427528.2013.786775

CITATIONS READS

8 298

5 authors, including:

K. Kamfwa Mick Sikaenyi. Mwala

University of Zambia University of Zambia
27 PUBLICATIONS   219 CITATIONS    24 PUBLICATIONS   52 CITATIONS   

SEE PROFILE SEE PROFILE

Patrick Okori Paul Gibson

International Crops Research Institute for Semi Arid Tropics Makerere University
111 PUBLICATIONS   583 CITATIONS    118 PUBLICATIONS   1,179 CITATIONS   

SEE PROFILE SEE PROFILE

Some of the authors of this publication are also working on these related projects:

Population Genetics View project

Biofortified Crops for Improved Human Nutrition View project

All content following this page was uploaded by Clare Mukankusi on 26 May 2014.

The user has requested enhancement of the downloaded file.

This article was downloaded by: [Michigan State University]
On: 14 June 2013, At: 19:43
Publisher: Taylor & Francis
Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered
office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK

Journal of Crop Improvement

Publication details, including instructions for authors and
subscription information:
http://www.tandfonline.com/loi/wcim20

Identification of QTL for Fusarium Root

Rot Resistance in Common Bean
a b c c d
K. Kamfwa , M. Mwala , P. Okori , P. Gibson & C. Mukankusi
a
Department of Plant, Soil and Microbial Sciences , Michigan State
University , East Lansing , Michigan , United States
b
Department of Crop Science, School of Agriculture , University of
Zambia , Lusaka , Zambia
c
Department of Crop Science, Faculty of Agriculture , Makerere
University , Kampala , Uganda
d
CentroI Iinternacional de Agricultura Tropical (CIAT) , Kampala ,
Uganda

To cite this article: K. Kamfwa , M. Mwala , P. Okori , P. Gibson & C. Mukankusi (2013): Identification
of QTL for Fusarium Root Rot Resistance in Common Bean, Journal of Crop Improvement, 27:4,
406-418

To link to this article: http://dx.doi.org/10.1080/15427528.2013.786775

PLEASE SCROLL DOWN FOR ARTICLE

Full terms and conditions of use: http://www.tandfonline.com/page/terms-and-conditions

This article may be used for research, teaching, and private study purposes. Any
substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing,
systematic supply, or distribution in any form to anyone is expressly forbidden.

The publisher does not give any warranty express or implied or make any representation
that the contents will be complete or accurate or up to date. The accuracy of any
instructions, formulae, and drug doses should be independently verified with primary
sources. The publisher shall not be liable for any loss, actions, claims, proceedings,
demand, or costs or damages whatsoever or howsoever caused arising directly or
indirectly in connection with or arising out of the use of this material.
 Journal of Crop Improvement, 27:406–418, 2013
Copyright © Taylor & Francis Group, LLC
ISSN: 1542-7528 print/1542-7536 online
DOI: 10.1080/15427528.2013.786775

Identification of QTL for Fusarium Root

Rot Resistance in Common Bean

K. KAMFWA1 , M. MWALA2 , P. OKORI3 , P. GIBSON3 ,

and C. MUKANKUSI4
1
Department of Plant, Soil and Microbial Sciences, Michigan State University,
East Lansing, Michigan, United States
2
Downloaded by [Michigan State University] at 19:43 14 June 2013

Department of Crop Science, School of Agriculture, University

of Zambia, Lusaka, Zambia
3
Department of Crop Science, Faculty of Agriculture, Makerere
University, Kampala, Uganda
4
CentroI Iinternacional de Agricultura Tropical (CIAT), Kampala, Uganda

Resistance to Fusarium root rot (FRR) in common bean ( Phaseolus

vulgaris L.) has been determined to be a quantitative trait. The
objective of this study was to identify quantitative trait loci (QTL)
for resistance to FRR in a resistant line MLB-49-89A of com-
mon bean. A mapping population of 62 F4:5 recombinant inbred
lines (RILs) derived from cross of K132 × MLB-49-89A was eval-
uated. A second population of 90 F4:5 RILs derived from cross of
K20 × MLB-49-89A was used to validate the QTL identified in
K132 population. A major QTL with a logarithm of odds (LOD)
score of 6.1 and R2 of 34% was detected between PVBR87 and
PVBR109 markers in the K132 population The same markers were
significantly associated with resistance in the K20 population ( R2 =
14%, P < 0.001). The QTL could facilitate marker-assisted selection
to introgress resistance for FRR into the highly susceptible Andean
genotypes widely grown in Uganda.

Received 23 December 2012; accepted 12 March 2013.

We acknowledge the financial support from the Regional University Forum for Capacity
Building in Agriculture (RUFORUM) in Uganda. We also thank Dr. James D. Kelly of Michigan
State University for his helpful comments during the research and manuscript preparation.
Address correspondence to K. Kamfwa at Department of Plant, Soil and Microbial
Sciences, Michigan State University, East Lansing, MI, 48824, USA. E-mail: kamfwake@msu.edu

406
 Fusarium Root Rot Resistance in Common Bean 407

KEYWORDS Phaseolus vulgaris, Fusarium root rot resistance,

quantitative trait loci, recombinant inbred lines, simple sequence
repeat markers

INTRODUCTION

Common bean (Phaseolus vulgaris L.) is considered to be the most important

grain legume for direct human consumption, and beans comprise 50% of the
grain legumes consumed worldwide (Broughton et al. 2003). The productiv-
ity of this crop is constrained by many diseases that include bean root rots.
Bean root rots are caused by a complex of soil-borne pathogens including
Pythium sp., Rhizoctonia solani, and Fusarium solani fsp. phaseoli (Abawi
Downloaded by [Michigan State University] at 19:43 14 June 2013

and Pastor-Corrales 1990). Bean root rots have been reported throughout
the world (Abawi and Pastor-Corrales 1990) and are considered one of the
major bean production constraints in East Africa and Central Africa, particu-
larly in the highland areas (Spence 2003; CIAT 2005), with significant losses
occurring to susceptible varieties. The disease is considered the most impor-
tant constraint to bean production in the southwestern highland regions of
Uganda (Tusiime 2003; CIAT 2005; Mukankusi et al. 2011). The disease com-
plex is likely to spread to other bean production regions and is predicted to
be even more destructive in the coming years due to climate change.
Fusarium root rot (FRR) caused by Fusarium solani fsp. phaseoli is
one of the most important disease of the bean root rot disease com-
plex in the southwestern highland regions of Uganda, causing significant
yield losses (Tusiime 2003; CIAT 2005; Mukankusi et al. 2011). FRR symp-
toms appear as characteristic reddish-brown lesions along the taproot and
hypocotyls, and the disease is particularly severe on large-seeded Andean
bean genotypes because of a lack of genetic resistance (Abawi and Pastor-
Corrales 1990; Roman-Aviles et al. 2011). The use of resistant varieties is the
most effective control measure for FRR, especially for small-scale farmers
with limited access to fungicides (Abawi et al. 2006). Genetic resistance to
FRR is quantitatively inherited and is strongly influenced by environmental
factors (Schneider et al. 2001; Roman-Aviles and Kelly 2005). These factors
make it difficult to evaluate and the efficiency of phenotypic selection is low,
resulting in limited progress in breeding for resistance (Roman-Aviles et al.
2011).
Identifying major QTL for the traits difficult to evaluate phenotyp-
ically can enhance efficiency and progress in plant breeding programs.
This approach overcomes some of the common limitations encountered
by conventional selection for quantitative traits (Collard et al. 2005; Kelly
and Vallejo 2005). Indirect selection for FRR resistance based on genetic
markers associated with QTL for resistance would facilitate improvement,
given the limitations of field selection, which are laborious, inconsistent
 408 K. Kamfwa et al.

across environments, and require destructive sampling. Previous studies had

identified QTL for FRR resistance on bean chromosome Pv02, Pv03, and
Pv05 (Schneider et al. 2001; Roman-Aviles and Kelly 2005). The objective
of this study was to identify and validate QTL associated with resistance to
Fusarium root rot in common bean genotype, MLB-49-89A.

MATERIALS AND METHODS

Germplasm and Mapping Populations
Crosses were made between a FRR resistant line MLB-49-89A and two highly
susceptible varieties, K20 and K132, which are widely grown in the Uganda.
MLB-49-89A belongs to the Mesoamerican gene pool and is a medium-
Downloaded by [Michigan State University] at 19:43 14 June 2013

seeded black bean with an indeterminate type-III growth habit. K20 and
K132 belong to the Andean gene pool and exhibit type I upright determi-
nate bush growth habit with large red mottled-seed types. Both populations,
K132 (K132 × MLB-49-89A) and K20 (K20 × MLB-49-89A), were developed
by advancing F2 progeny to the F4 generation through single seed descent.
Thereafter, individual F4 plants were harvested and seed from each plant
bulked to constitute the F4:5 RILs. No selection was done for any traits dur-
ing the development of either population. Initially, 100 F2 individuals were
planted to develop each population, but the final population numbers were
reduced to 62 and 90 F4:5 lines of K132 and K20 populations, respectively,
because of germination problems and seedling death of some F2 and F3
individuals. During evaluation some lines in the K132 population died from
FRR before DNA could be extracted for QTL analysis, further reducing the
number of RILs. The two populations and their parents were evaluated for
FRR resistance in a screen house in Uganda. The experiment was conducted
as a randomized complete block design with two replications in wooden
trays measuring 0.74 × 0.42 × 0.12 m3 . Each experimental unit consisted of
14 plants per row, in 0.42-m-long rows for each population, with each tray
having nine RILs, including susceptible and resistant parents.

Preparation of the Inoculum, Inoculation, and Disease Evaluation

An isolate of Fusarium solani f.sp. phaseoli, coded FSP-3, which was origi-
nally obtained from bean fields infected with FRR in southwestern Uganda
and maintained by Centro Internacional de Agricultura Tropical (CIAT) in
Uganda, was used as a source of inoculum. Pure colonies of the isolate,
stored on slants of Potato Dextrose Agar at 5◦ C, were sub-cultured for a
period of 21 days and then used to prepare inoculum. Infested sorghum seed
colonized with FSP-3 for four weeks was used as the source of inoculum. The
inoculum was then added to the soil at a rate of 500 g of infested sorghum
kernels per tray and thoroughly mixed with the soil in a tray to ensure an
 Fusarium Root Rot Resistance in Common Bean 409

even distribution of the pathogen. To increase disease pressure immediately

after soil inoculation, the susceptible variety K132 was grown in the trays
for 28 days and then uprooted. Subsequently, the two populations were
planted and disease reaction was visually estimated at 28 days after planting.
Six randomly selected plants from each RIL in a row were uprooted, and
levels of infection on their roots and hypocotyls were observed and disease
severity estimated using the CIAT 1-9 scale (Abawi and Pastor-Corrales 1990).
In this scale: 1 = no visible symptoms; 3 = light discoloration either with-
out necrotic lesions or with approximately 10% of the hypocotyl and root
tissue covered with lesions; 5 = approximately 25% of the hypocotyl and
root tissue covered with lesions though the tissues remain firm, with some
deterioration of the root system; 7 = approximately 50% of the hypocotyls
and root tissues covered with lesions combined with considerable soften-
Downloaded by [Michigan State University] at 19:43 14 June 2013

ing, rotting, and reduction of root system; and 9 = approximately 75% or

more of the hypocotyls and root tissues affected with advanced stages of
rotting, combined with severe reduction in the root system. Score of 1-3 was
considered as resistant, 4-5 was moderately resistant and 6-9 was susceptible.

Statistical Analyses of Phenotypic Data

The mean disease score for each RIL was calculated and analysis of vari-
ance (ANOVA) was calculated using GenStat Discovery Edition 3. Where
significant differences were found, the means were compared using Fisher’s
protected least significant difference (LSD) test. Heritability estimates for FRR
resistance scores were calculated on an entry-mean basis from two replica-
tions (Bernardo 2002). Broad-sense heritability was calculated based on the
mean of the line as:

σG2
h2B = ,
σG2 + (σe2 /r)

where σG2 = the genetic variance, σe2 = variance due to the environment, and
r = the number of replications.

Identification of Polymorphic SSR Markers

Previous studies had identified QTL for FRR on bean chromosome Pv02,
Pv03, and Pv05, so only 35 SSR markers previously mapped to these chro-
mosomes (Grisi et al. 2007) were selected and tested for polymorphism
among K132, K20, and MLB 49-89A parents. DNA was extracted from fresh
leaf tissues of parents and RILs at the first trifoliate leaf stage following
the modified protocol of Dellaporta et al (1983). An equal quantity of leaf
tissue from five plants of each RIL was bulked for DNA extraction. PCR
was performed in 20 µL final volume containing 50 ng of DNA, 0.5 µM
 410 K. Kamfwa et al.

each of forward and reverse primers, 0.25 mM of dNTP mix, 1 unit of

Taq polymerase, 10 × Taq buffer, and 2mM of MgCl2 . The PCR products
were loaded onto 5% w/v agarose metaphor gels in TBE buffer. The DNA
bands were visualized by ethidium-bromide staining, using gel documenta-
tion system. Only 12 SSR markers were polymorphic among the three parents
and were genotyped on the K132 population. To validate the marker trait
associations identified in the K132 population, SSR markers that were signif-
icantly associated with resistance in K132 population were used to genotype
K20 population.

Linkage Map Construction and QTL Detection

Partial linkage groups were constructed using MAPMAKER/EXP programme
Downloaded by [Michigan State University] at 19:43 14 June 2013

version 3.0 (Lander et al. 1987). Linkage groups of the markers were deter-
mined by the group command of MAPMAKER/EXP at a logarithm of odds
(LOD) score of 2.0 and a maximum distance of 50 cM using the Haldane
units (Lander et al. 1987).
Both single-marker analysis and composite interval mapping were used
to identify the QTL. The relationship between molecular markers and
phenotypic scores was first analyzed using single-marker analysis in both
populations using a F-test. Composite interval mapping was done to map
the QTL for FRR using QTL Cartographer version 2.0 (Basten et al. 2003).
Permutation analysis was performed to identify the significance threshold
of LOD score for individual QTL at P ≤ 0.05. The window size was set to
10 cM. The presence of a QTL was declared significant whenever the LOD
score exceeded the threshold levels. The estimated position of the QTL was
the point at which the maximum LOD score was found in the region under
consideration.

RESULTS
Disease Reactions to Fusarium Root Rot in K20 Population
Significant genetic variation (P < 0.01) was observed among the 90 F4:5
RILs of K20 population for reaction to Fusarium solani fsp. phaseoli. Root
rot scores for the RILs ranged from 1.8 to 8.8 (Table 1) with a popula-
tion mean 4.1, which was less than the mid-parent value of 5.4. Susceptible
parent K20 had scores between 7 and 9 with a mean of 8.8, while scores
for the resistant parent MLB-49-89A ranged from 1 to 3 with a mean of
2.3. The K20 population was generally skewed toward the resistant par-
ent (Figure 1). Sixty-seven (67) out of 90 lines scored less than 5, which
was considered the threshold for resistance reaction. There was a con-
tinuous normal distribution observed among susceptible genotypes, while
resistant lines were concentrated near the resistant parent with scores
 Fusarium Root Rot Resistance in Common Bean 411

TABLE 1 Fusarium root rot scores of parents and progeny

means, range, and heritability estimates of resistance in two
common bean RIL populations consisted of 90 F4:5 (K20 ×
MLB-49-89A) in 62 F4:5 (K132 × MLB-49-89A) individuals

Genotypes K20 K132

Parents
MLB-49-89A (resistant parent) 2.3 1.7
K20 (susceptible parent) 8.8 −
K132 (susceptible parent) − 9.0
a
Mid-parent value 5.6 5.3
Progeny
Lowest score 1.8 1.1
Highest score 9.0 9.0
b
Mean (F4:5 RILs) 4.1 5.3
LSD (P ≤ 0.05) 0.2 0.2
Downloaded by [Michigan State University] at 19:43 14 June 2013

CV (%) 26.0 8.0

c 2
hB 0.86 0.99
a
Disease score was visually rated on a scale of 1-9. The scores are based
on the CIAT 1-9 (Abawi and Pastor-Corrales 1990), where 1 = very
resistant and 9 = very susceptible.
b
Mean of 90 F4:5 RILs in K20 population, and 62 F4:5 RILs in K132 popu-
lation; c h2 B = broad-sense heritability based on expected mean squares,
entry-mean basis from two replications (Bernardo 2002).

45

40

35

30
Number of Lines

RILs
25
MLB49
20
K20
15

10

0
1 2 3 4 5 6 7 8 9
Fusarium Score

FIGURE 1 Frequency of Fusarium root rot ratings for a F4:5 K20 × MLB-49-89A population.
MLB-49-89A is the resistant parent and K20 is the susceptible parent. Disease score was
visually rated on a scale of 1-9 from CIAT, where 1 = very resistant and 9 = very susceptible
(Abawi and Pastor-Corrales 1990) (color figure available online).
 412 K. Kamfwa et al.

of 2. Transgressive segregation toward both resistance and susceptibility

was observed, suggesting the presence of both positive and negative FRR
resistance alleles in both parents.

Disease Reactions to Fusarium Root Rot in K132 Population

There was highly significant (P < 0.001) genetic variation for reaction to
Fusarium solani fsp. phaseoli among the 62 F4:5 lines in the K132 popula-
tion. Scores for this population ranged from 1.1 to 9 with a mean of 5.3
(Table 2). The susceptible parent K132 had a mean score of 9 and the resis-
tant parent had scores ranging from 1 to 3 with a mean of 1.7 across trays.
The frequency distribution for FRR data exhibited a bi-modal pattern with
Downloaded by [Michigan State University] at 19:43 14 June 2013

two peaks, resembling the resistance and susceptible groupings (Figure 2).
The RILs followed a normal distribution within the resistant category (lines
with a score less than 5).

Linkage Analysis of the SSR Markers

Genetic mapping placed 9 of the 12 polymorphic SSR markers into three
partial linkage groups that were representative of bean chromosomes Pv02,
Pv03, and Pv05. Each of the three partial linkage groups had three markers
representing only 7.5% coverage of the common bean genome, which has an
estimated total size of 1200 cM. The total length of these three partial linkage
groups was 90.1 cM, with intervals between markers ranging from 0.9 cM to
28.9 cM. The other three SSR markers (BM139, BM167, and BM172) were not
associated with any linkage group.

TABLE 2 Putative QTL for resistance Fusarium root rot in two RIL populations evaluated in
a greenhouse in Uganda

LGa Proximal Marker Pr(F)b LODc R2 (%)d

Single-marker analysis
K132 Pv03 PvBR109 0.0001∗∗∗ − 34
K132 Pv03 PvBR8 0.0001∗∗∗ − 34
K132 Pv03 PvBR255 0.016∗ − 12
K20 Pv03 PvBR109 0.0001∗∗∗ − 14
K20 Pv03 PvBR8 0.0001∗∗∗ − 14
Composite interval mapping
K132 Pv03 PvBR109 − 6.1 34
a
Linkage group.
b
Probability value for the F statistic.
c
Logarithm of odds score.
d
Coefficient of determination.
∗ ∗∗∗
, Significant at the 5% and the 0.01% level of significance, respectively.
 Fusarium Root Rot Resistance in Common Bean 413

FIGURE 2 Frequency of Fusarium root rot ratings for a K132 × MLB-49-89A RILs (F4:5 )
Downloaded by [Michigan State University] at 19:43 14 June 2013

population. MLB-49-89A is the resistant parent and K132 is the susceptible parent. Disease
score was visually rated on a scale of 1-9 from CIAT, where 1 = very resistant and 9 = very
susceptible (Abawi and Pastor-Corrales 1990) (color figure available online).

QTL Detection
Among the twelve polymorphic SSR markers tested in the K132 population,
single-marker analysis identified two closely linked markers (PVBR87 and
PVBR109) on Pv03 that were significantly associated with FRR scores (P <
0.001, Table 2). A third marker, PVBR255 on the same chromosome, had
significant effects at P < 0.05. The other nine markers did not show any sig-
nificant association with resistance to FRR. All three marker alleles associated
with resistance to FRR resistance came from the resistant parent MLB-49-
89A. Single-marker analysis attributed a substantial proportion (34%) of the
phenotypic variance to each of the two closely linked markers that had
the strongest association with FRR scores (Table 2). Due to the tight link-
age between these two markers (0.9 cM), multiple regression analysis also
attributed the same R 2 value (0.34) to the two markers jointly as was indicated
for each marker individually.
A QTL was detected in K132 population by composite interval mapping
in the vicinity of PVBR109 and PVBR87 markers, with a LOD score of 6.1
(Table 2). Composite interval mapping eliminated marker PVBR255 as having
an independent effect on FRR so the location of the QTL is much closer to
PVBR109 and PVBR87 region than to the PVBR255 region on Pv03. No QTL
were identified on the other two linkage groups.
PVBR87 and PVBR109 markers showed strong significant association
(P < 0.001) in K20 population (Table 2). The R 2 values for these markers
were moderate, with each accounting for 14% of the phenotypic vari-
ance for FRR. Joint regression jointly attributed the same value to this
pair of markers (R 2 = 0.14) because the two markers were tightly linked.
The other two markers detected in the K132 population, BM156 and
 414 K. Kamfwa et al.

BM172, did not show significant association with FRR (P < 0.05) in
K20 population.

DISCUSSION

In this study, the bimodal frequency distribution pattern of FRR scores

observed in both populations suggests that major genes may be contributing
to resistance. Mukankusi et al. (2011) reported similar bimodal frequency
distributions for FRR resistance in F3 populations in which MLB-49-89A was
used as a resistant parent. In the current study, K20 × MLB49-89A pop-
ulation was skewed toward resistance, with a majority of RILs having a
disease severity score of less than 5, while the K132 × MLB49-89A was
Downloaded by [Michigan State University] at 19:43 14 June 2013

skewed to susceptibility, with many lines having a score of 9. This distri-

bution trend is different from the one reported by Mukankusi et al. (2011),
where K20 appears to contribute more resistance alleles to F3 progeny than
K132 in crosses with MLB-49-89A. These results suggest a complex pattern
of inheritance with some quantitative and/or multi-gene inheritance in addi-
tion to at least one major gene. Complex inheritance of resistance to FRR
involving many loci with epistatic interactions has been widely reported
(Mukankusi et al. 2011, Roman-Aviles et al. 2011). Our results clearly show
differences between the parental effects of K20 and K132. Such differ-
ences in means and distributions between the two populations suggest that
K20 possesses one or more genes that interact in an epistatic manner with
two or more resistance loci in MLB-49-89A. In contrast, K132 apparently
lacks the beneficial allele, or has an alternate allele that interacts towards
susceptibility.
The heritability estimates of 0.86 and 0.99 for K20 and K132, respec-
tively, were extremely high again, suggesting major gene effects. The high
heritability estimates and fewer number of QTL but with large effect may sug-
gest that a fewer number of genes could be controlling resistance to FRR in
the K132 and K20 populations. Mukankusi et al. (2011) used a F2 population
derived from K132 X MLB 49-89A and estimated two as the number of genes
controlling resistance to FRR. Although the effect of the environment on
FRR resistance is significant, the high heritability estimates obtained in this
study suggest that, if selections are made in controlled environment such
as the greenhouse, the gains from selections could be significant. Hassan
et al. (1971) reported broad sense heritability of resistance to FRR vary-
ing from 61.5% to 64.3% under greenhouse conditions and 77.9% to 79.7%
under field conditions, while narrow sense heritability varied from 25.9% to
44.3% for inter-gene-pool crosses. Relatively high narrow-sense heritability
estimates for resistance to FRR, ranging from 0.48 to 0.71 in the F4 -derived
RILs developed within the same gene pool, have been noted in previ-
ous studies (Schneider et al. 2001). Narrow-sense heritability estimates for
 Fusarium Root Rot Resistance in Common Bean 415

FRR resistance ranged from 0.10 to 0.51 for kidney beans and from 0.2 to
0.82 for the cranberry-inbred backcrossed populations (Román-Avilés and
Kelly 2005).
Results from both single-marker analysis and composite interval map-
ping indicate the presence of a major QTL for resistance to FRR on Pv03.
The QTL, associated with closely linked markers PVBR87 and PVBR109 in
the K132 population, could be considered major due to the high R 2 (34%)
and LOD score of 6.1. The bi-modal frequency distribution of the phenotypic
scores in this study also points to a major gene effect for resistance in the
K132 × MLB-49-89A, and the susceptible and resistant frequency peaks are
strongly associated with the K132 and MLB-49-89A alleles at these marker
loci. Further studies are needed to accurately establish the chromosomal
location of this major genetic factor. The small population size (n = 62) may
Downloaded by [Michigan State University] at 19:43 14 June 2013

have generated an upward bias in QTL effect estimation. The large effect
QTL might actually be a series of linked QTL, each of small effect (Flint and
Mott 2001), hence the need for fine mapping of such genomic regions.
The same two SSR markers (PVBR87 and PVBR109) that were sig-
nificantly associated with FRR resistance in K132 population also showed
significant associations (R 2 = 14%, P < 0.001) in the K20 population. This
is further confirmation of the presence of a major QTL on Pv03 that condi-
tions resistance to FRR. However, the overall contribution to the phenotype
in the K20 population was relatively low (R 2 = 14%) compared to the QTL
detected in K132 population (R 2 = 34%). This result suggests the role of
parent background effects and supports the phenotypic data that showed
the K20 population to have a lower disease severity index than K132 pop-
ulation. The significant associations of these two markers in two different
genetic backgrounds also show that the QTL detected in K132 population is
stable in different genetic backgrounds. Stability of QTL in different genetic
backgrounds is important in marker-assisted selection because it improves
the usability of the markers in different genetic background.
The major QTL identified in this study appears to map close to the
same region of Pv03, where QTL for FRR resistance was previously mapped
(Schneider et al. 2001). In that study, RAPD markers were used to identify
the QTL, so a direct comparison is not possible with the SSR markers used
in our study, which were based on the available genetic maps of common
bean (Grisi et al. 2007). The QTL identified in this study appears to be in a
different location from the QTL for FRR identified by Schneider et al. (2001),
as that QTL was located close to the PVPR-1 gene on Pv03. We propose
naming the QTL conditioning resistance to FRR on Pv03 as FRR3.1KM since
no previously QTL were named in this region. The results of this study cor-
roborate the importance of a genomic region on Pv03, where a QTL for
resistance to Pythium ultimum and Aphanomyces euteiches was identified
previously by Navarro et al. (2008), close to the FRR3.1KM QTL. The mark-
ers used by Navarro et al. (2008), which flanked the QTL for resistance to
 416 K. Kamfwa et al.

Pythium and Aphanomyces root rots, were found between the RFLP markers
D1020 and D1132 of the integrated linkage map (Yu et al. 2000). This is the
same region in which the SSR markers (PVBR87 and PVBR109) identified in
the current study are located. Other major genes for resistance to anthrac-
nose, common bacterial blight, and bacterial brown spot have been mapped
to this same region of Pv03 (Miklas et al. 2006). The co-localization of QTL
for resistance to several diseases suggests similar defense response genes
or resistance mechanisms and supports earlier findings on the clustering of
resistance genes within the common bean genome (Kelly et al. 2003). Other
studies have detected a relatively large number of QTL for FRR in common
bean (Roman-Aviles et al. 2011). Schneider et al. (2001) identified 16 QTL for
resistance to FRR, using F4:5 RILs, but none of the individual RAPD markers
explained more than 15% of the phenotypic variation. Two QTL for FRR with
Downloaded by [Michigan State University] at 19:43 14 June 2013

high LOD scores of 5 and 8 that accounted for 20% and 30% of the variability
were reported by Chowdhury et al. (2002), but direct comparisons cannot
be made, as the QTL were not mapped. A single major QTL for Fusarium
wilt resistance with a LOD score of 23.9 that accounted for 63.5% of the
phenotypic variability was detected on Pv10 (Fall et al. 2001). Nine QTL that
explained 5% to 53% of the total phenotypic variability for FRR resistance in
the field and greenhouse were mapped to Pv02 and Pv05 (Román-Avilés and
Kelly 2005). In the current study, no QTL was detected on Pv02 and Pv05,
and may represent the different genetic background of the resistant parents
used in each study.
A major QTL FRR3.1KM that explained 14% to 34% of the total phenotypic
variability for resistance to FRR was detected on bean chromosome Pv03.
Two closely linked SSR markers (PVBR87 and PVBR109) associated with
this major QTL in two different genetic backgrounds would be useful for
marker-assisted selection to introgress resistance to Fusarium root rot from
Mesoamerican genotypes to locally adapted Andean bean genotypes in
Uganda.

REFERENCES

Abawi, G. S., J. W. Ludwig, and B. K. Gugino. 2006. Bean root evaluation protocols
currently used in New York. Ann. Rep. Bean Improv. Coop. 49:83–84.
Abawi, G. S., and M. A. Pastor Corrales. 1990. Root rots of beans in Latin America
and Africa: Diagnosis, research methodologies and management strategies. Cali,
Colombia: Centro Internacional de Agricultura Tropical (CIAT).
Basten, C. J., B. S. Weir, and Z. B. Zeng. 2003. WinQTL Cartographer v. 2.0. Raleigh,
NC: Department of Statistics, North Carolina State Univ.
Bernardo, R. 2002. Breeding for quantitative traits in plants. Woodbury, MN: Stemma
Press.
Broughton, W. J., G. Hernandez, M. Blair, S. Beebe, P. Gepts, and J. Vanderleyden.
2003. Beans (Phaseolus spp.): Model food legumes. Plant Soil 252:55–128.
 Fusarium Root Rot Resistance in Common Bean 417

Chowdbury, M. A., K. Yu, and S. J. Park. 2002. Molecular mapping of root rot
resistance in common bean. Ann. Rep. Bean Improv. Coop. 45:96–97.
Centro Internacional de Agricultura Tropical (CIAT) 2005. Pathology in Africa. CIAT
Annual report 2005. Cali, Colombia: CIAT Bean Programme.
Collard, B. C. Y., M. Z. Z. Jahufer, J. B. Brouwer, and E. C. K. Pang. 2005. An intro-
duction to markers, quantitative trait loci (QTL) mapping and marker-assisted
selection for crop improvement: The basic concepts. Euphytica 142:169–196.
Dellaporta, S. L., and J. B. Woodand. 1983. A plant DNA minipreparation: version II.
Plant Mol. Biol. Rep. 14:19–21.
Fall, A. L., P. F. Byrn, G. Jung, D. P. Coyne, M. A. Brick, and H. F. Schwartz.
2001. Detection and mapping of a major locus for Fusarium wilt resistance
in common bean. Crop Sci. 41:1,494–1,498.
Flint, J., and R. Mott. 2001. Finding the molecular basis of quantitative traits:
Successes and pitfalls. Nat. Rev. Genet. 2(6): 437–445.
Downloaded by [Michigan State University] at 19:43 14 June 2013

Grisi, M. C. M., M. W. Blair, P. Gepts, C. Brondani, P. A. A. Pereira, and R. P. V.

Brondani. 2007. Genetic mapping of a new set of microsatellite markers in a
reference common bean (Phaseolus vulgaris) population BAT93 × Jalo EEP558.
Genet. Mol. Res. 6:691–706.
Hassan, A. A., R. E. Wilkinson, and D. H. Wallace. 1971. Genetics and heritability of
resistance to Fusarium solani f. sp. phaseoli in beans. HortSci. 96:623–627.
Kelly, J. D., P. Gepts, P. N. Miklas, and D. P. Coyne. 2003. Tagging and mapping of
genes and QTL and molecular marker-assisted selection for traits of economic
importance in bean and cowpea. Field Crops Res. 82:135–154.
Kelly, J. D., and V. A. Vallejo. 2005. QTL analysis of multigenic disease resistance in
plant breeding. In Multigenic and induced systemic resistance in plants, edited
by S. Tuzun and E. Bent, 21–48. New York: Springer.
Lander, E. S., P. Green, J. Abrahamson, A. Barlow, M. Daly, S. E. Lincoln, and
L. Newburg. 1987. MAPMAKER: An interactive computer package for construct-
ing primary genetic linkage maps of experimental and natural populations.
Genomics 1:174–181.
Miklas, P. N., J. D. Kelly, S. E. Beebe, and M. W. Blair. 2006. Common bean breeding
for resistance against biotic and abiotic stresses: from classical to MAS breeding.
Euphytica 147:105–131.
Mukankusi, C., J. Derera, R. Melis, P. T. Gibson, and R. Buruchara. 2011. Genetic
analysis of resistance to Fusarium root rot in common bean. Euphytica
182:11–23.
Navarro, F., M. E. Sass, and J. Nienhuis. 2008. Identification and confirmation of
quantitative trait locus for root rot resistance in snap bean (Phaseolus vulgaris
L.). Crop Sci. 48:962–972.
Román-Avilés, B., and J. D. Kelly. 2005. Identification of quantitative trait loci
C=conditioning resistance to Fusarium root rot in common bean. Crop Sci.
45:1,881–1,890.
Schneider, K. A, K. F. Grafton, and J. D. Kelly. 2001. QTL analysis of resistance to
Fusarium root rot in bean. Crop Sci. 41:535–542.
Roman-Avilés, B., J. M. Lewis, and J. D. Kelly. 2011. Fusarium genetic control: A
long-term strategy. In Control of Fusarium diseases, Research Signpost 37/661,
 418 K. Kamfwa et al.

edited by F. M. Alves-Santos and J. J. Diez, 65–108. Kerala, India: Research

Signpost.
Spence, N. 2003. Root rot diseases of Phaseolus beans in Uganda. (Abstract)
Bean crop protection research. R7568 Crop protection programme (CPP). Cali,
Colombia: CIAT Bean Programme.
Tusiime, G. 2003. Variation and detection of Fusarium solani f.sp. phaseoli and
quantification of soil inoculum in common bean fields. Dissertation, Makerere
University, Kampala, Uganda.
Yu, K., S. J. Park, V. Poysa, and P. Gepts. 2000. Integration of simple sequence
repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus
vulgaris L.). Heredity 91:429–434.
Downloaded by [Michigan State University] at 19:43 14 June 2013

View publication stats