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‘Forrest’ Resistance to the Soybean Cyst Nematode Is Bigenic: ‘Forrest’ Resistance to the Soybean Cyst Nematode Is Bigenic:
Saturation Mapping of the Rhg1 and Rhg4 Loci Saturation Mapping of the Rhg1 and Rhg4 Loci
K. Meksem
Southern Illinois University
, meksemk@siu.edu
P. Pantazopoulos
Southern Illinois University
V. N. Njiti
Southern Illinois University
D. L. Hyten
Southern Illinois University
, david.hyten@unl.edu
P. R. Arelli
University of Missouri - Columbia
, prakash.arelli@ars.usda.gov
See next page for additional authors
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Meksem, K.; Pantazopoulos, P.; Njiti, V. N.; Hyten, D. L.; Arelli, P. R.; and Lightfoot, D. A., "‘Forrest’
Resistance to the Soybean Cyst Nematode Is Bigenic: Saturation Mapping of the Rhg1 and Rhg4 Loci"
(2001).
Agronomy & Horticulture -- Faculty Publications
. 774.
https://digitalcommons.unl.edu/agronomyfacpub/774
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Published in Theoretical and Applied Genetics 103:5 (October 2001), pp. 710–717;
doi: 10.1007/s001220100597
Copyright © 2001 Springer-Verlag. Used by permission.
Submitted November 5, 2000; accepted January 23, 2001.
‘Forrest’ Resistance to the Soybean
Cyst Nematode Is Bigenic:
Saturation Mapping of the Rhg1 and Rhg4 Loci
K. Meksem,
1
P. Pantazopoulos,
1
V. N. Njiti,
1
D. L. Hyten,
1
P. R. Arelli,
2
and
D. A. Lightfoot
1
1. Department of Plant Soil and General Agriculture, Center for Excellence in Soybean Research,
Teaching and Outreach, Southern Illinois University at Carbondale, Room 176, Carbondale, IL
62901-4415, USA
2. Department of Agronomy, 104 Curtis Hall. University of Missouri, Columbia, MO 65211, USA
Corresponding author – K. Meksem, email meksemk@siu.edu
Abstract
Field resistance to cyst nematode (SCN) race 3 (Heterodera glycines I.) in soybean [Glycine max (L.)
Merr.] cv ‘Forrest’ is conditioned by two QTLs: the underlying genes are presumed to include Rhg1
on linkage group G and Rhg4 on linkage group A2. A population of recombinant inbred lines (RILs)
and two populations of near-isogenic lines (NILs) derived from a cross of Forrest × Essex were used
to map the loci affecting resistance to SCN. Bulked segregant analysis, with 512 AFLP primer com-
binations and microsatellite markers, produced a high-density genetic map for the intervals carrying
Rhg1 and Rhg4. The two QTLs involved in resistance to SCN were strongly associated with the AFLP
marker E
ATGMCGA87 (P = 0.0001, R
2
= 24.5%) on linkage group G, and the AFLP marker ECCGMAAC405
(P = 0.0001, R
2
= 26.2%) on linkage group A2. Two-way analysis of variance showed epistasic inter-
action (P = 0.0001, R
2
=16%) between the two loci controlling SCN resistance in Essex × Forrest re-
combinant inbred lines. Considering the two loci as qualitative genes and the resistance as female
index FI < 5%, jointly the two loci explained over 98% of the resistance. The locations of the two QTLs
were confirmed in the NILs populations. Therefore SCN resistance in Forrest × Essex is bigenic.
High-efficiency marker-assisted selection can be performed using the markers to develop cultivars
with stable resistance to SCN.
K. MEKSEM ET AL., T HEORETICAL AND A PPLIED GENETICS 103 (2001)
2
Keywords: soybean cyst nematode, AFLP, high-resolution genetic mapping, marker-assisted breed-
ing, Rhg1, Rhg4, qualitative mapping
Introduction
The soybean cyst nematode (SCN), Heterodera glycines, is a widespread pest of soybeans
and causes substantial yield losses worldwide (Wrather et al. 1996). Soybean plant intro-
ductions that are resistant to SCN suppress reproduction of the nematode but do not elim-
inate damage (Rao-Arelli and Anand 1988). During selection, SCN populations often
develop the ability to overcome resistance (Riggs and Schmidt 1988).
Resistance to SCN is often found in unadapted germplasm and the genetics of resistance
can be complex (Rao-Arelli et al. 1992). Transfer of the underlying genes to adapted
germplasm is a laborious process since the resistance phenotype is oligogenic and quanti-
tative. Furthermore, introgression may be complicated by linkage drag on yield (Mudge et
al. 1996) and variability in the pathogen population (Riggs and Niblack 1999). DNA mark-
ers detect loci underlying resistance to SCN as QTLs (Webb et al. 1995; Concibido et al.
1996; Chang et al. 1997). DNA markers within 1–5 cM of the loci can be used to select for
resistance during soybean breeding (Prabhu et al. 1999). Compared to phenotypic selec-
tion, DNA markers expedite gene introgression, minimize linkage drag, and maximize re-
covery of the target genome.
There are very few different sources for soybean cyst nematode resistance genes and
their alleles in the U.S. soybean crop (PI 88788, PI 437.654, Peking, PI90763 and PI209332).
More than 85% of SCN-resistant cultivars are derived from PI88788 due to superior agro-
nomic performance (Skorupska et al. 1994). DNA marker analysis has shown that re-
sistance to SCN was quantitative when derived from PI437654 (Webb et al. 1995; Vierling
et al. 1997; Prabhu et al. 1999), Peking (Mahalingam and Skorupska 1995; Chang et al.
1997), PI88788 (Concibidio et al. 1997; Matthews et al. 1998), PI90763 and PI209332 (Conci-
bidio et al. 1996, 1997). One locus, on linkage group G, is common among the sources of
resistance to SCN and is thought to correspond to rhg1 that was identified by classical ge-
netics as a recessive gene (Rao-Arelli et al. 1992). Among crosses deriving resistance to SCN
from Peking and PI437654, the second locus on linkage group A2 is thought to correspond
to Rhg4. Rhg4 was originally identified by classical genetics (Myers and Anand 1991; Rao-
Arelli et al. 1992). Other loci (Qiu et al. 1999) implicated in resistance to SCN differ by their
position on the genetic map (linkage groups B, E, F, H, I and J) and the nature of the path-
ogen population to which they confer resistance (often categorized as race 1, 3, 5 or 14)
(Riggs and Schmidt 1988). These QTLs have not been confirmed in multiple mapping stud-
ies.
When multiple QTLs segregate, the error associated with inference of a QTL may be
inflated by the effects of the other QTLs, recombination, non-genetic variation and errors
in scoring (Kearsey and Farquhar 1998). Furthermore, linked QTLs can cause biased esti-
mates of QTL position. Using methods of QTL analysis that can simultaneously account
for multiple QTLs (Knapp and Bridges 1990) it is possible to create a model that contains
parameters for multiple QTLs and simultaneously estimate the most-likely positions of
QTLs within two or more intervals (Knott and Haley 1992). QTL analysis can show the
K. MEKSEM ET AL., T HEORETICAL AND A PPLIED GENETICS 103 (2001)
3
presence of linked or coincident QTLs for target and non-target traits (Tanksley and Nel-
son 1996). Although linkage and pleiotropy may be indistinguishable at the level of reso-
lution afforded by common population sizes and marker densities, information regarding
the frequency of coupling vs repulsion relationships can be invaluable in developing a
breeding strategy.
The development of SCN-resistant soybean cultivars with durable resistance is a com-
plex challenge for breeders due to the multiple QTLs, the resistance sources and the SCN
populations involved. Breeding for quantitative traits by marker-assisted selection can be
further complicated unless a large number (3–5) of markers tightly linked (>1 cM) to loci
conferring SCN resistance are available. Sufficient marker density can be developed by
high-resolution mapping of the QTLs conferring resistance to SCN (Meksem et al. 1999)
and targeted marker development (Meksem et al. 1998, 2000a; Cregan et al. 1999). In this
report we have focused on SCN resistance in cv ‘Forrest,’ derived from Peking, reported
to be inherited quantitatively due to segregation of two QTLs (Chang et al. 1997). The two
QTLs were fine-mapped using AFLP and bulked segregant analysis. Using the closest
markers (0.5–1 cM) to each gene, Mendelian inheritance of Rhg1 and Rhg4 was examined
and the positions of the two QTLs were confirmed using nearisogenic lines.
Materials and methods
Plant material
A population of 100 F
5 derived recombinant inbred lines (RILs) from the cross ‘Essex’
(Smith and Camper 1973) × ‘Forrest’ (Hartwig and Epps 1973) was used to construct a ge-
netic linkage map. Forrest is resistant to the soybean cyst nematode (SCN) while Essex is
susceptible. Forrest derived its resistance to SCN from Peking. Soybean seeds derived from
F
5:13 recombinant inbred lines were planted at the agronomy research center, Southern Illi-
nois University, Carbondale, in a soil defined as Stoy Fine-silty, mixed, mesic, Aquic, Hap-
ludalfs (Hnetkovsky et al. 1996). Soybean genomic DNA was extracted from a pooled
sample of leaves from five plants per genotype. The RILs were advanced to the F
5:13 gener-
ation from never less than 300 plants per RIL per generation during these studies.
Fine mapping of genes controlling the SCN resistance was performed in two near-
isogenic line (NIL) populations, E × F6 and E × F34, that were developed from 40 individual
plants at the F
5:9 generation from within heterogeneous RILs by plant seed-to-row descent
(Njiti et al. 1998; Meksem et al. 1999, 2000c). E × F34 segregated for a region encompassing
Rhg1 on linkage group G (Meksem et al. 1999). E × F6 segregated for a region encompassing
Rhg4 which derives resistance to SCN on linkage group A2. Individual NILs from E × F34,
line 6 (Resistant line) and line 29 (Susceptible line) were crossed to produce F1 and F2 pop-
ulations.
Soybean genomic DNA used for AFLP and microsatellite analysis was extracted and
purified using the Qiagen Plant Easy DNA Extraction Kit (Qiagen, Hilden, Germany).
DNA probes and microsatellite primers
The Bng122 RFLP probe was provided by Dr. E. Vallejos (University of Florida, USA). The
microsatellite primers (BARC-Satt 309, BARC-Satt 275, and BARC-Satt 163) were provided
