TH E CR OP J OUR NA L 8 ( 2 0 20 ) 89 2 –9 0 4

Available online at www.sciencedirect.com

ScienceDirect

Soybean cyst nematode-resistance: Gene

identification and breeding strategies

Abdulwahab S. Shaibua,b , Bin Lia,⁎, Shengrui Zhanga , Junming Suna,⁎

a
The National Engineering Laboratory for Crop Molecular Breeding/Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean
Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
b
Department of Agronomy, Bayero University, Kano, Nigeria

AR TIC LE I N FO ABS TR ACT

Article history: Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most economically
Received 25 October 2019 damaging disease of soybean worldwide, and breeding host plant resistance is the most
Received in revised form 30 January feasible option for SCN management. In this review, we summarise the progress made so
2020 far in identifying nematode-resistance genes, the currently available sources of resistance,
Accepted 10 March 2020 possible mechanisms of SCN resistance and strategies for soybean breeding. To date, only
Available online 21 March 2020 two sources of SCN resistance have been widely used, from the accessions PI 88788 and
Peking, which has resulted in a shift in SCN resistance and created a narrow genetic base for
Keywords: SCN resistance. These resistant germplasms for SCN are classified into two types according
Soybean cyst nematode (Heterodera to their copy number variation in a 31-kb genomic region: PI 88788-type resistance requires
glycines Ichinohe) high copy numbers of a rhg1 resistance allele (rhg1-b) and Peking-type resistance requires
Candidate gene both low copy numbers of a different rhg1 resistance allele (rhg1-a) and a resistant allele at
Functional analysis another locus, Rhg4. Resistance related to rhg1 primarily involves impairment of vesicle
Marker-assisted selection trafficking through disruption of soluble NSF-attachment protein receptor (SNARE)
Resistance complexes. By contrast, resistance via Rhg4 involves disturbance of folate homeostasis at
SCN feeding sites due to alteration of the enzymatic activity of serine
hydroxymethyltransferase (SHMT). Other potential mechanisms, including plant defences
mediated by salicylic acid (SA) and jasmonic acid (JA) signalling modulation, have also been
suggested for SCN resistance. Indeed, genome-wide association studies (GWAS) have
identified other candidate SCN resistance genes, such as GmSNAP11. Although gene
functional analysis in a transient expression system could increase the efficiency of
candidate gene identification, information on novel genes and mechanisms for SCN
resistance remains limited. Any beneficial candidate genes identified might, when fully
exploited, be valuable for improving the efficiency of marker-assisted breeding and
dissecting the molecular mechanisms underlying SCN resistance.
© 2020 Crop Science Society of China and Institute of Crop Science, CAAS. Production and
hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access
article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

⁎ Corresponding authors.
E-mail addresses: libin02@caas.cn, (B. Li), sunjunming@caas.cn. (J. Sun).
Peer review under responsibility of Crop Science Society of China and Institute of Crop Science, CAAS.

https://doi.org/10.1016/j.cj.2020.03.001
2214-5141 © 2020 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi
Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
 TH E C ROP J O U R NA L 8 (2 0 2 0) 89 2 –9 0 4 893

Contents

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 893
2. The life cycle of soybean cyst nematode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 893
3. SCN population and race . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 893
4. Distribution of SCN. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 894
5. Management of SCN in soybean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 894
6. Cytological and histological process of syncytium . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 894
7. Germplasm screening and sources of SCN resistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 895
8. Identification of SCN-resistance QTL and genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 895
9. Functional gene analysis for SCN resistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 898
10. Molecular mechanisms of SCN resistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 899
11. Strategies for soybean breeding for resistance to SCN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 899
12. Conclusions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 900
Declaration of competing interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 901
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 901
Author contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 901
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 901

1. Introduction 2. The life cycle of soybean cyst nematode

Soybean (Glycine max L. Merrill) is a widely used legume crop
accounting for about 70% of total protein meal and 28% of
total vegetable oil consumption worldwide (www.soystats.
com, 2019). It also serves as a source of fuel. The USA
produces the highest percentage (34%) of the world’s
soybeans annually, followed by Brazil (32%), Argentina
(15%), and China (4%) (www.soystats.com, 2019). Soybean
average yield in the USA increased annually by 22 kg ha−1
from 1924 (740 kg ha−1) to 2013 (2959 kg ha−1) [1] and rose to
3500 kg ha−1 in 2018 (www.soystats.com, 2019). Biotic and
abiotic constraints are the two major challenges limiting
soybean production. Management practices can prevent
some abiotic stresses, but most, such as drought and floods,
cannot be easily controlled [2]. Biotic stresses, meanwhile,
have negative effects on the growth and development of
soybean that often result in significant yield losses and
cannot be easily controlled using management practices.
The use of fertilizers and pesticides can reduce the inci-
dence of biotic stresses; however, host plant resistance/
tolerance is a more promising alternative for farmers.
The soybean cyst nematode (SCN, Heterodera glycines
Ichinohe) is an economically important pest of soybean
causing estimated annual losses valued at billions of dollars
worldwide [3]. The damage is often devastating because
aboveground symptoms are not always visible and infesta-
tions are usually recognized at the later stage of infection
when a significant proportion of the damage has already
occurred and the nematode is difficult to eradicate; as a result,
yields are significantly reduced due to inhibited root growth
and reduced nodule formation [4,5]. The use of resistant
varieties and crop rotation practices are the most effective
strategies for controlling SCN [4].
This review assesses the trends and progress in the
identification of nematode-resistance genes, available
sources of resistance, and mechanisms underlying SCN
resistance. Management strategies for SCN resistance and
gene function analysis are also discussed.
The life cycle of SCN can be separated into four juvenile stages
and one adult stage. Development from one stage to another
usually begins in the egg and is interposed by moulting. SCN
at the second-stage juvenile (J2) stage penetrates into the root
of the host plant and migrates until it reaches the vascular
cylinder. The J2 nematode initiates the formation of a
permanent feeding cell (syncytium) and becomes sedentary
[5]. The syncytium provides the nutrients for growth and
development of SCN and is metabolically active as well as
important for a complete life cycle. Sexual dimorphism
usually becomes prominent in the third stage (J3) before the
nematode moves to the fourth stage (J4). The adult females
are visible on the host root surface because of their large size.
The vermiform male migrates out of the root to fertilize the
female before dying. The cyst is formed from dead females
and protects the eggs in the soil for many years when there is
no available host. In the presence of a favourable host, the
eggs hatch and the life cycle continues [5]. The life cycle of
SCN is usually completed in three to four weeks depending on
nutrient availability, soil temperature, and location. Because
SCN requires a living host to complete its life cycle, it is
classified as a biotrophic pathogen.
3. SCN population and race
The abilities of SCN populations to develop on resistant soybean
varieties are diverse because of differences in generation time,
fecundity, and extent of host damage [5]. The race description
published in 1970, which was based on the ability of SCN to
reproduce on four indicator lines (Pickett, Peking, PI 88788, and PI
90763), is still widely used for SCN classification [6]. When the
number of nematodes produced on a particular line is equal to or
greater than 10% of the number produced on cultivar Lee
(susceptible to SCN), the race is designated “+”, whereas when
the number is less than 10%, the race is designated “–” [7].
However, the race scheme has faced various criticisms [8]. For
894 TH E CR OP J OUR NA L 8 ( 2 0 20 ) 89 2 –9 0 4
one thing, according to that scheme, the virulence of a
population on one differential line is linked to virulence on
another, a situation that is impossible to test because of the
obligate parasitic nature of SCN [5]. Another SCN classification
scheme, the HG (Heterodera glycines) type classification
scheme, was later developed to circumvent the challenges
posed by the race scheme description. The HG type
classification is based on the ability of SCN to reproduce
on a larger and more diverse set of soybean indicator lines
(seven), which also aids in management decisions for SCN
[8]. The HG scheme allows the addition of new soybean
lines and is flexible for different environments.
4. Distribution of SCN
Soybean cyst nematode is believed to have evolved in either
China or Japan before spreading to other parts of the world [9].
Riggs and Schmitt [7] reported 16 races of SCN, the first
identified in 1954; a new race was also recently reported in
the Shanxi province of China [10]. H. glycine is widespread in
many countries, including the USA and China, where soy-
beans are grown on a large commercial scale. In the USA, Hg
Type 0 or 7 (race 3) and Hg Type 1.2.5– (races 4 and 14) are
primarily found in latitudes south and north of 37°N,
respectively [11]. In China, eight races of SCN are predominant
(races 1, 2, 3, 4, 5, 6, 9, and 14) [9]. Hg Type 0 is the most
common in the northeastern provinces of China (north of
41°N latitude), while Hg Type 1.2.5– is one of the two most
common races in the Huang-Huai-Hai valley region (between
32°N and 41°N latitude) [9,12].
Until recently, race 4 was reported to be the most virulent
race in China, but the new race 12 has recently been reported
to be more virulent than race 4 [10]; however, so far it is not
known to have spread broadly across China, having been
reported only in Shanxi province.
5. Management of SCN in soybean
Soybean cyst nematode causes the most substantial yield
reduction of any soybean disease or pest [13]. Damage by SCN
to soybean plants is reported to have a positive association with
the initial numbers of SCN present in the soil. Reducing the
initial numbers and preventing the spread of SCN to non-
infected areas are important aspects of its management that
can minimize yield loss [13]. Tillage and removal of root and soil
debris from farm implements can also help reduce SCN
numbers and its transfer to non-infested areas. Faghihi [14]
reported that a one-year rotation with non-host crops (such as
alfalfa [Medicago sativa], corn [Zea mays], sorghum [Sorghum
bicolor], barley [Hordeum vulgare], and oat [Avena sativa]) in the
absence of weeds could lead to a 55% decrease in SCN
population. The use of nematicides can also control SCN but it
is currently not feasible due to safety issues [13]. Biological
control methods, when identified, can also be used to control or
manage SCN. However, host plant resistance has always been
the favoured choice for controlling pests and diseases because it
is economically feasible and poses no threat to the
environment. A summary of the integrated disease
management (IDM) approaches that can be used for SCN control
is presented in Fig. 1.
6. Cytological and histological process of syncytium
Before SCN parasitism, root diffusate from soybean can cause
increased hatching of SCN eggs. Moreover, the diffusate from
susceptible varieties increases hatching more than that from
resistant varieties [15]. Successful parasitism in soybean roots
by SCN usually involves important physiological and morpho-
logical changes that result in the formation of a specialized
feeding cell called a syncytium. The syncytium serves as the
only source of nutrients during the life cycle of SCN, making it
very important for the nematode's survival, and it has to be
constantly replenished with nutrients that are required by the
developing SCN [16]. In susceptible plants, the syncytia develop
into mature functional feeding sites sustained by the plants.
This interaction occurs for weeks and, when successful, leads
to failure in plant defence [17]. During the maturation of the
syncytium into functional nurse cells, two developmental
phases are observed. In the first or parasitism phase, SCN
establishes the molecular circuitry to create a well-matched
interaction with the plant cell; during this phase, the cytolog-
ical features of syncytia for a susceptible or resistant process
are similar. The second phase of syncytium maturation
involves either a susceptible or resistant reaction, depending
on the outcome of the plant’s defence [17].
Inhibition of syncytium formation and growth is linked to
plant resistance. Syncytium formation in both susceptible and
resistant soybean includes the features of wall perforations,
increased cytoplasm density, and increased abundance of the
endoplasmic reticulum [18]. In susceptible plants, the syncy-
tium undergoes a continuous development up to nematode
maturity, which is usually accompanied by hypertrophy of
nuclei, an increase in the rough endoplasmic reticulum, and the
formation of wall ingrowths in early and late stages of infection
[15]. Moreover, the syncytium cell in a susceptible variety of
soybean is considerably larger than those in resistant varieties.
In the resistant reaction, different mechanisms based on the
syncytium have been proposed: necrosis of cells surrounding
the immature juvenile SCN due to lack of syncytium formation
[18], degeneration of syncytium [19], and formation of cell wall
thickenings that seal off the syncytium [20].
In regard to their resistance reactions to SCN, soybeans
are categorized into two main groups, the Peking and PI
88788 types, on the basis of their different histological
responses to SCN infection. The Peking type includes the
accessions Peking, PI 90763, PI 89772, PI 438489B, Pickett,
Huipizhiheidou (ZDD2315), and Yuanboheidou (ZDD10261)
[18,21,22], and the PI 88788 type includes typical genotypes
such as PI 88788, PI 209332, and PI 548316 [22]. The effect of
the resistant reaction on SCN development occurs much
earlier in the Peking type than in the PI88788-type of
resistance. The Peking-type resistant reaction causes
mortality of SCN at the J2 stage [17–19,21,23], while in PI
88788-type resistance, SCN development can proceed to
the J3 and J4 stages [21,24]. Thus, in PI 88788, syncytium
function is not greatly affected in the early stage of
resistance process.
 TH E C ROP J O U R NA L 8 (2 0 2 0) 89 2 –9 0 4
Regulatory
(field
sanitaon)
Host plant
resistance
IDM
Biological
(crop
rotaon)
Fig. 1 – Integrated disease management (IDM) strategies against soybean cyst nematode.
7. Germplasm screening and sources of SCN
resistance
The major genetic groups of SCN are separated based on
host compatibility described using the HG classification [8].
The HG classification gives information on the standard
indicator lines (SCN-resistant lines used in breeding for SCN
resistance) on which the nematode population can reproduce.
Thus, resistant cultivars derived from these indicator lines
will harbour nematode populations that can reproduce on the
indicator lines [25]. In some instances, resistance to a
minimum of one SCN HG type has been reported for 158
soybean accessions across soybean germplasm collections
(National Plant Germplasm System, NPGS, 2016; Crop: Soy-
bean, Descriptors: Nematcyst_1, 2, 3, 4, 5, and 14, Observation:
Resistant) [25]. Numerous resistant sources of germplasm
(Table S1) have been identified from abundant soybean
germplasm collections [26–28]. Notably, some germplasms,
such as PI 437654, Huipizhiheidou, and Wuzhaiheidou, have a
broad spectrum of resistance to SCN races. However, only a
few of these have been used in soybean breeding because
most of these collections carry undesirable traits that are
difficult to improve through conventional breeding tech-
niques [29].
Soybean varieties with SCN resistance that are available
for commercial purposes are derived primarily (90%) from
three plant introduction (PI) accessions; PI 88788, PI 209332,
and Peking [30]. Other resistant germplasms, including PI
437654, Huipizhiheidou, and Haerbinxiaoheidou, are also
sources of resistance for some resistant soybean varieties
[31]. Peking- and PI 88788-type sources of resistance are the
most widely used against SCN. However, many breeding
programs are primarily using PI 88788 as their major sources
of SCN resistance. Joos et al. [32] reported that out of 336 SCN-
895
Cultural
(llage and
ferlizer
applicaon)
Chemical
(use of
nemacides)
resistant entries evaluated, only 10 had resistance traits from
sources other than PI 88788, and about 90% of SCN-resistant
varieties in the central USA have PI 88788-type resistance [33].
There has been a population shift in SCN resistance which led
to new biotypes [34,35] and made the selection of new sources
of SCN resistance difficult. Niblack et al. [36] observed that
SCN could reproduce on PI 88788 in 70% of soil samples
infested with SCN in Illinois, and similar population shifts
have been reported in other soybean-producing regions
[14,37]. Thus, PI 88788-type resistance has become less
effective in reducing yield loss because SCN populations
have adapted to overcome this type of resistance [38,39].
Resistances from PI 437654 and Peking are effective, but
combining them with increased yield and other agronomic
traits is a major challenge [25]. Thus, there is currently a great
need to breed commercially viable varieties with resistance
derived from different resistant sources.
8. Identification of SCN-resistance QTL and genes
Not all quantitative trait loci (QTL) mediating SCN resistance
have been detected because of limited coverage of resistance
sources, size of mapping population, and lack of adequate
statistical techniques. However, the availability of soybean
reference genome sequences [40] coupled with high-
throughput single-nucleotide polymorphism (SNP) tools has
provided insight for association mapping (AM), which has
been used to study important soybean traits such as yield,
disease resistance, and quality [41,42]. Breeding for SCN
resistance in soybean will entail understanding the mecha-
nism(s) underlying SCN resistance and mapping related QTL
or genes. The first Rhg (resistance to H. glycines) locus was
identified in the early 1960s [43], and since then, with the
896 TH E CR OP J OUR NA L 8 ( 2 0 20 ) 89 2 –9 0 4

rapid developments in QTL mapping, many SCN-resistance
loci have been mapped by utilizing different germplasms
[44–65]. Table 1 shows some of these QTL with their relatively
high logarithm of the odds (LOD) values. Of these QTL, two loci
found on chromosomes (Chr.) 18 and 8 (rhg1 and Rhg4,
respectively) that are involved in resistance to SCN races 1 to
5 have been studied extensively [51,59,64,65]. The rhg1 locus
has been consistently mapped to a subtelomeric region on
Chr. 18 in diverse soybean germplasms, including Peking [13].
About 9%–28% of the total phenotypic variation observed in
resistance to SCN HG types 2.5.7 (race 1) and 0 (race 3) is
explained by Rhg4 genes from various resistant sources [38].
Meksem et al. [51] reported that in the Forrest cultivar, rhg1
and Rhg4 together explain 98% of the observed phenotypic
variance in resistance to SCN race 3. The resistance conferred
by Rhg4 is primarily linked to SCN race 3 but also includes
minor resistance to HG types 1.2.5.7 (race 2), 2.5.7, and 1.3.6.7
(race 14). The Rhg4 and rhg1 loci are required to confer full
resistance to some SCN races in cv. Peking and PI 437654
[22,33,66,67].
In 2010, Vuong et al. [35] mapped two SCN-resistance
QTL on Chrs. 10 and 18 in PI 567516C that are not related to
rhg1 or Rhg4 loci. These QTL confer resistance against SCN
races 1, 2, 3, and LY1. The QTL on Chr. 18 is physically
distant from the rhg1 locus [35]. Furthermore, this is the
first evidence of an SCN-resistance QTL on Chr. 10; all
previously reported QTL for SCN resistance had been
mapped to 15 of the soybean chromosomes, with none
reported on Chrs. 2, 7, 10, 12, or 13 [7,38,50,57,68]. Kim et al.
[13] also mapped two QTL on Chrs. 10 and 18 in PI 567305,
which is highly resistant to multiple SCN HG types, similar
to what was reported by Vuong et al. for 567516C [35]. Thus,
both PI 567516C and PI 567305 may harbour novel QTL that
can mediate SCN resistance independently of the rhg1 and
Rhg4 loci.
Genome-wide association studies (GWAS) have also been
used to detect resistance loci. A study of 282 soybean
accessions detected three resistance loci for SCN race 3 on
chromosome 18, two of which corresponded to rhg1 and to
another previously identified SCN-resistance locus, FGAM1,
while the third was located at the other end of Chr. 18 [69].
Vuong et al. [63] also reported eight novel QTL for resistance to
SCN race 3. Zhang et al. [69] reported 13 significant SNPs for
SCN resistance in seven different genomic regions. Three of
these corresponded to previously mapped QTL including rhg1
and Rhg4, while the other 10 were novel. A study by Zhao et al.
[70] revealed that 13 SNPs distributed on five chromosomes
are associated with resistance to SCN race 1, four of which
were novel loci. From these studies, more candidate genes for
SCN resistance have been identified. Recently, 12 SNPs located
on Chrs. 7, 8, 10, and 18 were reported to be significantly
associated with SCN resistance, among which three were
located near the rhg1 locus [71]. Liu et al. [72] reported 27
mutations among 10 genes, and three of these genes
overlapped between the two phenotypic mutants used in the
study. These genes were reported to be possible candidate
genes for SCN resistance [72]. A summary of some associated
loci is presented in Table 2.

Table 1 – List of QTL with LOD ≥ 3.0 reported for resistance to soybean cyst nematode.
Race/HG Resistance Linkage group Population type Analysis References
Type source method

3 PI 209332 A2, G, J F2:3 ANOVA, IM Concibido et al. [53]

3 Peking A2 F2:3, F2:4 ANOVA, IM Mahalinggam and Skorupska
[62]
3 PI 437654 A2, G, M RILs IM Webb et al. [56]
1, 3, 6 PI 209332 D2, G RILs, F2:3 ANOVA, IM Concibido et al. [52]
3 Hartwig B1 F2:3 ANOVA Vierling et al. [58]
1, 3, 6 PI 90763 G, J F2:3 ANOVA Concibido et al. [51]
1, 3, 6 Peking G, N F2:3 ANOVA Concibido et al. [51]
1, 3, 6 PI 88788 G F2:3 ANOVA Concibido et al. [51]
1, 3, 5 J87-233 A2, G F2:3 ANOVA, IM Heer et al. [47]
1, 3, 5 Peking B2 F2:3 ANOVA, IM Qiu et al. [60]
3 Peking A2, G RILs, NILs ANOVA, IM Meksem et al. [61]
14 Hartwig D2 F2:3 ANOVA Schuster et al. [59]
3 PI 468916 (G. soja) C2, E, G RILs, BC1F2 CIM Wang et al. [57]
1, 2, 3, 5, 14 PI 438489B A2, B1, C1, C2, D1a, E, F2:3 IM Yue et al. [45]
G
1, 2, 3, 5 PI 89772 B1, D2, E, G F2:3 ANOVA, IM Yue et al. [44]
3, 14 PI 88788 G, J RILs, NILs CIM, ANOVA Glover et al. [50]
2, 3, 5 PI 90763 A2, B1, E, G, J, L F2:3 CIM Guo et al. [65]
1, 2, 3, 5, 14 PI 438489B A2, C1, G RILs, F2:3 IM, MQM Vuong et al. [55]
3, 14 Hartwig A2, C2, G RILs BIM Arriagada et al. [54]
3,4 – B2, D1b, I Accessions of landraces and MLM Han et al. [48]
cultivars
2, 3, 14, LY2 PI 437655 A1, C1, E, G, I, J, N RILs IM, MQM Jiao et al. [46]
3 Zhongpin03-5373 B1 RILs CIM Li et al. [63]

ANOVA, analysis of variance; IM, interval mapping; CIM, composite interval mapping; MQM, multi-QTL method; BIM, Bayesian interval
mapping; MLM, mixed linear model.
 TH E C ROP J O U R NA L 8 (2 0 2 0) 89 2 –9 0 4 897

Table 2 – List of SNPs associated with resistance to soybean cyst nematode races 3 and 4.
Race QTL Associated locus Chromosome Position Linkage group

SCN3 SCN 3-g1 RS:7631207 Gm07 7,631,207 M

SCN 3-g2 RS:7640250 Gm07 7,640,250 M
SCN 3-g3 RS:7671170 Gm08 7,671,170 A2
SCN 3-g4 RS:7662003 Gm08 7,662,003 A2
SCN 3-g5 RS:7664479 Gm08 7,664,479 A2
SCN 3-g6 RS:7622492 Gm08 7,622,492 A2
SCN 3-g7 RS:7661660 Gm08 7,661,660 A2
SCN 3-g8 RS:46625879 Gm08 46,625,879 A2
SCN 3-g9 RS:36423980 Gm08 36,423,980 A2
SCN 3-g10 RS:3853672 Gm08 3,853,672 A2
SCN 3-g11 RS:35898587 Gm14 35,898,587 B2
SCN 3-g12 RS:16268025 Gm15 16,268,025 E
SCN 3-g13 RS:38522986 Gm18 38,522,986 G
SCN4 SCN 4-g1 ss715594958 Gm06 48,870,408 C2
SCN 4-g2 ss715594959 Gm06 48,871,996 C2
SCN 4-g3 ss715597374 Gm07 36,036,751 M
SCN 4-g4 ss715597376 Gm07 36,048,636 M
SCN 4-g5 ss715597408 Gm07 36,368,238 M
SCN 4-g6 ss715597409 Gm07 36,371,468 M
SCN 4-g7 ss715597410 Gm07 36,376,909 M
SCN 4-g8 ss715597413 Gm07 36,399,537 M
SCN 4-g9 ss715597431 Gm07 36,449,014 M
SCN 4-g10 ss715597444 Gm07 36,544,826 M
SCN 4-g11 ss715597487 Gm07 36,869,304 M
SCN 4-g12 ss715602745 Gm08 8,240,979 A2
SCN 4-g13 ss715602753 Gm08 8,287,226 A2
SCN 4-g14 ss715602757 Gm08 8,323,966 A2
SCN 4-g15 ss715606985 Gm10 40,672,699 O
SCN 4-g16 ss715610391 Gm11 32,834,795 B1
SCN 4-g17 ss715610392 Gm11 32,835,041 B1
SCN 4-g18 ss715610393 Gm11 32,837,437 B1
SCN 4-g19 ss715610396 Gm11 32,849,185 B1
SCN 4-g20 ss715610402 Gm11 32,855,711 B1
SCN 4-g21 ss715610417 Gm11 32,959,788 B1
SCN 4-g22 ss715610420 Gm11 32,960,792 B1
SCN 4-g23 ss715610421 Gm11 32,978,048 B1
SCN 4-g24 ss715628625 Gm18 1,187,349 G
SCN 4-g25 ss715628770 Gm18 1,277,584 G
SCN 4-g26 ss715628786 Gm18 1,286,863 G

The data given were retrieved from soybase database (soybase.org) and Tran et al. [71].

The rhg1 copy number has been classified into high (> 6
repeats, e.g. PI 88788) and low (3 repeats, e.g. Peking) copy
numbers [33]. Yu et al. [73] observed that for rhg1, both copy
number and polymorphism type are important for SCN
resistance. Among the resistance sources carrying rhg1,
those with higher rhg1 copy numbers have greater resistance.
Thus, the rhg1 locus may mediate SCN resistance by copy
number variation (CNV) of multiple genes encoding an amino
acid transporter (AAT), an α-soluble N-ethylmaleimide-sensi-
tive factor (NSF) attachment protein (α-SNAP), and a WI12
protein (wound-inducible protein) [33,67]. Therefore, Kadam
et al. [74] differentiated the CNV at rhg1 into resistant-high
copy (PI 88788-type), resistant-low copy (Peking type), and
susceptible-single copy (Williams 82) numbers. The Peking-
type resistance is suggested to be bigenic, comprising rhg1-a
and Rhg4 [67], whereas PI 88788 requires only rhg1-b for
resistance to SCN. Moreover, one gene in rhg1-a locus, the
GmSNAP18 is fully required for Peking-type resistance [67].
Patil et al. [75] further classified the rhg1-b locus into two
categories, rhg1-b (similar to those in PI 88788-type lines) and
rhg1-b1 (similar to those in Cloud-type lines).
Serine hydroxymethyltransferase (SHMT), which catalyses
the reversible conversion of serine and tetrahydrofolate to
glycine and tetrahydrofolate, respectively, contributes to the
resistance at the Rhg4 locus [76]. The gene GmSHMT08 has two
polymorphisms located in the first and second exons, 389 G/C
and 1165 A/T, which result in amino acid variations of
arginine vs. proline and tyrosine vs. asparagine, respectively,
and affect the kinetic properties of the enzyme [76]. Kandoth
et al. [77] further suggested that GmSHMT08 has additional
functions aside from its main enzymatic role in SCN resis-
tance and interacts with the GmSNAP18 protein. Further
evidence from Kandoth et al. [77] showed that even after
many years of selection on the recombinant inbred line (RIL)
EXF63 (rhg1F rhg4E), the SCN population did not change,
whereas SCN selected on the RIL EXF67 (rhg1F Rhg4F) shifted
to HG type 1.3.6.7, suggesting a shift in virulence upon
exposure to Peking-type resistance.
898 TH E CR OP J OUR NA L 8 ( 2 0 20 ) 89 2 –9 0 4

Table 3 – List of candidate genes for resistance to soybean cyst nematode.

Gene Protein Reference

Glyma.02g260400 α-soluble N-ethylmaleimide-sensitive factor attachment protein Lakhssassi et al. [79]

Glyma.06g130300 Tetratricopeptide repeat (TPR)-like superfamily protein Liu et al. [72]
Glyma.07g193900 Dof-type zinc-finger DNA-binding family protein Zhao et al. [70]
Glyma.07g194400 Cytochrome P450 Tran et al. [71]
Glyma.07g195400 RING gene Zhao et al. [70]
Glyma.07g196000 RING gene Tran et al. [71]
Glyma.07g196500 Phosphate 2 Zhao et al. [70]
Glyma.07g196800 Lipoxygenase 3 Zhao et al. [70]
Glyma.07g199500 (LRR) receptor gene Tran et al. [71]
Glyma.08g097300 Aldolase-type TIM barrel family protein Zhao et al. [70]
Glyma.08g108900 Serine hydroxymethyltransferase Liu et al. [76]
Glyma.08g119200 LRR and NB-ARC domains-containing disease-resistance protein Liu et al. [72]
Glyma.08g200100 HAD superfamily, subfamily IIIB acid phosphatase Zhao et al. [70]
Glyma.08g200200 HAD superfamily, subfamily IIIB acid phosphatase Zhao et al. [70]
Glyma.08g202300 Integrase-type DNA-binding superfamily protein Zhao et al. [70]
Glyma.08g303900 Sterol regulatory binding element Zhang et al. [69]
Glyma.09g054000 Ankyrin repeat family protein Liu et al. [72]
Glyma.11g151500 Catechol oxidase activity Zhang et al. [69]
Glyma.11g234500 α-soluble N-ethylmaleimide-sensitive factor attachment protein Lakhssassi et al. [79]
Glyma.13g175200 GTP-binding protein Zhang et al. [69]
Glyma.14g047900 Leucine-rich repeat receptor-like protein kinase family protein Zhao et al. [70]
Glyma.14g051600 Copper transport protein family Zhao et al. [70]
Glyma.14g054900 α-soluble N-ethylmaleimide-sensitive factor attachment protein Lakhssassi et al. [79]
Glyma.15g141800 Unknown Liu et al. [72]
Glyma.15g237200 Leucine-rich repeat receptor-like protein kinase family protein Liu et al. [72]
Glyma.17g010200 Homeobox transcription factor Zhang et al. [69]
Glyma.18g022400 Amino acid transporter Cook et al. [33]
Glyma.18g022500 α-soluble N-ethylmaleimide-sensitive factor attachment protein Cook et al. [33]
Glyma.18g022700 Wound induced protein Zhang et al. [69]
Glyma.18g095000 Protein of unknown function Zhang et al. [69]

Nonsynonymous SNPs distributed in GmSNAP11, which is a
paralogous gene of GmSNAP18, have been identified as novel
alleles contributing to SCN resistance [33,78]. Whole-genome
sequencing revealed that a truncated α-SNAP was encoded by
GmSNAP on chromosome 11 and not GmSNAP on chromosome
18 [79]. Also, Li et al. [53] demonstrated that a nonsynonymous
SNP (map-5149) closely associated with resistance to SCN race 3
mapped to GmSNAP11. Thus, GmSNAP11 is a novel gene that can
also confer SCN resistance.
Glycine max salicylic acid methyltransferase (GmSAMT)
mediates the resistance of soybean to SCN. Lin et al. [80]
showed that overexpression of GmSAMT1 in susceptible lines
reduces the number of SCN, and it also affects the expression
of genes responsible for salicylic acid (SA) biosynthesis and
signal transduction. Other genes involved in SA biosynthesis
and signalling also confer partial resistance on SCN. Mathew
et al. [81] showed that overexpression of AtNPR1, AtTGA2, and
AtPR-5 in soybean roots reduced cyst count to less than 50% of
that in controls not overexpressing these genes. Youssef et al.
[82] reported that ectopic expression of Arabidopsis phytoalexin-
deficient4 (AtPAD4) can broaden resistance to SCN. Therefore,
the genes involved in SA biosynthesis and signalling play
important roles in SCN resistance.
In addition, Yang et al. [83] characterized the soybean WRKY
gene family and identified five WRKY genes (GmWRKY154,
GmWRKY62, GmWRKY36, GmWRKY28, and GmWRKY5) confer-
ring high SCN resistance (>70% reduction in cyst number) and
four (GmWRKY52, GmWRKY53, GmWRKY86, and GmWRKY136)
conferring moderate SCN resistance (40% to 60% reduction in
cyst number). A list of some identified candidate genes with
their associated proteins is presented in Table 3.
9. Functional gene analysis for SCN resistance
Reverse genetics strategies, such as T-DNA insertion mutagen-
esis [84], targeting-induced local lesions in genomes (TILLING)
[85], RNA interference (RNAi) [86], and virus-induced gene
silencing (VIGS) [87–89], have been developed in recent decades.
Also, the soybean hairy root transient transformation system has
been developed and used to study SCN resistance [33,67,76,90].
The early work on the functional analysis of SCN-resistance
genes was done by Cook et al. [33], who used gene silencing in
soybean hairy roots to show that three genes in a 31-kb segment
at rhg1-b contribute to SCN resistance. Overexpression of these
genes together, but not individually, in soybean hairy roots
significantly increased SCN resistance [33]. Yang et al. [83] used
transgenic hairy roots to show that the overexpression of WRKY
genes could increase SCN resistance.
A DNA-based VIGS vector based on bean pod mottle virus
(BPMV) has been developed [87,88] and used to detect genes
for resistance to Asian soybean rust (Phakopsora pachyrhizi)
[89]. Liu et al. [76] used mutation analysis, BPMV-VIGS, and
transgenic complementation in soybean hairy roots to show
that the Rhg4 locus gene GmSHMT08 confers SCN resistance.
Kandoth et al. [77] showed that the GmSHMT08 protein has
 TH E C ROP J O U R NA L 8 (2 0 2 0) 89 2 –9 0 4
other functions aside from mediating in SCN resistance using
mutagenesis.
These reverse genetics strategies, as well as the soybean
hairy root transient expression system, have significantly
increased the efficiency with which SCN-resistance candidate
genes can be identified and will facilitate future understand-
ing of the molecular mechanisms of SCN resistance.
10. Molecular mechanisms of SCN resistance
The molecular mechanisms of SCN resistance are compli-
cated and still not fully understood. GWAS results have
suggested that numerous disease-resistance proteins are
associated with SCN resistance, including leucine-rich region
(LRR)-containing proteins, zinc-finger domain proteins, pro-
tein kinases, cytochrome P450s, RING domain proteins, and
members of the MYB and WRKY transcription activation
families [56]. Comparative RNA sequencing analysis using
wild soybean (Glycine soja) suggested that amounts of defence-
related differentially expressed genes (DEGs) are associated
with SCN resistance; these included genes involved in
pathogen recognition, the MAPK signalling cascade, Ca2+/
calmodulin-mediated signalling, phytohormone-mediated
signalling, WRKY-involved transcription regulation, cell wall
remodelling, and various other defence-associated signalling
processes [91]. Gene ontology (GO) enrichment analyses
revealed that the serine and arginine metabolic processes
may also be vital for SCN race 4 resistance [29]. To date, the
rhg1- and Rhg4-mediated mechanisms have received the most
attention due to their high contributions to SCN resistance,
although other mechanisms have also been investigated.
For the rhg1 locus, Cook et al. [78] suggested that the protein
product of the resistance-associated gene GmSNAP18 may not
function as classical α-SNAP, but instead may mediate resis-
tance through a novel mechanism. Bayless et al. [92] have
shown that the disruption of SNARE complexes and vesicle
trafficking resulting from the significant accumulation of
abnormal α-SNAP protein at the syncytium confers resistance.
Moreover, an unusual NSF allele (rhg1-associated NSF on
chromosome 07; NSFRAN07) was discovered only in rhg1+
germplasm. The protective effect against rhg1 α-SNAP cytotox-
icity from NSFRAN07 coexpression in planta is much greater than
that of the WT NSFCh07. An examination of segregation
distortion between rhg1 and NSFRAN07 across 855 soybean
accessions and rhg1+ progeny showed a 100% coinheritance of
NSFRAN07 and rhg1 alleles [93]. These results suggest that rhg1-
mediated SCN resistance may be accomplished through im-
pairment of SNARE complexes, and NSFRAN07 enables the
sustainability of nematode resistance in rhg1 cultivars.
For the Rhg4 locus, Liu et al. [76] suggested that the
GmSHMT08 gene responsible for Rhg4 resistance has two
genetic polymorphisms that alter the function of the enzyme
and thereby lead to the resistant or susceptible reaction. The
enzyme plays an important role in oneQcarbon folate metab-
olism, and its alteration leads to folate deficiency, which can
trigger hypersensitive-response-like programmed cell death
of developing syncytia and also of the nematode [76].
The SA and jasmonic acid (JA) signalling pathways may
also be involved in SCN resistance. AtPAD4 encodes a lipase-
899
like protein that acts in mediating SA signalling, and its
ectopic expression in soybean roots can reduce the number of
SCN cysts [82]. The overexpression of GmSAMT1 induces the
expression of the genes Isochorismate synthase (ICS) and
Nonexpressor of pathogenesis-related 1 (NPR1), which modulate
the SA biosynthesis and signal transduction pathway before
SCN infection [80]. The ectopic expression of some
Arabidopsis genes (AtNPR1, AtTGA2, and AtPR-5) influencing
SA synthesis, regulation, and signalling can also confer SCN
resistance [81]. The JA synthesis and signalling pathway may
also be involved in SCN resistance. The ectopic expression of
AtAOS, AtAOC, and AtJAR1 in soybean provides some level of
resistance to SCN [81]. Guo et al. [94] reported that overex-
pression of rhg1-GmAAT increases the transportation of
glutamate from shoots to roots, resulting in the accumulation
of free glutamate in the roots and upregulation of the JA
pathway, which may contribute to SCN resistance.
In brief (Fig. 2), the main molecular mechanisms of SCN
resistance in soybean can be summarised as (1) Disruption of
SNARE complexes and vesicle trafficking (involving SNAP and
NSF) by cytotoxic effects of the extensive accumulation of
abnormal α-SNAP protein at the syncytium can mediate SCN
resistance; (2) Disturbance of folate homeostasis, which may
trigger hypersensitive-response-like programmed cell death
of developing syncytia, causes the death of the nematode,
thereby preventing its growth and reproduction; and (3)
Modulation of SA and JA signalling triggers defence processes
against SCN.
11. Strategies for soybean breeding for resistance
to SCN
Based on the mechanisms of SCN resistance mentioned
above, although there are several existing strategies for
breeding crops for resistance, the multigenic and widespread
nature of SCN will require more reliable and efficient methods
to breed SCN-resistant soybean varieties.
A conventional approach is to screen large collections of
soybean accessions and select lines that are resistant to SCN.
These lines can be employed in traditional breeding programs
as the donor parents in developing SCN-resistant varieties.
Another approach is the marker-assisted selection (MAS),
which is the most economical, fast, and reliable strategy, and
whose efficiency and accuracy could be further enhanced by
the development of high-throughput markers. Shi et al. [95]
have reported three functional Kompetitive allele-specific PCR
(KASP) marker assays (GSM381 and GSM383 at rhg1 and
GSM191 at Rhg4) that can be used for high-throughput MAS
for SCN resistance with high accuracy [95]. Tian et al. [96]
developed cleaved amplified polymorphic sequences (CAPS)
markers targeting GmSNAP11 with a high selection efficiency.
The race structure of the SCN population requires the use of
gene pyramiding in developing resistant soybean varieties.
The use of linkage and association mapping will allow the
identification of numerous markers linked to SCN resistance
[53] and will provide a basis for developing simple and
effective markers for SCN resistance breeding.
Reverse genetic tools have facilitated the identification of
SCN-resistance genes such as rhg1 [33,76,93] and Rhg4 [67,76].
900 TH E CR OP J OUR NA L 8 ( 2 0 20 ) 89 2 –9 0 4

Fig. 2 – An illustration of proposed mechanisms for resistance to soybean cyst nematode. NSF, N-ethylmaleimide-sensitive
factor; SNAP, soluble N-ethylmaleimide-sensitive factor attachment protein; SNARE, soluble N-ethylmaleimide-sensitive
factor attachment protein receptor; SHMT, serine hydroxymethyltransferase; THF, tetrahydrofolate; MTHF, 5,10-methylene
tetrahydrofolate; PCD, programmed cell death; SA, salicylic acid; ICS, isochorismate; SID2, salicylic-acid-induction-deficient 2;
NPR1, nonexpressor of pathogenesis-related 1; EDS1, enhanced disease susceptibility 1; PAD4, phytoalexin-deficient 4; JA,
jasmonic acid; JAile, jasmonoyl-isoleucine; AOS, allene oxide synthase; AOC, allene oxide cyclase; OPR, 12-oxophytodienoic
acid reductase; JAR, jasmonic acid-amido synthetase.

The identified genes will facilitate the development of
resistant varieties through gene editing, allowing the im-
provement of SCN-susceptible lines that are desirable for
other traits. Therefore, genome-editing tools such as zinc-
finger nucleases (ZFNs), transcription-activator-like effector
nucleases (TALENs), and clustered regularly interspaced short
palindromic repeats–CRISPR-associated proteins (CRISPR-
Cas9) deserve more attention from soybean breeders, given
their ability to knock out or modify specific targeted
sequences [97]. These techniques can be used to develop
SCN-resistant varieties through targeted editing of rhg1, Rhg4,
and other resistance genes, given that nucleotide transitions
or deletions in GmSNAP18, GmSNAP11, and GmSHMT08 are
known to significantly influence SCN resistance. Moreover,
editing these genes, individually or together, will produce a
series of soybean materials with different levels of SCN
resistance, which could be useful in soybean breeding.
12. Conclusions
With the availability of soybean genome sequence informa-
tion and efficient rapid techniques for gene function studies,
previously unknown resistance genes (GmSNAP18 and
GmSHMT08) for SCN have been identified in soybean. Also,
new discoveries about the mechanisms of gene resistance are
in progress. Apart from the previously identified rhg1 gene on
chromosome 18, other genes, such as GmSNAP11 on chromo-
some 11, have been identified as being associated with SCN
resistance. These identified candidate genes are important
tools for improving marker-assisted breeding efficiency and
understanding the molecular basis of SCN resistance. The
phylogenetic information about SCN-resistance loci and gene/
QTL-specific markers that have been developed will acceler-
ate breeding programs targeting SCN-resistance. Gene func-
tional analysis using techniques such as RNAi, VIGS, and
mutagenesis will also increase the efficiency of candidate
gene identification. The mechanisms underlying SCN resis-
tance identified to date primarily involve disruption of SNARE
complexes and vesicle trafficking, disturbance of folate
homeostasis, and regulation of the biosynthesis and signal-
ling of plant hormones such as SA and JA, suggesting possible
avenues of approach for developing novel sources of SCN
resistance. The combination of conventional breeding, MAS,
and genomic editing tools is highly promising for future
soybean breeding programs for SCN resistance.
 TH E C ROP J O U R NA L 8 (2 0 2 0) 89 2 –9 0 4
Supplementary data to this article can be found online at
https://doi.org/10.1016/j.cj.2020.03.001.
Declaration of competing interest
Authors declare that there are no conflicts of interest.
Acknowledgments
This study was supported by the National Key Research and
Development Program of China (2016YFD0100504,
2016YFD0100201, and 2017YFD0101400), the National Natural
Science Foundation of China (No. 31301345 and No. 31671716),
the National Major Science and Technology Project of China
(2016ZX08004-003), and the Agricultural Science and Technol-
ogy Innovation Program of CAAS.
Author contributions
Abdulwahab S. Shaibu wrote the manuscript. Bin Li concep-
tualized and supervised this work, and edited the manuscript,
Shengrui Zhang edited the manuscript. Junming Sun super-
vised and financed this work, and edited the manuscript.
REFERENCES
[1] J.E. Specht, B.W. Diers, R.L. Nelson, J. Francisco, F. de Toledo, J.
A. Torrion, P. Grassini, Soybean, in: S. Smith, B. Diers, J.
Specht, B. Carver (Eds.), Yield Gains Major U.S. Field Crops,
CSSA Spec. Publ. 33, American Society of Agronomy, Inc.,
Crop Science Society of America, Inc., and Soil Science
Society of America, Inc, Madison, WI, USA 2014, pp. 311–356.
[2] G.L. Hartman, E.D. West, T.K. Herman, Crops that feed the
world 2. Soybean-worldwide production, use, and constraints
caused by pathogens and pests, Food Secur. 3 (2011) 5–17.
[3] S.R. Koenning, J.A. Wrather, Suppression of Soybean Yield
Potential in the Continental United States by Plant Diseases
from 2006 to 2009, Plant Heal, Prog, 2010https://doi.org/10.
1094/PHP-2010-1122-01-RS.
[4] E.L. Davis, G.L. Tylka, Soybean Cyst Nematode Disease, Plant
Health Instructor 2000https://doi.org/10.1094/PHI-I-2000-
0725-01.
[5] T.L. Niblack, K.N. Lambert, G.L. Tylka, A model plant
pathogen from the kingdom animalia: Heterodera glycines, the
Soybean Cyst Nematode, Annu. Rev. Phytopathol. 44 (2006)
283–303.
[6] G.L. Am, J. Epps, R. Riggs, L. Duclos, J. Fox, R. Bernard,
Terminology and identity of infraspecific forms of the
soybean cyst nematode (Heterodera glycines), Plant Dis. Rep. 54
(1970) 544–546.
[7] R.D. Riggs, D.P. Schmitt, Complete characterization of the
race scheme for Heterodera glycines, J. Nematol. 20 (1988)
392–395.
[8] T.L. Niblack, P.R. Arelli, G.R. Noel, C.H. Opperman, J.H. Orf, D.
P. Schmitt, J.G. Shannon, G.L. Tylka, A revised classification
scheme for genetically diverse populations of Heterodera
glycines, J. Nematol. 34 (2002) 279–288.
[9] X.Z. Liu, J.Q. Li, D.S. Zhang, History and status of soybean cyst
nematode in China, Int. J. Nematol. 7 (1997) 18–25.
901
[10] Y. Lian, J. Guo, H. Li, Y. Wu, H. Wei, J. Wang, J. Li, W. Lu, A new
race (X12) of soybean cyst nematode in China, J. Nematol. 49
(2017) 321–326.
[11] D.G. Kim, R.D. Riggs, R.T. Robbins, L. Rakes, Distribution of
races of Heterodera glycines in the Central United States, J.
Nematol. 29 (1997) 173–179.
[12] Q. Yan, P. Chen, L. Wang, The verification of race 4 of soybean
cyst nematode in suburban, Beijing, Soybean Sci. 14 (1995)
355–359(in Chinese with English abstract).
[13] K.S. Kim, T.D. Vuong, D. Qiu, R.T. Robbins, J. Grover
Shannon, Z. Li, H.T. Nguyen, Advancements in breeding,
genetics, and genomics for resistance to three nematode
species in soybean, Theor. Appl. Genet. 129 (2016)
2295–2311.
[14] J. Faghihi, P.A. Donald, G. Noel, T.W. Welacky, V.R. Ferris,
Soybean Resistance to Field Populations of Heterodera glycines
in Selected Geographic Areas, Plant Health Prog, 2010https://
doi.org/10.1094/PHP-2010-0426-01-RS.
[15] Q. Yan, P. Chen, L. Wang, The effect of soybean root
diffusates on the hatching of Heterodera glycines race 4, Acta
Phytopathol. Sin. 27 (1997) 269–274(in Chinese with English
abstract).
[16] H. Bohlmann, M. Sobczak, The plant cell wall in the feeding
sites of cyst nematodes, Front. Plant Sci. 5 (2014) 89.
[17] V.P. Klink, P. Hosseini, M.H. MacDonald, N.W. Alkharouf, B.F.
Matthews, Population-specific gene expression in the plant
pathogenic nematode Heterodera glycines exists prior to
infection and during the onset of a resistant or susceptible
reaction in the roots of the Glycine max genotype Peking, BMC
Genomics 10 (2009) 111.
[18] Q. Yan, L. Wang, P. Chen, Nature of resistance to race 4 of
Heterodera glycines in Chinese black soybeans III. Histological
responses in roots of resistant and susceptible varieties
infected with Heterodera glycines, Soybean Sci. 16 (1997) 34–37
(in Chinese with English abstract).
[19] B.Y. Endo, Histopathological responses of resistant and
susceptible soybean varieties, and backcross progeny to entry
and development of Heterodera glycines, Phtytopathology 55
(1965) 375–381.
[20] R.D. Riggs, K.S. Kim, I. Gipson, Ultrastructural changes in
Peking soybeans infected with Heterodera glycines,
Phtytopathology 63 (1973) 76–84.
[21] J. Halbrendt, S. Lewis, E. Shipe, A technique for evaluating
Heterodera glycines development in susceptible and resistant
soybean, J. Nematol. 24 (1992) 84–91.
[22] A.L. Colgrove, T.L. Niblack, Correlation of female indices from
virulence assays on inbred lines and field populations of
Heterodera glycines, J. Nematol. 40 (2008) 39–45.
[23] J.P. Ross, Host-parasite relationship of the soybean cyst
nematode in resistant soybean roots, Phtytopathology 48
(1958) 578–579.
[24] V.P. Klink, P. Hosseini, P.D. Matsye, N.W. Alkharouf, B.F.
Matthews, Syncytium gene expression in Glycine max ([PI
88788]) roots undergoing a resistant reaction to the parasitic
nematode Heterodera glycines, Plant Physiol. Biochem. 48
(2010) 176–193.
[25] K. Rincker, T. Cary, B.W. Diers, Impact of soybean cyst
nematode resistance on soybean yield, Crop Sci. 57 (2017)
1373–1382.
[26] Y. Li, Z. Wang, G. Jiao, R. Chang, Studies on resistance of
soybean germplasm resources to race 4 of soybean cyst
nematode, Sci. Agric. Sin. 24 (1991) 64–69(in Chinese with
English abstract).
[27] T.N. Aeny, R.D. Riggs, Susceptibility of soybean introductions
to races 1, 2, 3, and 4 of Heterodera glycines, J. Nematol. 25
(1993) 34–37.
[28] W. Cui, Advances in study of breeding for resistance to
soybean cyst nematode of China, Soybean Sci. 17 (1998) 79–82
(in Chinese with English abstract).
902 TH E CR OP J OUR NA L 8 ( 2 0 20 ) 89 2 –9 0 4
[29] B. Li, J. M. Sun, L. Wang, R.J Zhao, L.Z Wang, Comparative
analysis of gene expression profiling between resistant and
susceptible varieties infected with soybean cyst nematode
race 4 in Glycine max, J. Integr. Agric. 13 (2014) 2594–2607.
[30] S. Winter, I. Rajcan, B. Shelp, Soybean cyst nematode:
challenges and opportunities, Plant Sci. 86 (2006) 25–32.
[31] C. Yuan, B. Shen, Y. Dong, Released soybean varieties
resistant to cyst nematode in China and their resistance
genetic derivation, Soybean Sci. 28 (2009) 1049–1053(in
Chinese with English abstract).
[32] D.K. Joos, R.W. Esgar, B.R. Henry, E.D. Nafziger, Soybean
Variety Test Results in Illinois-2014, Crop Sciences Special
Reports, University of Illinois, Urbana, Illinois, USA, 2014.
http://vt.cropsci.illinois.edu/soybean.html.
[33] D.E. Cook, T.G. Lee, X. Guo, S. Melito, K. Wang, A.M. Bayless, J.
Wang, T.J. Hughes, D.K. Willis, T.E. Clemente, B.W. Diers, J.
Jiang, M.E. Hudson, A.F. Bent, Copy number variation of
multiple genes at Rhg1 mediates nematode resistance in
soybean, Science 338 (2012) 1206–1209.
[34] B.W. Diers, P.R. Arelli, Management of parasitic nematodes of
soybean through genetic resistance, in: H.E. Kauffman (Ed),
Proceedings of the World Soybean Research Conference VI,
August 4–7, Chicago, Illinoil, USA, 1999 300–305.
[35] T.D. Vuong, D.A. Sleper, J.G. Shannon, H.T. Nguyen, Novel
quantitative trait loci for broad-based resistance to soybean
cyst nematode (Heterodera glycines Ichinohe) in soybean PI
567516C, Theor. Appl. Genet. 121 (2010) 1253–1266.
[36] T.L. Niblack, A.L. Colgrove, K. Colgrove, J.P. Bond, Shift in
Virulence of Soybean Cyst Nematode Is Associated with Use
of Resistance from PI 88788, Plant Health Prog, 2008https://
doi.org/10.1094/PHP-2008-0118-01-RS.
[37] M.G. Mitchum, J.A. Wrather, R.D. Heinz, J.G. Shannon, G.
Danekas, Variability in distribution and virulence pheno-
types of Heterodera glycines in Missouri during 2005, Plant Dis.
91 (2007) 1473–1476.
[38] V.C. Concibido, B.W. Diers, P.R. Arelli, A decade of QTL
mapping for cyst nematode resistance in soybean, Crop Sci.
44 (2004) 1121–1131.
[39] J.G. Shannon, P.R. Arelli, L.D. Young, Breeding for soybean
cyst nematode resistance, in: D.P. Schmitt, J.A. Wrather, R.D.
Riggs (Eds.), Biology and Management of Soybean Cyst
Nematode, Second editionSchmitt & Associates of Marceline,
Marceline, MO, USA 2004, pp. 155–180.
[40] J. Schmutz, S.B. Cannon, J. Schlueter, J. Ma, T. Mitros, W.
Nelson, D.L. Hyten, Q. Song, J.J. Thelen, J. Cheng, D. Xu, U.
Hellsten, G.D. May, Y. Yu, T. Sakurai, T. Umezawa, M.K.
Bhattacharyya, D. Sandhu, B. Valliyodan, E. Lindquist, M.
Peto, D. Grant, S. Shu, D. Goodstein, K. Barry, M. Futrell-
Griggs, B. Abernathy, J. Du, Z. Tian, L. Zhu, N. Gill, T. Joshi, M.
Libault, A. Sethuraman, X.C. Zhang, K. Shinozaki, H.T.
Nguyen, R.A. Wing, P. Cregan, J. Specht, J. Grimwood, D.
Rokhsar, G. Stacey, R.C. Shoemaker, S.A. Jackson, Genome
sequence of the palaeopolyploid soybean, Nature 463 (2010)
178–183.
[41] M. Bastien, H. Sonah, F. Belzile, Genome wide association
mapping of Sclerotinia sclerotiorum resistance in soybean with
a genotyping-by-sequencing approach, Plant Genome 7
(2014) 0030.
[42] Z. Wen, R. Tan, J. Yuan, C. Bales, W. Du, S. Zhang, M.I.
Chilvers, C. Schmidt, Q. Song, P.B. Cregan, D. Wang, Genome-
wide association mapping of quantitative resistance to
sudden death syndrome in soybean, BMC Genomics 15 (2014)
809.
[43] B.E. Caldwell, C.A. Brim, J.P. Ross, Inheritance of resistance of
soybeans to the cyst nematode, Heterodera glycines, Agron. J.
52 (1960) 635–636.
[44] P. Yue, D.A. Sleper, P.R. Arelli, Mapping resistance to multiple
races of Heterodera glycines in soybean PI 89772, Crop Sci. 41
(2001) 1589–1595.
[45] P. Yue, P.R. Arelli, D.A. Sleper, Molecular characterization of
resistance to Heterodera glycines in soybean PI 438489B, Theor.
Appl. Genet. 102 (2001) 921–928.
[46] Y. Jiao, T.D. Vuong, Y. Liu, C. Meinhardt, Y. Liu, T. Joshi,
P.B. Cregan, D. Xu, J.G. Shannon, H.T. Nguyen, Identifi-
cation and evaluation of quantitative trait loci underly-
ing resistance to multiple HG types of soybean cyst
nematode in soybean PI 437655, Theor. Appl. Genet. 128
(2015) 15–23.
[47] H.T. Heer, J.A., Knap, R. Mahalingam, E.R. Shipe, P.R. Arelli, B.
Mathews, Molecular markers for resistance to
Heteroderaglycines in advanced soybean germplasm, Mol.
Breed. 4 (1998) 359–367.
[48] Y. Han, X. Zhao, G. Cao, Y. Wang, Y. Li, D. Liu, W. Teng, Z.
Zhang, D. Li, L. Qiu, H. Zheng, W. Li, Genetic characteristics of
soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the
cyst nematode analyzed by genome-wide association map-
ping, BMC Genomics 16 (2015) 598.
[49] B. Guo, D.A. Sleper, P. Lu, J.G. Shannon, H.T. Nguyen, P.R.
Arelli, QTLs associated with resistance to soybean cyst
nematode in soybean meta-analysis of QTL locations, Crop
Sci. 46 (2006) 595–602.
[50] K.D. Glover, D. Wang, P.R. Arelli, S.R. Carlson, S.R. Cianzio, B.
W. Diers, Near isogenic lines confirm a soybean cyst
nematode resistance gene from PI 88788 on linkage group J,
Crop Sci. 44 (2004) 936–941.
[51] V.C. Concibido, D.A. Lange, R.L. Denny, J.H. Orf, N.D. Young,
Genome mapping of soybean cyst nematode resistance genes
in Peking, PI 90763, and PI 88788 using DNA markers, Crop Sci.
37 (1997) 258–264.
[52] V.C. Concibido, N.D. Young, D.A. Lange, R.L. Denny, J.H. Orf,
RFLP mapping and marker-assisted selection of soybean cyst
nematode resistance in PI 209332, Crop Sci. 36 (1996)
1643–1650.
[53] V.C. Concibido, R. Denny, S.R. Boutin, R. Hautea, J. Orf, N.D.
Young, DNA marker analysis of loci underlying resistance to
soybean cyst nematode (Heterodera glycines Ichinohe), Crop
Sci. 34 (1994) 240–246.
[54] O. Arriagada, F. Mora, J.C. Dellarossa, M.F.S. Ferreira, G.D.L.
Cervigni, I. Schuster, Bayesian mapping of quantitative trait
loci (QTL) controlling soybean cyst nematode resistant,
Euphytica 186 (2012) 907–917.
[55] T.D. Vuong, D.A. Sleper, J.G. Shannon, X. Wu, H.T. Nguyen,
Confirmation of quantitative trait loci for resistance to
multiple-HG types of soybean cyst nematode (Heterodera
glycines Ichinohe), Euphytica 181 (2011) 101–113.
[56] D.M. Webb, B.M. Baltazar, P.R. Arelli, J. Schnupp, K. Clayton, P.
Keim, W.D. Beavis, Genetic mapping of soybean cyst nema-
tode race 3 resistance loci in soybean PI 437654, Theor. Appl.
Genet. 91 (1995) 574–581.
[57] D. Wang, P.R. Arelli, R.C. Shoemaker, B.W. Diers, Loci
underlying resistance to race 3 of soybean cyst nematode in
Glycine soja plant introduction 468916, Theor. Appl. Genet. 103
(2001) 561–566.
[58] R.A. Vierling, J. Faghihi, V.R. Ferris, J.M. Ferris, Association of
RFLP markers with loci conferring broad-based resistance to
the soybean cyst nematode (Heterodera glycines), Theor. Appl.
Genet. 92 (1996) 83–86.
[59] I. Schuster, R.V. Abdelnoor, S.R.R. Marin, V.P. Carvalho, R.A.S.
Kiihl, J.F.V. Silva, C.S. Sediyama, E.G. Barros, M.A. Moreira,
Identification of a new major QTL associated with resistance
to soybean cyst nematode (Heterodera glycines), Theor. Appl.
Genet. 102 (2001) 91–96.
[60] B.X. Qiu, P.R. Arelli, D.A. Sleper, RFLP markers associated with
soybean cyst nematode resistance and seed composition in a
“Peking” × “Essex” population, Theor. Appl. Genet. 98 (1999)
356–364.
[61] K. Meksem, P. Pantazopoulos, V.N. Njiti, L.D. Hyten, P.R.
Arelli, D.A. Lightfoot, ‘Forrest’ resistance to the soybean cyst
 TH E C ROP J O U R NA L 8 (2 0 2 0) 89 2 –9 0 4
nematode is bigenic: saturation mapping of the Rhg1 and
Rhg4 loci, Theor. Appl. Genet. 103 (2001) 710–717.
[62] R. Mahalingam, H.T. Skorupska, DNA Markers for resistance
to Heterodera glycine I. Race 3 in soybean cultivar Peking,
Breed. Sci. 45 (1995) 435–443.
[63] Y. Li, X. Shi, H. Li, J.C. Reif, J. Wang, Z. Liu, S. He, B. Yu, L. Qiu,
Dissecting the genetic basis of resistance to soybean cyst
nematode combining linkage and association mapping, Plant
Genome 9 (2016) 0020.
[64] B.F. Matthews, M.H. MacDonald, J.S. Gebhardt, T.E. Devine,
Molecular markers residing close to the Rhg4 locus conferring
resistance to soybean cyst nematode race 3 on linkage group
A of soybean, Theor. Appl. Genet. 97 (1998) 1047–1052.
[65] B. Guo, D.A. Sleper, P.R. Arelli, J.G. Shannon, H.T. Nguyen,
Identification of QTLs associated with resistance to soybean
cyst nematode races 2, 3 and 5 in soybean PI 90763, Theor.
Appl. Genet. 111 (2005) 965–971.
[66] E. Brucker, T. Niblack, F.J. Kopisch-Obuch, B.W. Dier, The
effect of rhg1 on reproduction of Heterodera glycines in the field
and greenhouse and associated effects on agronomic traits,
Crop Sci. 45 (2005) 1721–1727.
[67] S. Liu, P.K. Kandoth, N. Lakhssassi, J. Kang, V. Colantonio, R.
Heinz, G. Yeckel, Z. Zhou, S. Bekal, J. Dapprich, B. Rotter, S.
Cianzio, M.G. Mitchum, K. Meksem, The soybean GmSNAP18
gene underlies two types of resistance to soybean cyst
nematode, Nat. Commun. 8 (2017) 14822.
[68] S.M.J. Winter, B.J. Shelp, T.R. Anderson, T.W. Welacky, I.
Rajcan, QTL associated with horizontal resistance to soybean
cyst nematode in Glycine soja PI464925B, Theor. Appl. Genet.
114 (2007) 461–472.
[69] J. Zhang, Z. Wen, W. Li, Y. Zhang, L. Zhang, H. Dai, D. Wang, R.
Xu, Genome-wide association study for soybean cyst nema-
tode resistance in Chinese elite soybean cultivars, Mol. Breed.
37 (2017) 60.
[70] X. Zhao, W. Teng, Y. Li, D. Liu, G. Cao, D. Li, L. Qiu, H. Zheng, Y.
Han, W. Li, Loci and candidate genes conferring resistance to
soybean cyst nematode HG type 2.5.7, BMC Genomics 18
(2017) 462.
[71] D.T. Tran, C.J. Steketee, J.D. Boehm Jr., J. Noe, Z. Li, Genome-
wide association analysis pinpoints additional major geno-
mic regions conferring resistance to soybean cyst nematode
(Heterodera glycines Ichinohe), Front. Plant Sci. 10 (2019) 401.
[72] S. Liu, F. Ge, W. Huang, D.A. Lightfoot, D. Peng, Effective
identification of soybean candidate genes involved in resis-
tance to soybean cyst nematode via direct whole genome re-
sequencing of two segregating mutants, Theor. Appl. Genet.
132 (2019) 2677–2687.
[73] N. Yu, T.G. Lee, D.P. Rosa, M. Hudson, B.W. Diers, Impact of
Rhg1 copy number,type, and interaction with Rhg4 on
resistance to Heterodera glycines in soybean, Theor. Appl.
Genet. 129 (2016) 2403–2412.
[74] S. Kadam, T.D. Vuong, D. Qiu, C.G. Meinhardt, L. Song, R.
Deshmukh, G. Patil, J. Wan, B. Valliyodan, A.M. Scaboo,
Genomic-assisted phylogenetic analysis and marker devel-
opment for next generation soybeancyst nematode resis-
tance breeding, Plant Sci. 242 (2016) 342–350.
[75] G.B. Patil, N. Lakhssassi, J. Wan, L. Song, S.S. Kahil, S. Piya, T.
D. Vuong, H.J. Rice, Z. Zhou, H.T. Nguyen, V. Colantonio, T.
Hewezi, R.M. Stupar, A.O. Stec, M. Klepadlo, K. Meksem, B.
Valliyodan, Whole genome re-sequencing reveals the impact
of the interaction of copy number variants of the rhg-1 and
Rhg4 genes on broad-based resistance to soybean cyst
nematode, Plant Biotechnol. J. 17 (2019) 1595–1611.
[76] S. Liu, P.K. Kandoth, S.D. Warren, G. Yeckel, R. Heinz, J. Alden,
C. Yang, A. Jamai, T. El-Mellouki, P.S. Juvale, J. Hill, T.J. Baum,
S. Cianzio, S.A. Whitham, D. Korkin, M.G. Mitchum, K.
Meksem, A soybean cyst nematode resistance gene points to
a new mechanism of plant resistance to pathogens, Nature
492 (2012) 256–260.
903
[77] P.K. Kandoth, S. Liu, E. Prenger, A. Ludwig, N. Lakhssassi, R.
Heinz, Z. Zhou, A. Howland, J. Gunther, S. Eidson, A. Dhroso,
P. LaFayette, D. Tucker, S. Johnson, J. Anderson, A. Alaswad,
S.R. Cianzio, W.A. Parrott, D. Korkin, K. Meksem, M.G.
Mitchum, Systematic mutagenesis of serine
hydroxymethyltransferase reveals an essential role in nem-
atode resistance, Plant Physiol. 175 (2017) 1370–1380.
[78] D.E. Cook, A.M. Bayless, K. Wang, X. Guo, Q. Song, J. Jiang, A.F.
Bent, Distinct copy number, coding sequence, and locus
methylation patterns underlie Rhg1-mediated soybean resis-
tance to soybean cyst nematode, Plant Physiol. 165 (2014)
630–647.
[79] N. Lakhssassi, S. Liu, S. Bekal, Z. Zhou, V. Colantonio, K.
Lambert, A. Barakat, K. Meksem, Characterization of the
soluble NSF attachment protein gene family identifies two
members involved in additive resistance to a plant pathogen,
Sci. Rep. 7 (2017) 45226.
[80] J. Lin, X. Zhuang, M. Mazarei, P.R. Arelli, W. Liu, N. Zhao, F.
Chen, V.R. Pantalone, C.N. Stewart, J.J. Zhu, Overexpression of
a soybean salicylic acid methyltransferase gene confers
resistance to soybean cyst nematode, Plant Biotechnol. J. 11
(2013) 1135–1145.
[81] B.F. Matthews, H. Beard, E. Brewer, S. Kabir, M.H. MacDonald,
R.M. Youssef, Arabidopsis genes, AtNPR1, AtTGA2 and AtPR-5,
confer partial resistance to soybean cyst nematode
(Heterodera glycines) when overexpressed in transgenic soy-
bean roots, BMC Plant Biol. 14 (2014) 96.
[82] R.M. Youssef, M.H. MacDonald, E.P. Brewer, G.R. Bauchan, K.
H. Kim, B.F. Matthews, Ectopic expression of AtPAD4
broadens resistance of soybean to soybean cyst and root-
knot nematodes, BMC Plant Biol. 13 (2013) 67.
[83] Y. Yang, Y. Zhou, Y. Chi, B. Fan, Z. Chen, Characterization of
soybean WRKYgene family and identification of soybean
WRKYgenes that promote resistance to soybean cyst nema-
tode, Sci. Rep. 7 (2017) 17804.
[84] R. Azpiroz-Leehan, K.A. Feldmann, T-DNA insertion muta-
genesis in Arabidopsis: going back and forth, Trends Genet. 13
(1997) 152–156.
[85] S. Henikoff, TILLING. Traditional mutagenesis meets func-
tional genomics, Plant Physiol. 135 (2004) 630–636.
[86] K. McGinnis, V. Chandler, K. Cone, H. Kaeppler, S. Kaeppler, A.
Kerschen, C. Pikaard, E. Richards, L. Sidorenko, T. Smith, N.
Springer, T. Wulan, Transgene-induced RNA interference as a
tool for plant functional genomics, Methods Enzymol. 392
(2005) 1–24.
[87] C. Zhang, C. Yang, S.A. Whitham, J.H. Hill, Development and
use of an efficient DNA-based viral gene silencing vector for
soybean, Mol. Plant-Microbe Interact. 22 (2009) 123–131.
[88] C. Zhang, J.D. Bradshaw, S.A. Whitham, J.H. Hill, The
development of an efficient multipurpose bean pod mottle
virus viral vector set for foreign gene expression and RNA
silencing, Plant Physiol. 153 (2010) 52–65.
[89] A.K. Pandey, C. Yang, C. Zhang, M.A. Graham, H.D. Horstman,
Y. Lee, O.A. Zabotina, J.H. Hill, K.F. Pedley, S.A. Whitham,
Functional analysis of the asian soybean rust resistance
pathway mediated by Rpp2, Mol. Plant-Microbe Interact. 24
(2011) 194–206.
[90] X. Wang, A. Replogle, E.L. Davis, M.G. Mitchum, The tobacco
Cel7 gene promoter is auxin-responsive and locally induced
in nematode feeding sites of heterologous plants, Mol. Plant
Pathol. 8 (2007) 423–436.
[91] H. Zhang, S. Kjemtrup-Lovelace, C. Li, Y. Luo, L.P. Chen, B.H.
Song, Comparative RNA-seq analysis uncovers a complex
regulatory network for soybean cyst nematode resistance in
wild soybean (Glycine soja), Sci. Rep. 7 (2017) 9699.
[92] A.M. Bayless, J.M. Smith, J. Song, P.H. McMinn, A. Teillet, B.K.
August, A.F. Bent, Disease resistance through impairment of
α-SNAP–NSF interaction and vesicular trafficking by soybean
Rhg1, Proc. Natl. Acad. Sci. U. S. A. 113 (2016) E7375–E7382.
904 TH E CR OP J OUR NA L 8 ( 2 0 20 ) 89 2 –9 0 4
[93] A.M. Bayless, R.W. Zapotocny, D.J. Grunwald, K.K. Amundson,
B.W. Diers, A.F. Bent, An atypical N-ethylmaleimide sensitive
factor enables the viability of nematode-resistant Rhg1
soybeans, Proc. Natl. Acad. Sci. U. S. A. 115 (2018)
E4512–E4521.
[94] W. Guo, F. Zhang, A. Bao, Q. You, Z. Li, J. Chen, Y. Cheng, W.
Zhao, X. Shen, X. Zhou, Y. Jiao, The soybean Rhg1 amino acid
transporter gene alters glutamate homeostasis and jasmonic
acid-induced resistance to soybean cyst nematode, Mol. Plant
Pathol. 20 (2019) 270–286.
[95] Z. Shi, S. Liu, J. Noe, P. Arelli, K. Meksem, Z. Li, SNP
identification and marker assay development for high-
throughput selection of soybean cyst nematode resistance,
BMC Genomics 16 (2015) 314.
[96] Y. Tian, B. Liu, X. Sha, J.C. Reib, R. Guan, Y. Li, L. Qiu, Deep
genotyping of the gene GmSNAP facilitates pyramiding
resistance to cyst nematode in soybean, Crop J. 7 (2019)
677–684.
[97] K. Zhang, N. Raboanatahiry, B. Zhu, M. Li, Progress in genome
editing technology and its application in plants, Front. Plant
Sci. 8 (2017) 177.