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Crop Protection 77 (2015) 74e86

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Advancements in molecular marker development and their

applications in the management of biotic stresses in peanuts
Gyan P. Mishra*, T. Radhakrishnan, Abhay Kumar, P.P. Thirumalaisamy, Narendra Kumar,
Tejas C. Bosamia, Bhagwat Nawade, Jentilal R. Dobaria
Directorate of Groundnut Research, Post Box No. 05, Junagadh 362 001, Gujarat, India

a r t i c l e i n f o

a b s t r a c t

Article history:
Received 31 March 2015
Received in revised form
17 July 2015
Accepted 20 July 2015
Available online xxx

Peanut is grown extensively in different parts of world, where various biotic and abiotic factors limit its
productivity and quality. The major fungal biotic constraints to peanut production include rust (Puccinia
arachidis Speg.), stem-rot (Sclerotium rolfsii), collar-rot (Aspergillus niger Van Teighem), aa-root (Aspergillus avus), and late leaf spot (Phaeoisariopsis personata Ber. and M A Curtis), while viral disease constraints are peanut bud necrosis disease (PBND) caused by peanut bud necrosis virus (PBNV) and peanut
stem necrosis disease (PSND) caused by tobacco streak virus (TSV). Since, only a few sources of resistance
are available in cultivated peanut for some diseases, which has resulted in the limited success of conventional breeding programmes on disease resistance. Moreover, even marker assisted breeding in
peanut is in the nascent stage and identication of some major quantitative trait loci (QTLs) for a few
fungal disease resitance genes has only recently been reported. Substantial efforts are underway to
develop PCR-based markers for the construction of high-density genetic linkage maps. This will enable
the breeders to effectively pyramid various biotic stress resistance genes into different agronomically
superior breeding populations, in a much shorter time. It is expected that the availability of various costeffective genomic resources (SNPs, whole genome sequencing, KASPar, GBS etc.) and more effective
mapping populations (NAM, MAGIC etc.) in the coming years will accelerate the mapping of complex
traits in peanut. This review provides an overview of the current developments and future prospects of
molecular marker development and their applications for improving biotic-stress resistance in peanut
2015 Elsevier Ltd. All rights reserved.

Diseases and pests
Marker assisted selection

1. Introduction
Peanuts (Arachis hypogaea L.), also known as groundnuts, are
grown in more than 120 countries with different agro-climatic
zones between latitudes 40  S and 40  N on approximately
21e24 M ha of land annually (Sarkar et al., 2014). It is cultivated
predominantly by small farms under low input conditions and
ranks third and fourth as a source of protein and edible oil,
respectively (Bhauso et al., 2014). Several biotic stresses are known
to limit peanut productivity, and their severity and extent of distribution vary with the cropping system, growing season, and region. Among biotic stresses, several diseases including rust
(Puccinia arachidis Speg.), early leaf spot (ELS, Cercospora arachidicola), late leaf spot (LLS, Phaeoisariopsis personata Ber. and M A

* Corresponding author.
E-mail address: (G.P. Mishra).
0261-2194/ 2015 Elsevier Ltd. All rights reserved.

Curtis), and aatoxin contamination by Aspergillus avus and

Aspergillus parasiticus are global constraints against peanut production (Subrahmanyam et al., 1984; Waliyar, 1991). Rust, stem-rot
(Sclerotium rolfsii), collar-rot (Aspergillus niger Van Teighem), and
leaf spots are also quite serious and together may cause the loss of
50e60% of pod yield in India (Dwivedi et al., 2003; Subrahmanyam
et al., 1985). In the peanut growing regions, high yielding, welladapted cultivars contain multiple resistances to biotic stresses
that can provide enhanced and sustainable peanut production
(Dwivedi et al., 2003).
The world's largest peanut germplasm collection with more
than 15,000 accessions is housed at the International Crops
Research Institute for the Semi-Arid Tropics (ICRISAT) in India
(Gowda et al., 2013). These accessions have many differences in
their vegetative, reproductive, physiological, and biochemical traits.
The global Arachis gene pool possesses the source of resistance to
many biotic stresses, including rust, ELS, LLS, Groundnut Rosette
Disease [GRD, caused by a complex of three agents: groundnut

G.P. Mishra et al. / Crop Protection 77 (2015) 74e86

rosette virus (GRV), its satellite RNA (sat RNA), and a groundnut
rosette assistor virus (GRAV)], Peanut Bud Necrosis Virus (PBND), A.
avus induced aatoxin contamination, bacterial wilt (Ralstonia
solanacearum), leafminer (Aproaerema modicella), Spodoptera, jassids (Empoasca kerri Pruthi), thrips (Frankliniella schultzei Trybom)
and termites (Odontotermes sp.) (Rao et al., 2002; Basu and Singh,
2004; Amin et al., 1985; Rao et al., 2014).
Since the 1960s, interspecic hybridization has received much
attention in peanuts because several wild Arachis species show a
very high level of resistance to many biotic stresses, such as rust,
ELS, LLS, and stem rot (Holbrook and Stalker, 2003; Singh et al.,
1984). However, success in transferring the resistance to cultivated peanuts has been limited mainly because of cross compatibility barriers, linkage drag, and long periods required for
developing stable tetraploid interspecic derivatives (Wynne et al.,
1991; Singh et al., 1997). Moreover, the partial and polygenic nature
of biotic stresses makes the identication of resistant and susceptible lines very tedious using conventional screening techniques
(Leal-Bertioli et al., 2009). Because of the frequent occurrence of
multiple diseases, peanut yields are often signicantly lower than
their potential (Holbrook and Stalker, 2003). In the future, cultivars
with multiple disease and pest resistances will be needed, which
appears to be a very difcult endeavour for this crop species (Basu
and Singh, 2004).
Marker-assisted selection (MAS) offers great promise for
improving the efciency of conventional plant breeding (Janila
et al., 2013), including the potential to pyramid resistance genes
in peanuts (Mishra et al., 2009; Varshney et al., 2014; Pandey et al.,
2012). For any molecular breeding program, assessment of genetic
diversity and development of genetic linkage maps are two very
important steps (Dwivedi et al., 2003). Abundant polymorphisms in
wild Arachis species have been observed, but progress in the molecular breeding of cultivated peanuts is greatly constrained due to
the low level of detectable molecular genetic variation (Mondal
et al., 2005; Herselman, 2003; Raina et al., 2001; He and Prakash,
2001). Therefore, the use of more robust assays such as single
nucleotide polymorphisms (SNPs), competitive allele-specic PCR
(KASPar) and genotyping by sequencing (GBS) approaches are
needed. However, cost-effective SNP genotyping platforms are not
readily available for tetraploid peanuts, but a large number of
robust markers such as SSRs and SNPs (including KASPar) would be
valuable. SSRs are still considered the marker of choice in peanuts
(Pandey et al., 2012), and a wide range of genotypes have been used
for mapping (Table 1) of many important biotic and abiotic traits
using SSR markers (Table 2).
Despite being an important oilseed crop, very limited work in
the area of molecular genetics and breeding of peanuts has been
performed (Dwivedi et al., 2002; Raina et al., 2001). However, over
the last decade, signicant developments have been made in the
use of various molecular approaches for biotic stress management
in peanuts, and new efforts such as functional genomics are likely
to play key roles in the future (Wang et al., 2011; Varshney et al.,
2014; Gajjar et al., 2014). Recently, Kanyika et al. (2015) has


identied 376 polymorphic SSR markers in 16 African groundnut

cultivars with a wide range of disease resistance. These identied
markers can be used to improve the efciency of introgression of
resistance to multiple important biotic constraints into farmerpreferred varieties of Sub-Saharan Africa. In this review, we made
an attempt to capture the recent updates in molecular marker
development and their applications in the management of various
biotic stresses in peanut.
2. Markers associated with rust and LLS resistance gene(s)
Rust and leaf spots are economically very important foliar fungal
diseases of peanuts that often occur together and not only reduce
the yield but also adversely affect the fodder and seed quality
(Subrahmanyam et al., 1985; Waliyar, 1991). Despite the economic
importance of rust and LLS, very limited work has been carried out
on hostefungus interaction, fungal genetic diversity, and physiological specialization (Mondal and Badigannavar, 2015). Several
studies have emphasized the application of different types of molecular markers, construction of peanut linkage maps, or tagging of
important agronomic traits, such as disease resistance (Wang et al.,
2011; Gajjar et al., 2014). Recently, many DNA markers have been
found to be putatively linked to rust and LLS resistance genes
(Mondal et al., 2012a; Khedikar et al., 2010; Shoba et al., 2012; Sujay
et al., 2012) (Table 2), a few of which have been validated and used
in the breeding programme (Sujay et al., 2012; Gajjar et al., 2014;
Varshney et al., 2014). Location of markers on the various linkage
groups in Table 2, is derived after doing intensive meta-analysis of
all the published literature, including the most comprehensive and
consensus linkage maps available in peanut.
Validation of other linked markers will accelerate the process of
introgression of disease resistance into preferred peanut genotypes
(Sujay et al., 2012; Gajjar et al., 2014). Near isogenic lines (NILs)
developed for rust resistance were thoroughly screened with both
foreground and background molecular markers (Yeri et al., 2014).
For the identication of LLS resistance, Luo et al. (2005b) identied
genes in the resistant genotype that were more highly expressed
than in the susceptible genotype (in response to Cercosporidium
personatum infection) by microarray analysis and validated them by
real-time PCR. In a recombinant inbred line (RIL) population (VG
9514  TAG 24), two transposable element (TE) markers, TE 360
and TE 498, were found to be associated with the rust resistance
gene. These two markers need further validation before they could
be effectively applied for MAS of rust resistance in different backgrounds (Mondal et al., 2013).
3. Soil-borne fungal diseases and associated markers
(Collar rot, Stem rot, Aspergillus spp., Bacterial wilt and Sclerotinia blight)
Among soil-borne diseases, collar rot (A. niger) and stem-rot (S.
rolfsii) are very important (Farr et al., 1989; Kolte, 1984). The search
for peanut cultivars resistant to S. rolfsii originates all the way back

Table 1
List of a few genotypes, used for mapping of various resistance gene(s) (Dwivedi et al., 2003; Shoba et al., 2012;
Sujay et al., 2012).


Early leaf spot

Late leaf spot
Rosette disease
Bacterial wilt
Aatoxin production

ICG 405, ICG 1705, ICG 6284, TMV 2

GPBD 4, ICGV 99001, ICGV 99004, COG 0437, TAG 24, TMV 2
GPBD 4, ICGV 99003, ICGV 99005, TG 26, TMV 2
ICG 6323, ICG 6466, ICG 11044, JL 24
ICG 7893, ICG 15222, and Chico
U 4-7-5, 55-437, J 11


G.P. Mishra et al. / Crop Protection 77 (2015) 74e86

Table 2
SSR markers and its linkage group known to be associated to the rust and/or LLS resistance gene(s).
S. No.


Linkage group






b07and a07

Rust and LLS




ICGV 99003  TMV 2

TMV 2  COG 0437 (F2)
and ICGV 99005  TMV 2
ICGV 99005  TMV 2
ICGV 99005  TMV 2 and 22 genotypes

Rust and LLS



ICGV 99005  TMV 2 and 22 genotypes

Rust and LLS



a03 and b03
a03 and b03
b10 and a09
a06 and b04

22 genotypes
22 genotypes
22 genotypes
22 genotypes
22 genotypes
TAG 24 xGPBD 4
TMV 2  COG 0437
TMV 2  COG 0437
TMV 2  COG 0437
TMV 2  COG 0437
TMV 2  COG 0437
TAG 24  GPBD 4
TG 26 xGPBD 4
TG 26 xGPBD 4
TG 26 xGPBD 4
20 genotypes
20 genotypes

Rust and LLS

Rust resistance
Rust and LLS


seq4A05 and


RILs from VG 9514  TAG 24

Varma et al., 2005

Shoba et al., 2012; Varma et al., 2005;
Shirasawa et al., 2013
Varma et al., 2005
Varma et al., 2005; Mace et al., 2006;
Shirasawa et al., 2013
Varma et al., 2005; Mace et al., 2006;
Shirasawa et al., 2013
Mace et al., 2006; Shirasawa et al., 2013
Mace et al., 2006
Mace et al., 2006
Mace et al., 2006
Mace et al., 2006
Khedikar et al., 2010
Shoba et al., 2012
Shoba et al., 2012; Shirasawa et al., 2013
Shoba et al., 2012; Shirasawa et al., 2013
Shoba et al., 2012
Shoba et al., 2012
Sujay et al., 2012; Shirasawa et al., 2013
Sujay et al., 2012
Sujay et al., 2012
Sujay et al., 2012
Mondal and Badigannavar, 2010
Mondal and Badigannavar, 2010;
Shirasawa et al., 2013
Mondal et al., 2012a



Subscript numerical values are for linked band size.

to 1918 (McClintock, 1918), but a high degree of resistance is yet to

be found. Recently, Thirumalaisamy et al. (2014) has reported some
sources for stem rot resistance in peanut, but the genetics of
resistance and markers linked with the resistance gene(s) are still
lacking. Thus, there is an urgent need to nd molecular markers
linked with the stem rot resistance QTLs, for its use in markerassisted breeding programme.
Very few published reports pertaining to the molecular characterization of S. rolfsii are available. Variations in the internal
transcribed spacer (ITS) regions have revealed 12 sub-specic
groupings, some of which correlated with their mycelial compatibility groups (MCGs) (Harlton et al., 1995). Punja and Sun (1997)
detected 68 MCGs while comparing 128 isolates of S. rolfsii from
36 host species collected from 23 geographic regions. Cilliers et al.
(2000) found Amplied Fragment Length Polymorphism (AFLP) as
a suitable technique for the assessment of genetic variability between isolates and MCGs of S. rolfsii. Genetic variability among the
virulent isolates of S. rolfsii was studied using molecular techniques,
such as RAPD, ITS-PCR and RFLP (Prasad et al., 2010). Several molecular markers associated with pod rot resistance and susceptibility in mutants and Giza5 peanut genotype were reported by
Azzam et al. (2007) using RAPD markers, although these markers
still need to be validated.
A. avus and A. parasiticus infect peanut seeds and produce aflatoxins, which are harmful to both domestic animals and humans
(Waliyar et al., 2015; Singh et al., 2015a,b; Liu et al., 2014). The
progress in peanut breeding for resistance to aatoxin is slow due
to the lack of a cost-effective method for resistance identication in
breeding materials or segregating progeny (Lei et al., 2006). Barros
et al. (2007) and Singh et al. (2015a,b) analysed Aspergillus isolates
collected from peanut elds in Argentina and India using AFLP,
where different levels of polymorphism in different groups of isolates were recorded. Guo et al. (2008) has identified up-regulation
of 8 resistance-related genes for Aspergillus infection. Lei et al.
(2006) reported an AFLP (E45/M53-440) converted SCAR marker

(AFs-412) to be closely linked to resistance of A. avus infection.

Screening of isolates using gene-specic PCR was found to be quite
effective for the identication of gene defects in A. avus, which
could be used as bio-control agents in peanut growing areas (Dodia
et al., 2014). Moreover, to date, the genetic basis of S. rolfsi and
A. avus stress resistance traits in peanuts is not fully understood.
Therefore, extensive efforts are required to rst identify the resistance sources and then to nd the markers associated with the
resistance genes/QTLs for their future use in marker assisted
breeding (Mishra et al., 2014).
Bacterial wilt (R. solanacearum) is an important constraint to
peanut production in several Asian and African countries, and
planting of bacterial-wilt resistant cultivars is the most feasible
method for disease control. Genetic diversity analysis using SSR and
AFLP markers among selected peanut genotypes identied certain
genotypes and primer combinations for developing mapping
populations and breeding for high yield, resistant cultivars (Jiang
et al., 2007a). In an attempt to understand the molecular mechanism of bacterial wilt resistance, 25 differentially expressed
candidate genes were identied by studying the differences in gene
expression between inoculated and control seeds. Conrmation of
the functions of these genes needs to be validated through transgenic studies (Ding et al., 2012). For Sclerotinia blight (Sclerotinia
minor) resistance, Kelly et al. (2010) characterized 96 US peanut
mini-core collections using a resistance-associated SSR marker, and
39 accessions as new potential sources of resistance were
4. Molecular studies on resistance to viral diseases
(Groundnut rosette disease, PBND and PSND)
Groundnut rosette disease is the most destructive viral disease
of peanuts causing serious yield losses. Single recessive gene control for resistance to the aphid vector (Aphis craccivora) was
observed in the breeding line ICG 12991, which was mapped 3.9 cM

G.P. Mishra et al. / Crop Protection 77 (2015) 74e86

from an AFLP marker on LG 01 (Herselman et al., 2004). Peanut bud

necrosis disease (PBND) caused by peanut bud necrosis virus
(PBNV) and vectored by Thrips (Vijayalakshmi et al., 1995) is a
major viral disease of peanuts. In 2000, a new threat to peanuts
emerged in the form of a viral disease named peanut stem necrosis
disease (PSND) caused by the peanut stem necrosis virus (PSNV),
which results in lethal necrosis (Rao et al., 2000). Tobacco streak
virus (TSV) was found to be associated with the disease (Reddy
et al., 2002). Despite several years of effort, a conrmed source of
genetic resistance/tolerance to TSV has not been identied in the
gene pool of cultivated peanuts. However, genetically engineered
resistance has been actively investigated in recent years as an
alternative to cope with this type of situation (Mehta et al., 2013).
Kamdar et al. (2014) studied 115 resistant and one susceptible line
to PBND using SSR, but no clear differentiation was observed.
Similarly, SSR-based diversity analysis among 15 peanut genotypes
(resistant and susceptible to PBND) grouped together based on
their origin rather than PBND resistance (Srinivasaraghavan et al.,
2012). In the future, the availability of more cost effective
genomic resources, such as SNPs and whole genome sequencing,
will hasten complex trait mapping efforts (especially for viral diseases) in this crop (Pandey et al., 2012).
5. Molecular studies on nematode resistance
In many peanut production areas across the world, the peanut
root-knot nematode causes signicant economic losses (Holbrook
and Stalker, 2003). Many sources of resistance were identied in
the germplasm, and lot of molecular work has been performed to
nd the linked gene(s)/QTLs (Mishra et al., 2009). For the root-knot
nematode (Meloidogyne arenaria), two dominant genes viz. Mae
(restricted egg number) and Mag (restricted galling) conditioning
resistance were identied, and a RAPD marker (Z3/265) was found
to be linked to these genes (Garcia et al., 1996).
Different types of DNA markers associated with root-knot
nematode resistance were also identied (Burow et al., 1996;
Garcia et al., 1996; Choi et al., 1999; Church et al., 2000; Wang
et al., 2008a) and are currently being used for the development of
resistant peanut cultivars. A DNA marker with 6% recombination
frequency to the resistance gene has been developed to screen the
segregating populations for nematode resistance (Chu et al., 2007).
The RFLP marker R2430E was found to link to a locus for resistance
of the peanut root-knot nematode M. arenaria (Neal) Chitwood race
1 (Ppolo et al., 2014). Genes controlling the resistance to nematodes were introgressed through interspecic hybridization and
resulted in the release of the rst nematode-resistant peanut
cultivar COAN (Simpson and Starr, 2001). Other works on the
development of nematode-resistant peanut cultivars are presented
in other sections of this review.
6. Single nucleotide polymorphism (SNP) technologies for
biotic stresses
Recent developments in SNP technologies for peanuts have
indicated that, in the near future, additional options may be
available for the rapid identication of large numbers of polymorphic markers in peanuts (Kanazin et al., 2002; Khera et al.,
2013). A single base pair extension (SBE) was found to be an efcient method for high-throughput SNP mapping in peanuts, and
ve candidate genes for resistance were identied on the genetic
map (Alves et al., 2008). Recently, Khera et al. (2013) used a set of 96
informative SNPs to develop competitive allele-specic PCR (KASPar) assays in peanuts, designated as GKAMs (Groundnut KASPar
Assay Markers), through which 90 GKAMs were validated for
different biotic stresses. A comprehensive list of the various


markers associated with different diseases and pests is given in

Table 3.
7. Advancements in linkage mapping
Peanut is a self-pollinated allotetraploid (2n 4x 40, AABB)
crop having ten basic chromosomes, harboring about 2813 Mb of
DNA content (Arumuganatham, 1991). Peanut genome is nearly 20
times larger than that of Arabidopsis thaliana and is somewhat
similar to Gossypium hirsutum and Zea mays. Variation in genome
size among accessions of A. hypogaea (2n 4x 40) and Arachis
duranensis (2n 2x 20) (Singh et al., 1996) and between
A. hypogaea and A. monticola (Temsch and Greilhuber, 2000) has
also been reported. The rst RFLP-based genetic linkage map of
peanuts was constructed using an F2 population (Halward et al.,
1993). A list of a few classical and the most recent genetic linkage
maps, including consensus maps, are given in Table 4.
Compared to that of many other legume crops, the development
of molecular markers in cultivated peanuts has progressed at a
relatively slow pace. Although many markers have been developed
in both wild and cultivated peanuts, the genetic linkage map is not
yet saturated. There is a need to saturate the linkage map to provide
sufcient markers for marker-assisted breeding (Dwivedi et al.,
2003). Constant increases in peanut marker identities and linkage
groups together with the availability of genome sequence data in
the recent past have opened up the possibility of integrating new
markers to some LGs and identifying closely linked markers
(Mondal et al., 2012a). Efforts are currently underway for applying
genomics to peanut biotic stress resistance breeding through
mapping and MAS for different biotic stresses (Pandey et al., 2012).
8. QTL analysis for biotic stress resistance
In peanuts, many markers were recently found to be associated
with QTLs for various biotic stresses, namely, rust and LLS (Sujay
et al., 2012; Mondal and Badigannavar, 2010), Cylindrocladium
black-rot and ELS (Stalker and Mozingo, 2001), nematodes (Chu
et al., 2007; Nagy et al., 2010), tomato spotted wilt virus (TSWV)
(Qin et al., 2012), aphid vector of GRD (Herselman et al., 2004). The
majority of the identied QTLs are not major and account for less
than 10% of the phenotypic variation explained (PVE). Major QTLs
identied for rust and LLS in the germplasm source (Khedikar et al.,
2010; Sujay et al., 2012) and for nematode resistance (Nagy et al.,
2010; Simpson, 2001) were of a wild species origin.
In peanuts, candidate genome regions controlling disease
resistance were identied by placing the 34 sequence-conrmed
candidate disease resistance genes and 05 QTLs against LLS on
the genetic map of the A-genome of Arachis. Upon grouping, these
genes and QTLs were found to be present on the upper and lower
regions of LG 04 and 02, respectively, indicating the prominence of
these regions for imparting disease resistance (Leal-Bertioli et al.,
2009). QTL analysis in a Tifrunner  GT-C20-derived mapping
population has identied 54 QTLs in the F2 map, including 02 for
thrips, 15 for TSWV, and 37 for LS. However, in the F5 map, 23 QTLs
could be identied, including 01 for thrips, 09 for TSWV, and 13 for
LS. This is the rst QTL study reporting novel QTLs for thrips, TSWV,
and LS, which needs renement in the future (Wang et al., 2013,
2014). Using RIL population (VG 9514  TAG 24), 13 main and 31
epistatic QTLs for total developmental period (TDP) were detected
for bruchid resistance. Two years screening identied two common
main QTLs, qTDP-b08 for TDP (57e82% PVE) and qAE2010/11-a02
for adult emergence (13e21% PVE) (Mondal et al., 2014).
Shoba et al. (2013) reported Ah 4-26 and PM 384 as the closest
markers for QTLs of 100 kernel weight and LLS severity, respectively. Because PMc 588 and Ah 4-26 are the anking markers for


G.P. Mishra et al. / Crop Protection 77 (2015) 74e86

Table 3
List of different markers associated with various biotic stresses.

Disease/Causal organism



Bacterial wilt
Rosette disease
A. avus
A. avus
Bacterial wilt
Sclerotinia blight
Rust and LLS
Rust and LLS
A. avus
A. avus
Rust and Leaf spots

Garcia et al., 1996; Burow et al., 1996

Choi et al., 1999; Church et al., 2000
Jiang et al., 2003; Ren et al., 2008
Herselman et al., 2004
Lei et al., 2005
Lei et al., 2006
Azzam et al., 2007
Chu et al., 2007
Mondal et al., 2007
Jiang et al., 2007a; Jiang et al., 2007b
Hou et al., 2007
Xia et al., 2007
Kelly et al., 2010
Mondal et al., 2008
Wang et al., 2008a
Mondal et al., 2009
Hong et al., 2009
Guo et al., 2011
Mondal et al., 2012b
Khera et al., 2013
Mondal et al., 2013

TE: Transposable Element; AS-PCR: Allele Specic-PCR.

Table 4
List some classical and latest genetic linkage maps.


Map distance (cM)


Back Cross
Arachis duranensis
02 RILs
02 RILs
10 RILs, 01 BC
03 RILs

1724 marker loci
324 marker loci
225 SSR
897 marker loci
3693 marker loci


Halward et al., 1993

Burow et al., 2001
Nagy et al., 2012
Qin et al., 2012
Sujay et al., 2012
Gautami et al., 2012
Shirasawa et al., 2013

PM 384, they can therefore be used for marker-assisted breeding of

LLS resistance. A genetic map derived from a SunOleic
97R  NC94022 cross (Qin et al., 2012) was developed, and multiple
phenotyping data have identied a total of 155 QTLs, of which, 01
and 03 major QTLs for TSWV and LLS resistance, respectively, were
identied (Guo et al., 2013).
A QTL region with 82.62% phenotypic variation for rust resistance (Sujay et al., 2012) was validated and introgressed in some
susceptible varieties using a marker-assisted backcrossing (MABC)
approach by employing four markers, namely IPAHM103, GM2079,
GM1536 and GM2301 (Varshney et al., 2014). It is expected that
multi-location testing of the promising introgressed lines will
result in the identication of entries for its possible release as varieties with enhanced disease resistance. This result emphasized
the utility of using markers for QTL selection through MAS for
improving the rust resistance of any elite varieties (Varshney et al.,
To date, neither background nor genome-wide selection has
been performed in peanuts, and this analysis must await the
development of high-throughput, economical assays for a large
number of markers (Holbrook et al., 2011). Details of some QTLs
that have been identied to be associated with biotic stress-related
traits in peanuts are given in Table 5. Identication of major QTLs
for various biotic stress resistances in peanuts will enable efcient
MABC for the development of resistant cultivars. Recently, 39
marker trait associations (MTAs) for A. avus, ELS, LLS, and GRD
were identied using genome wide association studies (GWAS). Of
these MTAs, 01 was for Aspergillus (24.69% PV), 31 for GRD
(10.25e39.29% PV), 06 for ELS (9.18e10.99% PV), and 01 for LLS
(18.10% PV). It is expected that upon validation these MTAs may be

deployed for marker-assisted improvement of peanut genotypes

(Pandey et al., 2014).
9. Biotic stresses and gene expression studies
(Transcriptome analysis, microRNAs, epigenetic regulation,
In cultivated peanuts, which do not have whole genome
sequence information available yet, transcriptome data are an
alternative source of information, and ESTs can be used to identify
candidate genes (Pandey et al., 2012). During recent years, a wealth
of genomic data has been generated in peanut by high throughput
transcriptome sequencing (Chopra et al., 2014, 2015). However, the
available transcriptome sequences are not complete; many have
low N50 values, ranging from 500 to 750 bp (Guimar~
aes et al., 2012;
Chopra et al., 2014). On the basis of gene annotations, Bosamia et al.
(2015) has identied 2784 SSR containing sequences, of which,
2027 (72.81%) were annotated and assigned in 4124 gene ontology
terms and 31.91% sequences were found to be associated with
response to stimulus encompassing biotic as well as abiotic
Transcriptome analysis of cDNA collections from Arachis stenosperma infected with C. personatum revealed a number of transcription factor families and defence-related genes. Additionally,
the expression of ve A. stenosperma resistance gene analogues
(RGAs) and four retrotransposon (FIDEL-related) sequences were
also analysed by qRT-PCR, which was used to design EST-SSRs of
~es et al., 2012).
which 214 were shown to be polymorphic (Guimara
Bertioli et al. (2003) generated 78 RGAs based on the nucleotidebinding site (NBS) regions from A. hypogaea and other wild

G.P. Mishra et al. / Crop Protection 77 (2015) 74e86


Table 5
List of QTLs identified for various biotic-stress related traits in peanut.

No of QTLs identied

Phenotypic variance explained (PVE) %





Leaf rust
Aspergillus avus
Bruchid resistance
Aphid vector of rosette disease
In F2 map
Leaf spot
In F5 map
Leaf spot

54 (Total)
23 (Total)


Khedikar et al., 2010;

Sujay et al., 2012
Khedikar et al., 2010; Sujay et al., 2012
Liang et al., 2009
Mondal et al., 2014
Herselman et al., 2004
Wang et al., 2013, 2014

relatives. A collection of peanut nucleotide binding site leucine-rich

repeat (NBSeLRR) resistance gene candidates (RGCs) were identied by mining the GenBank databases (Radwan et al., 2010).
Further, Yuksel et al. (2005) also isolated 234 RGAs based on the
primer sequence information from NBS-LRR and LRR-Toll-like
motif (LRR-TM) classes. On the similar note, Proite et al. (2007)
identied 35 putative non-redundant RGAs and 26 pathogenesis
related ESTs from an accession of A. stenosperma, resistant to
different foliar diseases.
At present, a total of 281,754 ESTs are available for Arachis spp.
on the NCBI website (, accessed January 24,
2015), of which the contribution of each species is as follows: A.
hypogaea (205,442), A. duranensis (35,291), Aipaensis ipaensis
(32,787), A. stenosperma (6264), Alberta magna (750), A. hypogaea
subsp. fastigiata (745), A. appressipila (400) and A. diogoi (75). Many
of these have been generated for the identication of biotic stress
resistance genes (e.g., 21,777 ESTs were identied from developing
seeds against Aspergillus infection (Guo et al., 2008), and 8000 ESTs
from the root tissues of A. stenosperma resistant to M. arenaria
(Proite et al., 2007). Guo et al. (2009) identied 17,376 ESTs from the
leaves of TSWV and leaf spot resistant and susceptible cultivars, of
which 5717 had unknown functions. In response to A. avus
infection under drought stress, 29 protein spots showing differential expression between resistant and susceptible cultivars were
identied and further validated using RT-PCR analysis (Wang et al.,
2010). In addition, some defense-related transcripts, such as putative oxalate oxidase (EU024476) and NBS-LRR domains, were also
Large numbers of available ESTs in the public databases were
used for EST-SSR marker development. From 16424 unigenes, using
MISA (MIcroSAtellite identication tool) search, a total of 2456
novel EST-SSR primer pairs were designed; of which 366 unigenes,
having relevance to various stresses and other functions were PCR
validated using a set of 11 diverse peanut genotypes (both resistant
and susceptible to various diseases). Of these, 340 primer pairs
yielded clear and scorable PCR products and 39 primer pairs
exhibited polymorphisms which are of potential use for the resistance breeding programme (Bosamia et al., 2015). Out of 411 sorghum EST-SSR (SbEST-SSR) markers tested in peanuts, 39% could be
successfully amplied, of which 14% showed polymorphism among
resistant and susceptible cultivars for rust and LLS diseases (Savadi
et al., 2012). Out of 259 EST-SSR markers, which were developed
using A. hypogaea ESTs (NCBI database), SSR_GO340445 and
SSR_HO115759 were found to be closely linked to the rust resistance gene (Mondal et al., 2012b). Chen et al. (2008a, 2008b, 2011)

Leal-Bertioli et al., 2009

Guo et al., 2013

identified and cloned the resistance gene to TSWV and characterized two peanut oxalate oxidase genes.
In response to A. avus infection, many genes were found to be
up-regulated in peanuts, of which PR-10 and pathogenesis-induced
protein (PIP) genes were cloned (Xie et al., 2009a,b). Resveratrol
imparts resistance in plants against both UV radiation and fungal
infection; the gene that synthesizes resveratrol synthase has been
cloned from peanuts, and expression analysis indicates that it is
expressed in the root (Zhou et al., 2008; Han et al., 2010). Lipid
transfer proteins (LTP), which were reported to be involved in
disease resistance in plants, have also been cloned from peanuts
(Zhao et al., 2009).
Transcriptome analysis of the migratory plant parasitic nematode Ditylenchus africanus (peanut pod nematode) from mixed
stages revealed the involvement of putative proteins in developmental and reproductive processes, as well as the role of unigenes
in oxidative stress and anhydrobiosis (Haegeman et al., 2009). Eight
differentially expressed genes were identified in A. stenosperma
roots in response to M. arenaria infection using in silico ESTs and
~es et al., 2010, 2011).
microarray analysis (Guimara
From non-protein coding genes, microRNAs were transcribed by
RNA polymerase II (Kim, 2005), and understanding of its functional
and regulatory roles could open new windows for crop improvement including disease tolerance. Zhao et al. (2010) and Pan and Liu
(2010) have identied 89 peanut miRNAs belonging to 14 new
miRNA and 22 conserved miRNA families, which can provide the
basis for peanut miRNA research for resistance to different stresses.
Relationships between functional molecules and plant phenotypes
can be studied more specically using proteomics (Wang et al.,
2011), and proteins that may play roles in aatoxin resistance in
imbedded peanut seeds have been discovered through proteomic
studies (Wang et al., 2008b).
In eukaryotes, epigenetic regulation is known to contribute to
gene silencing and plays critical roles in development and genome
defence against viruses, transposons, and transgenes (Lister et al.,
2008; Gehring et al., 2006; La et al., 2011). It has been observed
that bacterially infected plant tissue shows a net reduction in DNA
methylation, which may affect the disease resistance genes
responsible for surveillance against pathogens (Alvarez et al., 2010).
An investigation regarding epigenetic regulation mechanisms of
the peanut allergen gene Arah3 in developing peanut embryos
demonstrated an association between the loss of histone H3 from
the proximal promoter and high expression of Arah3 during embryo maturation (Fu et al., 2010). For better understanding and
management of various biotic stresses in peanuts, there is an urgent


G.P. Mishra et al. / Crop Protection 77 (2015) 74e86

need to determine the epigenetic regulatory mechanisms of

different biotic stress resistant genes and promoters.
For global gene expression proling, microarray analysis is a
powerful tool (Casson et al., 2005). Because a peanut gene chip is
commercial unavailability, high-throughput gene expression analysis is currently very limited. However, peanut microarrays have
been specically designed to solve particular issues, such as the
characterization of A. parasiticus infection-induced changes in gene
expression and gene expression proling in different peanut tissues
(Luo et al., 2005a; Payton et al., 2009). Approximately 25,000 ESTs
from cDNA libraries were constructed using the bacterial wilt
resistant peanut leaf before and after bacterial infection (Huang
et al., 2008). Shan et al. (2007) used soybean gene chips to analyse the differential gene expression of peanut varieties that are
resistant and susceptible to A. avus infection. Using microarray
analysis, Guo et al. (2011) identied 62 genes in Aspergillus resistant
peanut cultivars that were up-expressed in response to Aspergillus
infection, and 22 putative resistance genes that were constitutively
overexpressed. In addition to microarray-based gene expression
analysis, the expression and regulation of individual genes has also
been studied in peanuts (Wang et al., 2011). There is a need for the
development of a comprehensive genome-scale platform for
developing Aspergillus-resistant cultivars through targeted markerassisted breeding and genetic engineering.
10. Transgenic approach for biotic stress management
(Fungal, viral, bacterial and insect-pest resistance)
The lack of available resistance genes within crossable germplasms of peanuts necessitates the use of genetic engineering
strategies to impart genetic resistance against various biotic
stresses (Vasavirama and Kirti, 2012). Transgenic peanut lines
possessing fungal resistance genes offer an alternative to traditional
resistance and fungicide applications in managing fungal diseases
(Chenault et al., 2005). Vasavirama and Kirti (2012) generated
transgenic peanuts using a double gene construct with SniOLP
(Solanum nigrum osmotin-like protein) and Rs-AFP2 (Raphanus
sativus antifungal protein-2) genes under separate constitutive 35S
promoters, which then showed enhanced disease resistance to LLS.
Transgenic peanuts with rice chitinase-3 overexpression (with the
CaMV 35S promoter) exhibited a resistance for leaf spot that was
higher than that of the control, and a good correlation was observed
between chitinase activity and fungal pathogen resistance (Iqbal
et al., 2012).
Similarly, peanuts transgenic for the chitinase gene (Rchit) from
rice showed 2- to 14-fold higher chitinase activity than the wild
type, and a signicant negative correlation was observed between
the chitinase activity and the frequency of infection to the three
tested pathogens (A. avus, LLS and rust) (Prasad et al., 2013).
Transgenic peanut lines containing antifungal genes (rice chitinase
and/or alfalfa glucanase), when evaluated for their reaction to
Sclerotinia blight, showed varying degrees of resistance (Chenault
et al., 2005). Signicantly reduced lesion size was recorded in
transgenic plants expressing a barley oxalate oxidase gene
compared to the controls, which means that oxalate oxidase can
confer enhanced resistance to Sclerotinia blight in peanuts
(Livingstone et al., 2005). A non-heme chloroperoxidase gene (cpop) from Pseudomonas pyrrocinia, a growth inhibitor of mycotoxinproducing fungi, introduced into peanuts resulted in transgenic
plants that showed inhibition of A. avus hyphal growth and
reduced aatoxin contamination of peanut seeds (Niu et al., 2009).
The epidemiology of PBNV is yet to be fully understood for
peanut, including the search for linked markers for resistance
gene(s) and the development resistant transgenic lines for its
management. To this end, attempts have been made to develop

transgenic peanuts expressing PBNV genes using viral coat protein

(CP) genes (Satyanarayana et al., 1995). Evaluation of transgenic
peanuts with CP genes showed that resistance could be achieved
against PSND (Mehta et al., 2013). Transgenic peanut lines containing the CP gene of the peanut stripe virus (PStV) were less
susceptible to PStV. TSWV has a broad host range, and it spreads
through ubiquitous thrips. The nucleocapsid (N) protein gene of the
lettuce isolate of TSWV was inserted into the peanut genome,
which showed divergent levels of gene expression (Yang et al.,
1998). Transgenic peanuts expressing the N protein of TSWV and
subjected to natural infection of the virus under eld conditions
resulted in a signicantly lower incidence of spotted wilt compared
to that of non-transgenic lines (Yang et al., 2004). Increased insect
tolerance of the transgenic plants was recorded when the cowpea
trypsin inhibitor gene was transfected into peanuts (Xu et al., 2003;
Zhuang et al., 2003). The transgenic lines developed against various
diseases in peanuts are compiled and presented in Table 6, but to
date no transgenic peanut cultivars have been released
During the last decade, strong public opposition to genetically
modied (GM) food crops, especially in European countries, are
juxtaposed with issues such as freedom to operate related to
patented technologies (Holbrook et al., 2011). However, during last
two years, many patents have been approved in various countries
for eld trials of GM food crops. Two genetically modied types of
corn, namely TC1507 and SmartStax developed by the US companies Pioneer and Monsanto, respectively, won EU approval for
their cultivation in EU countries in February of 2014 and November
of 2013, respectively (Mcmanus, 2014). In India, the Union Ministry
of Environment and Forests (MoEF) has approved eld trials for GM
food crops (rice, wheat, maize, castor and cotton) to determine
their suitability for commercial production (Business Standard,
2014). Altogether, the possibility is good that various transgenic
peanut crops will be used in the next few years.
11. Achievements and future prospects
The dynamic challenges of peanut farming demand a quick
response from breeders to develop new cultivars, a process that can
be aided by the application of molecular markers (Chu et al., 2011).
NemaTAM is the rst root-knot nematode-resistant peanut variety
developed using the MABC approach in the USA (Simpson et al.,
2003). The Tifguard High O/L cultivar, with nematode resistance
and a high oleic:linoleic acid (high O:L) ratio in seeds, was developed using Tifguard (nematode-resistant cultivar) as the recurrent
female parent and Georgia-02C and Florida-07 (high O:L cultivars)
as donor parents after three rounds of accelerated backcrossing
using MAS (Chu et al., 2011).
A QTL region explaining up to 82.62% of the phenotypic variation for rust resistance was introgressed from cultivar GPBD 4 into
three rust susceptible varieties (ICGV 91114, JL 24 and TAG 24)
through MABC using four markers (IPAHM103, GM2079, GM1536,
GM2301). This has generated several promising introgression lines
with enhanced rust resistance and higher yields. These linked
markers may be used to improve rust resistance in peanut breeding
programmes across the world (Varshney et al., 2014). Through
validating LLS and rust resistance-linked markers in different
peanut genotypes, six superior genotypes were identied. Moreover, three lines that are superior for productivity traits and equal
for disease resistance to GPBD 4 (the resistant parent) are being
included in variety release trials for multi-location evaluation
(Sukruth et al., 2015). Gajjar et al. (2014) studied 22 SSR markers
reportedly linked to rust and LLS disease resistance on 95 diverse
genotypes for marker validation, from which 16 SSRs could be

G.P. Mishra et al. / Crop Protection 77 (2015) 74e86


Table 6
Transgenics developed for various biotic stress resistances in peanut.



Coat protein
Nucleocapsid (N)
Cowpea trypsin inhibitor gene
Coat protein
Chitinase and glucanase
Barley oxalate oxidase
cry1EC and Chi11
Coat Protein gene PStV
Mustard defensin
Chloroperoxidase (cpo-p)
Rice chitinase-3
Rchit and CHI
SniOLP and Rs-AFP2
Rice chitinase gene (Rchit)
Coat protein
Tfgd2-RsAFP2 fusion gene

Elasmopalpus lignoscellus
Tomato spotted wilt virus
Insect tolerance
Peanut stripe potyvirus
Sclerotinia blight
Sclerotinia blight
Spodoptera litura
Helicoverpa armigera and Spodoptera litura
Spodoptera litura and Phaeoisariopsis personata
A. avus
Leaf spot
Fusarium wilt and Cercospora arachidicola
A. avus, LLS and rust
Spodoptera litura
Holotrichia parallela

Satyanarayana et al., 1995

Singsit et al., 1997
Yang et al., 1998; Magbanua et al., 2000; Yang et al., 2004
Xu et al., 2003; Zhuang et al., 2003
Higgins et al., 2004
Chenault et al., 2005
Livingstone et al., 2005; Partridge-Telenko et al., 2011
Tiwari et al., 2008; Tiwari et al., 2011
Entoori et al., 2008
Beena et al., 2008
Hapsoro et al., 2008
Anuradha et al., 2008
Niu et al., 2009
Iqbal et al., 2012
Rohini and Sankara, 2001; Iqbal et al., 2011
Vasavirama and Kirti, 2012
Prasad et al., 2013
Mehta et al., 2013
Keshavareddy et al., 2013
Geng et al., 2013
Bala et al., 2015

Because of evolutionary selection pressure and their high

genetic-diversity, wild peanut species are considered to be excellent sources of various disease resistance genes that remain underutilized (Stalker and Simpson, 1995). A dense genetic linkage map
should enable breeders to effectively pyramid genes for various
biotic stress resistances, such as rust, LLS, and nematode resistance,
into agronomically superior lines in a much shorter time period
than would be possible by conventional techniques (Gajjar et al.,
2014). RILs are being developed to map various genes/QTLs underlying these traits. Currently, more than 14,000 SSR markers are
available from different sources; however, substantial efforts are
still required to develop sufcient PCR-based markers for the
construction of a high-density genetic linkage map and for routine
applications in the molecular breeding of peanuts (Mishra et al.,
2014; Bosamia et al., 2015).
The International Peanut Genome Initiative with a time line of
2012e2016 is working on different aspects of biotic stress management at the genome level, including screening peanut accessions for new sources of disease resistance, discovering new
sources of disease resistance, identifying a core set of informative
markers for their deployment in resistance breeding programmes,
searching and validating markers that can be used in pre-breeding
for disease and pest resistance, placing candidate genes for disease
resistance on the Arachis genetic map, and identifying core sets of
markers for QTLs associated with biotic stress resistance (http://
Nevertheless, the genomic progress made in peanuts over the last
few years has been quite encouraging, and it is expected that a
clearer genomic picture of peanuts will be available by the year
2016 for researchers to utilize.
Recently, the International Peanut Genome Initiative (IPGI) has
sequenced the genome of two wild species, A. duranensis (AA
genome) and A. ipaensis (BB genome), supposedly the ancestral
parents of cultivated peanut, which is an allotetraploid species. The
hope is that the available sequence information will provide researchers with approximately 96 percent of all peanut genomic
information and provide the molecular map needed to more
quickly breed drought-resistant, disease-resistant, lower-input and
higher-yielding varieties (; Mondal and Badigannavar,
However, compared to other crops such as rice, soybeans and

chickpeas, the ongoing molecular breeding programme for peanuts

is relatively slow primarily due to low genetic diversity among the
cultivated gene pool, introgression barriers between wild and
cultivated lines, non-availability of genome sequence information
until last year and inadequate funding. Because a draft sequence of
the Arachis genome (AA and BB) is available, the expectation is that
in the next few years the quality of peanuts will be improved
through the use of modern biotechnological approaches (Janila
et al., 2013). Ongoing research efforts across the world have not
only resulted in better understanding of the peanut genome but
also facilitated ongoing marker-assisted peanut breeding programs
(Holbrook et al., 2011). The use of biotechnological interventions in
peanut breeding for the development of resistance cultivars against
various biotic stresses is quite promising. Despite substantial advancements in the biotic management strategies, the global peanut
production is still threatened by a multitude of insect pests and
diseases. The situation demands judicious blending of conventional
and modern crop improvement technologies for more efcient and
rapid tackling of these problems (Krishna et al., 2015). An outline of
the tentative biotechnological interventions for peanuts is presented in Fig. 1.
12. Conclusions
We have reviewed the recent biotechnological developments
for the biotic stress management of peanut crops with special
preference given to genomic approaches. The goal of these studies
is to nd more effective and economical high-throughput tools to
manage various biotic stresses in peanuts. Conventional breeding
along with phenotyping tools have largely been used in peanut
improvement programs, and low genetic variability has been
considered one of the major bottlenecks. Therefore, mutations
were used to introduce variability, and wide-hybridizations were
attempted to determine the variability from wild Arachis species.
For the creation of new sources of genetic diversity, approaches that
are being explored include the development of transgenics, TILLING
(targeting-induced local lesions in genomes) populations and
synthetic allotetraploids (Holbrook et al., 2011). Additionally, a few
other robust mapping populations such as NAM (nested association
mapping) and MAGIC (multi-parent advanced generation intercross) are being developed by various institutions working on
peanut crops. To date, the genetic basis of many important traits in


G.P. Mishra et al. / Crop Protection 77 (2015) 74e86

Fig. 1. An outline of tentative biotechnological interventions proposed for the development peanut genotypes resistant to various biotic-stresses.

peanuts is not fully understood, and molecular mapping strategies

in cultivated peanut species for a few traits (e.g., rust, LLS, drought,
etc.) have only recently been developed. The development of integrated comprehensive linkage maps allows for the identication
of associated markers and QTLs more precisely on some of the
linkage groups.
Various genes and QTLs have been found to confer different
biotic stress tolerances; one of the challenges in this area is to
validate these gene(s)/QTLs on different backgrounds and to use
them for marker-assisted breeding to develop resistant cultivars.
Countries such as the USA, China, India, and Japan have used molecular breeding approaches to complement their ongoing peanut
breeding programs over the last decade (Janila et al., 2013). Cultivars developed using transgenic technologies have not yet been
released for commercial production, but several programs are
working towards achieving this goal. Based on the reports from
various labs across the world, it is expected that many peanut
cultivars developed using a variety of biotechnological interventions are going to be released very soon. Because biotechnological approaches have already shown great potential for
improving a variety of crop species (Varshney et al., 2006), it is
therefore expected that advancements in biotechnological interventions will also assist in selective breeding for enhancing the
biotic stress tolerance of peanut crops.
We thank Dr. J.B. Misra, Ex-Director, Directorate of Groundnut
Research, Gujarat, India for his critical suggestions. Financial support received from Directorate of Groundnut Research, Gujarat of
the Indian Council of Agriculture Research (ICAR), New Delhi, India
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