Received: 15 July 2017 | Accepted: 21 October 2017

DOI: 10.1111/pbr.12549

ORIGINAL ARTICLE

Marker-assisted backcrossing to develop foliar disease-

resistant genotypes in TMV 2 variety of peanut (Arachis
hypogaea L.)

Rohini M. Kolekar1 | Mallenahally Sukruth1 | Kenta Shirasawa2 | Hajisaheb L. Nadaf3 |

Babu N. Motagi3 | Sattigarahalli Lingaraju4 | Prakashgouda V. Patil4 | Ramesh S. Bhat1

1
Department of Biotechnology, University
of Agricultural Sciences, Dharwad, India Abstract
2
Department of Frontier Research, Kazusa TMV 2 is a very popular peanut variety among the Indian farmers, but it is highly
DNA Research Institute, Chiba, Japan
susceptible to fungal foliar diseases like late leaf spot (LLS) and rust. Marker-assisted
3
Department of Genetics and Plant
Breeding, University of Agricultural backcrossing (MABC) in TMV 2 using foliar disease-resistant donor, GPBD 4 and
Sciences, Dharwad, India the disease resistance-linked markers (GM2009, GM2079, GM2301, GM1839 and
4
Department of Plant Pathology, University
IPAHM103) resulted in a large number of backcross populations and also straight
of Agricultural Sciences, Dharwad, India
cross populations. Foreground selection followed by field evaluation under disease
Correspondence
epiphytotic conditions could identify a few superior genotypes. Two homozygous
Ramesh S. Bhat, Department of
Biotechnology, University of Agricultural backcross lines TMG-29 and TMG-46 showed enhanced resistance to LLS and rust
Sciences, Dharwad, India
diseases (score of 3.00 for both) along with 71.0% and 62.7% increase in the pod
Email: bhatrs@uasd.in
yield per plot, respectively, over the check, TMV 2. These foliar disease-resistant
Funding information
and productive lines can be released as commercial varieties or can be used as
Grant received from DBT, New Delhi
through the project BT/PR4195/AGR/2/ genetic resources in the peanut improvement.
836/2011, and DST-JSPS through the
project DST/INT/JSPS/P-227/2016 is KEYWORDS
gratefully acknowledged.
foreground selection, marker-assisted backcrossing, peanut, productivity, rust and late leaf spot
Communicated by: R. Varshney disease resistance

1 | INTRODUCTION
Cultivated peanut, an allotetraploid (2n = 4x = 40), is an important
oilseed and food crop worldwide. Globally, it is grown on an area
of 25.44 million hectares with a production of 45.22 million tons
(FAOSTAT, 2016). Foliar diseases like late leaf spot (LLS) caused by
Phaeoisariopsis personata, and rust caused by Puccinia arachidis are
the major biotic stresses limiting the peanut productivity since the
co-occurrence of these two diseases can cause a yield loss of 70%
(Subrahmanyam, Williams, McDonald, & Gibbons, 1984). Although
several fungicides are available to control these foliar diseases,
development of resistant cultivars is desirable considering the haz-
ardous effect of chemicals on environment. Breeding for foliar dis-
ease resistance in peanut has now reached a stage where
molecular markers can be successfully employed for genotypic
selection, which could enhance the breeding efficiency. This has
been possible due to the identification and validation of the QTL
and markers for foliar disease resistance. Two major QTL regions
were identified for LLS and rust resistance. A QTL region on A03
chromosome governed both LLS (67.98%) and rust (82.62%) resis-
tance with very high phenotypic variance explained (PVE). The QTL
region on A03 was further resolved to 3.06 Mb (131.60–
134.66 Mb) genomic region on the A03 pseudomolecule of A gen-
ome (Pandey et al., 2016), which carried ~25 putative candidate
genes associated with LLS and rust resistance. SSR (Sujay et al.,
2012), SNP (Pandey et al., 2016) and AhTE (Kolekar et al., 2016)
markers linked to the QTL/genes were identified. Some of these
markers were validated (Sukruth et al., 2015; Yeri et al., 2014) and
also used for developing foliar disease-resistant backcross lines
(Pasupuleti, Pandey, Manohar, et al., 2016; Varshney et al., 2014;
Yeri & Bhat, 2016). A 24.2 cM QTL region on A02 chromosome
governed only LLS resistance with a PVE of 62.34% (Sujay et al.,

948 | © 2017 Blackwell Verlag GmbH wileyonlinelibrary.com/journal/pbr Plant Breeding. 2017;136:948–953.

KOLEKAR ET AL.
2012) and 35.2% (Kolekar et al., 2016). GM1839 and GM1009 SSR
markers were linked to this region.
Among the major peanut-growing states of India, TMV 2 covers
a large area (Annonymous, 2014; IOPEPC and AICRP, 2016)
although it was released for commercial cultivation almost 70 years
back. TMV 2 is still popular among the farmers for its wide adapt-
ability and premium quality kernels. However, TMV 2 is highly sus-
ceptible to LLS and rust, thereby demanding the development of
foliar disease-resistant lines of TMV 2. For this purpose, we
employed the markers linked to LLS and rust for transferring the
two QTL regions (on A02 and A03) from the resistant donor GPBD
4. Marker-assisted backcrossing (MABC) resulted in the development
of a few foliar disease-resistant genotypes in TMV 2, which are cur-
rently undergoing multilocation trial for variety development and
commercial release.
2 | MATERIAL AND METHODS
2.1 | Development of backcross populations
Backcross populations were developed by crossing TMV 2 (recurrent
parent) with GPBD 4 (donor parent) following three cycles of back-
crosses (Figure 1) during 2012 to 2014. TMV 2 is an early maturing
and widely adapted variety, selected from “Gudiyatham bunch” and
released by Tamil Nadu Agricultural University, Coimbatore, India, in
1940. It is popular for its uniform pod and kernels, high oil content
(49%) and kernel taste, but it is susceptible for LLS and rust diseases.
The donor GPBD 4 is an improved Spanish bunch groundnut variety
with early maturity, high yielding ability with desirable pod and ker-
nel features, high oil and protein content, better oleic/linoleic ratio
(O/L), high pod growth rate and resistance to LLs and rust. It was
developed from KRG1 9 ICGV86855 at University of Agricultural
Sciences, Dharwad, India (Gowda, Motagi, Naidu, Diddimani, &
Sheshagiri, 2002).
F I G U R E 1 Scheme of marker-assisted backcrossing in TMV 2 variety of peanut (R: Rainy season; PR: Postrainy season) [Colour figure can
be viewed at wileyonlinelibrary.com]
| 949
Ten plants of TMV 2 were grown in the pots and crossed with
GPBD 4 during the postrainy season (January to April) of 2012. F1
plants were confirmed by foreground selection with LLS and rust
resistance-linked markers. These F1 plants were used as the male
parents to develop the BC1F1s. Likewise, two more rounds of back-
crosses were followed for TMV 2 9 GPBD 4 to produce BC3F1s
using MABC. Selfed generations of selected F1 and BCnF1 plants
were also developed for marker-assisted selection.
2.2 | Foreground selection
Genomic DNA was isolated from the young leaves using the modified
CTAB method (Cuc et al., 2008). TMV 2 and GPBD 4 were screened
with SSR markers linked to the LLS and rust resistance (Kolekar et al.,
2016), and the polymorphic markers, GM2009, GM2079, GM2301
and IPAHM103 linked to the QTL region on A03, and GM1839 linked
to the QTL region on A02, were employed for foreground selection in
the backcross lines as well as straight cross lines.
PCR amplification was carried out in a reaction volume of 20 ll con-
taining 5 ng of genomic DNA, 10 pmol of each primer, 2 mM of dNTPs,
2 mM MgCl2, 1 X amplification buffer and 1 U of Taq DNA polymerase.
Touch-down PCR of 35 cycles was performed with an initial denatura-
tion at 94°C for 5 min followed by denaturation at 94°C for 20 s,
annealing at 65°C for 20 s with a 1°C decrease in annealing tempera-
ture for first five cycles, extension at 72°C for 30 s and final extension
at 72°C for 20 min using Eppendorf mastercycler (Hamburg, Germany).
The PCR amplicons were separated on 4% agarose gel by electrophore-
sis. Fine resolution of the PCR products was accomplished using 4%
polyacrylamide gel electrophoresis (PAGE) wherever necessary.
2.3 | Evaluation for LLS and rust resistance
For evaluating the resistance to LLS and rust, disease epiphytotic
condition was created using the “Spreader Row Technique”
950 | KOLEKAR
(Subrahmanyam et al., 1995) in which the disease spreader plants
(TMV 2) were planted at every 10th row in the experimental plot.
LLS conidia and rust urediniospores were collected by soaking and
rubbing the infected leaves of susceptible plants in the water. When
the plants were 35 days old, they were sprayed with the inoculum
containing 20,000 conidia/urediniospores per ml water. Modified 9-
point scale (1–9 score) (Subbarao, Subramanyam, & Reddy, 1990)
was used for scoring LLS and rust disease at 70, 80 and 90 days
after sowing (DAS). The families were also evaluated for the produc-
tivity traits like pod yield per plot, shelling percentage, test weight
and sound mature kernel weight percentage and morphological traits
like plant height, number of primary branches, height of primary
branch, leaf length, leaf width and pod features as per the Ground-
nut Descriptor (IBPGR/ICRISAT, 1992). Productivity traits were
recorded on plot basis in each replication. However, the morphologi-
cal traits were observed on five randomly selected plants of each
family and the mean was used for analysis. Statistical analyses for
ANOVA, components of variance, heritability and genetic advance
were carried out using Windostat version 8.1 available at the
Department of Biotechnology, University of Agricultural Sciences,
Dharwad.
3 | RESULTS
TMV 2 was crossed with GPBD 4 during 2013 to produce 292 pro-
geny of which 40 were confirmed to be F1s. Subsequent MABC
could identify 33, 26 and 18 progeny from a total 276, 192 and 83
plants in BC1F1, BC2F1 and BC3Fl, respectively. A large number of
plants/families were raised in the backcross and straight cross gener-
ations. Selection in the backcross and straight cross generations was
exercised based on the foreground markers and phenotypic evalua-
tion in the field (2013 to 2015). With this breeding and evaluation
scheme, the superior plants (F2, BC1F2, BC2F2 and BC3F2) and lines
(F3, F4, BC1F3 and BC1F4) with resistance to LLS and rust were
identified.
3.1 | Selection of plants and families
Six hundred BC1F2 plants were evaluated for LLS and rust response,
which ranged from 3.0 to 8.0, for both the diseases. Sixteen superior
plants with LLS and rust scores ranging from 3.0 to 5.0 were
selected. The progeny of these plants were evaluated, and 11 fami-
lies were selected for resistance to LLS and rust and yield traits. Sim-
ilarly, 132 BC2F2 plants and 138 BC3F2 plants were selected for
foliar disease resistance and pod yield per plant from 550 and 670
BC2F2 and BC3F2 plants, respectively.
From the straight cross of TMV 2 9 GPBD 4, 990 F2s were
evaluated to select 119 plants. In F3, both plant and family selec-
tions were exercised. Further, 99 F4 families were evaluated in a
randomized block design (RBD) with two replications where each
family was grown in a plot of 1.36 m2 during the rainy season of
2015. LLS and rust were recorded from five randomly selected
ET AL.
plants in each family. Productivity traits were recorded on plot
basis. The ANOVA showed significant differences among these
families for the disease resistance and productivity traits. LLS, rust
and pod yield per plot showed high PCV, GCV, heritability and
genetic advance over mean (GAM) (Table 1). Three superior lines
(TMG-22-1, TMG-32-19 and TMG-51-2) were selected. They
exhibited high level of resistance to rust (3.0 to 3.5) and LLS (3.0
to 4.0). Selected superior lines recorded 76.3%–84.5% higher pod
yield per plot than TMV 2. These lines were marginally superior for
other traits like test weight, shelling percentage and sound mature
kernel weight percentage (Table 2).
3.2 | Selection of advanced backcross lines
Eleven (BC1F4) lines were evaluated in a RBD with two replications
where each line was grown in a plot of 1.35 m2 during the rainy sea-
son of 2015. Resistance to LLS and rust was observed on five plants
in each family. Productivity traits were recorded on plot basis.
ANOVA showed the significant differences between the genotypes
for LLS and rust resistance and productivity traits. High PCV and
GCV were observed for LLS and rust disease score at 90 DAS and
pod yield per plot (Table 1). High heritability and high GAM were
observed for LLS (78.99% and 61.99%, respectively) and rust reac-
tion (76.91% and 51.60%, respectively). Pod yield per plot exhibited
79.29% and 45.28% heritability and GAM, respectively, indicating
the scope for effective selection. Significant and positive correlation
was registered between LLS and rust disease score at 90 DAS, sug-
gesting scope for simultaneous improvement of the traits. Pod yield
per plot showed significant and negative correlation with LLS score,
whereas it was non-significant and negative for rust score. Pod yield
per plot exhibited significant and positive correlation with shelling
percentage and sound mature kernel weight percentage traits, which
contribute for high yield.
TMG-29 and TMG-46 recorded the score of 3.0 for LLS reac-
tion, while TMV 2 had a score of 7.0 for LLS reaction (Figure 2).
TMG-29 and TMG-46 had a score of 3.0 for rust response when
compared to the score of 8.0 for TMV 2, indicating enhanced LLS
and rust resistance among the two BC1F4 lines of TMV 2. These
two promising lines showed higher productivity when compared to
TMV 2. TMG-29 (458.75 g) and TMG-46 (436.55 g) showed 71.0%
and 62.7% increase in the pod yield per plot over TMV 2
(268.25 g). These lines recorded marginal superiority for test
weight, shelling percentage and sound mature kernel weight
percentage (Table 2).
Morphologically, the selected lines showed erect growth habit
like TMV 2 (Table 2) (Figure 2). Selected lines did not show any
significant difference for plant height, leaf length, leaf width,
height of primary branch and number of primary branches as
compared to TMV 2. Both the lines (TMG-29 and TMG-46) had
desirable pod features with medium pod constriction, medium
pod reticulation and slight pod beak. There was no remarkable
change for pod length and width (Figure 3). These lines showed
marginal superiority for pod yield per plot, test weight and
KOLEKAR ET AL. | 951

T A B L E 1 Estimates of genetic
Traits Mean Range PCV GCV h2bs (%) GA GAM
variability for foliar disease
reaction and productivity traits F4
among BC1F4 and F4 families LLS (90 DAS) 4.49 3.00–8.00 30.33 28.07 85.68 2.40 53.53
Rust (90 DAS) 3.74 3.00–7.00 24.04 21.64 80.83 1.50 40.02
PY/P (g) 196.03 245.46–509.00 26.92 24.57 83.27 90.53 46.18
TW (g) 38.43 32.83–42.65 10.35 7.97 59.24 4.86 12.64
SP 75.53 67.73–82.37 5.47 3.62 43.86 3.73 4.94
SMKW (%) 86.86 79.73–91.85 5.58 4.39 61.93 6.18 7.12
BC1F4
LLS (90 DAS) 5.61 3.00–7.00 38.11 33.86 78.99 3.98 61.99
Rust (90 DAS) 4.89 3.00–8.00 32.23 28.26 76.91 2.50 51.60
PY/P (g) 384.24 247.50–528.75 27.72 24.69 79.29 17.35 45.28
TW (g) 37.90 30.60–46.80 14.16 10.85 58.77 6.50 17.14
SP 73.15 64.87–82.80 8.70 6.04 49.18 6.13 8.63
SMKW (%) 82.90 67.50–91.68 9.88 8.78 78.97 13.33 16.07

LLS, late leaf spot; PY/P, pod yield per plot; TW, test weight; SP, shelling percentage; SMKW, sound mature ker-
nel weight percentage; PCV, phenotypic coefficient of variation; GCV, genotypic coefficient of variation; GA,
genetic advance; GAM, genetic advance over mean and h2bs (%): broad-sense heritability.

T A B L E 2 Foliar disease reaction, morphological features and yield performance of superior lines
LLS Rust PH HPB LL LW PY/P TW SMKW PL PW
Genotypes (90 DAS) (90 DAS) (cm) NPB (cm) (cm) (cm) (g) (g) SP (%) (cm) (cm) PCN PR PB
F4
TMG-22-1 3.50 4.00 32.50 6.50 34.75 4.60 2.80 473.00 42.00 78.41 84.00 2.90 1.20 M M S
TMG-32-19 3.00 4.00 32.25 6.50 33.75 4.15 2.15 495.00 35.94 77.00 91.06 2.64 1.22 M M S
TMG-51-2 3.00 3.00 29.75 5.00 33.25 3.75 2.35 484.50 44.54 73.68 91.08 2.70 1.10 M M S
CV (%) 11.37 10.17 8.74 14.45 5.70 13.51 12.98 11.05 6.61 4.10 3.44 4.49 8.30
LSD (0.05) 1.00 0.74 5.17 1.49 3.55 0.65 1.14 44.12 5.79 5.25 5.84 0.21 0.17
BC1F4
TMG-29 3.00 3.00 31.50 5.00 29.00 4.40 2.55 458.75 37.71 77.80 84.28 2.50 1.11 M M S
TMG-46 3.00 3.00 30.00 5.00 31.00 5.40 3.25 436.55 37.64 72.49 88.64 2.85 1.25 M M S
CV (%) 10.43 17.70 5.96 9.73 4.74 9.61 7.32 12.62 9.09 6.26 4.53 1.44 6.93
LSD (0.05) 0.74 1.04 3.99 1.18 3.31 1.04 0.43 104.45 7.44 9.00 8.12 0.08 0.16
TMV 2 7.00 8.00 31.50 5.00 30.50 5.50 3.65 268.25 43.12 73.38 87.25 2.80 1.25 M M S
GPBD 4 3.00 3.00 25.50 5.00 29.50 3.75 2.25 437.00 36.33 72.00 83.10 2.45 0.90 M M S

LLS, late leaf spot; PH, plant height; NPB, number of primary branches; HPB, height of primary branch; LL, leaf length; LW, leaf width; PY/P, pod yield
per plot; TW, test weight; SP, shelling percentage; SMKW, sound mature kernel weight percentage; PL, pod length; PW, pod width; PCN, pod constric-
tion; PR, pod reticulation; PB, pod beak; M, medium; S, slight; CV, coefficient of variation and LSD, least significant difference at p < .05.

shelling percentage over GPBD 4, the donor parent and an elite
and released variety.
These resistant lines were confirmed for the QTL regions on A03
and A02 by foreground screening with LLS and rust resistance-linked
markers. TMG-29 and TMG-46 had resistant-type alleles at
GM2009, GM2079, GM2301, GM1839 and IPAHM103 like those of
GPBD 4. Other lines such as TMG-48 and TMG-49 had resistant
allele at a few (2-3) marker loci. For example, TMG-48 had GPBD 4
type of allele at three loci (GM2009, GM2079 and IPAHM103) and
TMG-49 had GPBD 4 type of allele at two loci (GM2079 and
GM1839).
4 | DISCUSSION
This study reports the development of LLS- and rust-resistant back-
cross lines of TMV 2, an elite and farmer-friendly variety. GPBD 4, a
disease-resistant variety, was used as the donor parent to transfer
the QTL region on A02 and A03 chromosomes governing LLS and
rust resistance (Kolekar et al., 2016; Sujay et al., 2012). Previous
studies (Pasupuleti, Pandey, Manohar, et al., 2016; Varshney et al.,
2014) aimed at transferring the QTL from A03 only. The QTL region
on A03 chromosome of GPBD 4 was proposed to be contributed by
A. cardenasii (diploid with A genome) through the interspecific
952 | KOLEKAR ET AL.

FIGURE 2 Foliar disease response of the recurrent parent (TMV 2) and its backcross lines

FIGURE 3 Pod and kernel features of the recurrent parent (TMV 2) and its backcross lines

derivative, ICGV 86855 (Bertioli et al., 2016; Gowda et al., 2002).
Our unpublished results showed very high similarity for this region
between GPBD 4 and A. cardenasii.
Crossing and three rounds of backcrossing followed by selection
during 2012 to 2015 at F2, F3, F4, BC1F2, BC1F3, BC1F4, BC2F2 and
BC3F2 generations could identify 19.1% plants/lines, which showed
significant improvement for rust resistance, and 17.9% progeny
superior for LLS resistance. Recovery of more number of resistant
progeny for rust over LLS could be due to the simple genetic control
of rust resistance over the complex genetic control of LLS resistance
(Knauft, 1987; Nevill, 1981).
Evaluation of advanced backcross lines (BC1F4) identified two
(TMG-29 and TMG-46) genotypes, which were significantly superior
for LLS and rust resistance. They also recorded 71.0% and 62.7%
increase in the pod yield per plot, respectively, over TMV 2 and
were marginally superior for test weight, shelling percentage and
sound mature kernel weight percentage. TMV 2 gets a premium
price in the market because of its uniform pods and kernels. TMG-
29 and TMG-46 were comparable to TMV 2 for the pod and kernel
shape, size and uniformity. As the donor parent (GPBD 4) is an elite
variety, the undesirable linkage drags were not observed in any of
the backcross lines. In addition, our unpublished ddRAD-Seq data on
TMG-46 showed 99.99% genome similarity with TMV 2. TMG-29
and TMG-46 carried the resistant-type alleles at the QTL regions on
A02 and A03. Thus, TMG-29 and TMG-46 are promising for variety
development and commercial release.
Previously, Varshney et al. (2014) developed rust-resistant pea-
nut genotypes from three elite varieties (ICGV 91114, JL 24 and
TAG 24) using MABC. However, the backcross lines developed in
this study using TMV 2 as the recurrent parent are resistant to both
LLS and rust diseases. These superior backcross lines (TMG-29 and
TMG-46) are currently undergoing multilocation testing in eight dif-
ferent environments as per the variety development and release pro-
cedures. In the past, MABC has been successful in improving the
nematode resistance (Simpson, Starr, Church, Burow, & Paterson,
2003) and enhancing the oleic acid content in peanut (Chu et al.,
2011; Pasupuleti, Pandey, Shasidhar, et al., 2016). In future, with the
identification of QTL and markers for various productivity traits,
resistance to diseases and quality traits, MABC could be routine in
peanut.
CONFLICT OF INTEREST
There is no conflict of interests among the authors
KOLEKAR ET AL. | 953

ACKNOWLEDGEMENT Pasupuleti, J., Pandey, M. K., Manohar, S. S., Variath, M. T., Nallathambi,
P., Nadaf, H. L., . . . Varshney, R. K. (2016). Foliar fungal disease resis-
We thank Dr. M. V. C. Gowda, Professor, Genetics and Plant Breed- tant introgression lines of groundnut (Arachis hypogaea L.) record
ing, University of Agricultural Sciences, Dharwad, India, for sparing higher pod and haulm yield in multilocation testing. Plant Breeding,
135, 355–366.
the seeds of GPBD 4 and for his overall advice.
Pasupuleti, J., Pandey, M. K., Shasidhar, Y., Variath, M. T., Sriswathi, M.,
Khera, P., . . . Mishra, G. P. (2016). Molecular breeding for introgres-
sion of fatty acid desaturase mutant alleles (ahFAD2A and ahFAD2B)
ORCID
enhances oil quality in high and low oil containing peanut genotypes.
Mallenahally Sukruth http://orcid.org/0000-0002-9523-2925 Plant Science, 242, 203–213.
Simpson, C., Starr, J., Church, G., Burow, M., & Paterson, A. (2003).
Kenta Shirasawa http://orcid.org/0000-0001-7880-6221
Registration of ‘NemaTAM’ peanut. Crop Science, 43, 1561.
Babu N. Motagi http://orcid.org/0000-0001-6113-0667 Subbarao, P. V., Subramanyam, P., & Reddy, P. M. (1990). A modified nine
Ramesh S. Bhat http://orcid.org/0000-0002-1120-7088 points diseases scale for assessment of rust and late leaf spot of ground-
nut Second International Congress of French Phytopathological Society,
25. Montpellier, France: French Phyto-Pathological Society.
Subrahmanyam, P., McDonald, D., Waliar, F., Reddy, L. J., Nigam, S. N.,
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