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253
A. Pratap and J. Kumar (eds.), Alien Gene Transfer in Crop Plants, Volume 2:
Achievements and Impacts, DOI 10.1007/978-1-4614-9572-7_12,
© Springer Science+Business Media, LLC 2014
Abstract Groundnut or peanut is an important legume nut known for its multifarious
uses including oil production, direct human consumption as food and also animal
consumption in the form of hay, silage and cake. Being a grain legume, peanut has
an important nutritional value for human beings, and its nutritional value has been
exploited for combating malnutrition in children. The breeding objectives in groundnut
focus on increasing yield, incorporating resistance/tolerance to biotic and abiotic
stresses and improving oil and nutritional quality including safety of its consump-
tion by humans and animals. However, limited genetic variability in the cultivated
germplasm and diffi culties in hybridisation have slowed down the progress in
groundnut breeding. The wild relatives are considered as sources of several agricul-
turally important traits including resistance to pests and pathogens, tolerance to
abiotic stresses and variable nutritional value. These resources have been used in
groundnut breeding programmes for improving the above traits, simultaneously
addressing the constraint of reproductive barrier in successful hybridisation arising
due to different ploidy levels of A. hypogaea and its wild relatives. This has been
achieved through different routes: the hexaploid pathway, two different diploid/
tetraploid pathways and genetic engineering-based methods. Nonetheless, the use of
wild introgressions in groundnut improvement programmes has not been up to the
desired extent, and therefore concerted efforts for a large-scale generalised introgres-
sion programme are required. This chapter discusses the evaluation and utilisation of
alien introgressions in groundnut improvement, the achievements made hitherto
and the future strategies for initiating a large-scale introgression programme.
Chapter 12
Groundnut
Jean-François Rami , Soraya C. M. Leal-Bertioli , Daniel Foncéka ,
Marcio C. Moretzsohn , and David J. Bertioli
J.-F. Rami (*) • D. Foncéka
CIRAD , UMR AGAP , 108/3 Avenue Agropolis , Montpellier 34398 , France
e-mail: rami@cirad.fr
S. C. M. Leal-Bertioli • M. C. Moretzsohn
Embrapa Recursos Geneticos e Biotecnologia, Brasília , Distrito Federal , Brazil
D. J. Bertioli
Universidade de Brasìlia, Brasìlia , Distrito Federal , Brazil
254
Keywords A. hypogaea • A. cardenasii • AB-QTL • BSA • Diploid pathway • Gene
pools • Hexaploid pathway • Introgression
12.1 Introduction
Groundnut, also commonly known as peanut ( Arachis hypogaea ), is a tropical
legume mainly grown to produce oil and for human and animal consumption.
Peanut is grown in about 120 countries in the world in a total area of 24.6 million
ha, with a world production of 38.2 million tonnes (Mt). Asia is the major peanut-
producing region in the world. In this region, China and India are the major
contributors with 15.7 and 5.6 Mt in 2010, respectively ( FAOSTAT 2010 ). Africa
ranks second in the world peanut production. In this region, Nigeria (2.6 Mt),
Senegal (1.2 Mt) and Sudan (0.7 Mt) are the major producing countries ( FAOSTAT
2010 ). In Africa and Asia peanut is mainly grown by resource-poor farmers. In the
Americas, the USA and Argentina are the major producing countries with 1.8 and
0.6 Mt in 2010, respectively.
Peanut yields vary drastically between regions and between countries within a
region. Although Africa is the second region in terms of production, it has the lowest
yield (1 t/ha on average) as compared to Asia (1.8 t/ha) and to the Americas (3 t/ha).
In West Africa, peanut yields vary from 0.5 t/ha in Niger to 1 t/ha in Senegal and can
reach up to 1.5 t/ha in Nigeria. In Asia yields vary from 1.5 t/ha in India to 3 t/ha in
China. The low peanut yields observed in many countries in Africa and Asia are
related to rainfed and low-input growing conditions. In these countries where the
rainfall pattern is irregular, peanut is often subjected to drought.
Worldwide peanut production is principally dedicated to oil and food products.
Between 1996 and 2000, 49 % of world production has been used for oil and 41 % as
food product components (Revoredo and Fletcher 2002 ). Peanut is also used for feed
through the valorisation of oil cakes that represent an interesting source of proteins for
livestock. In most Sahelian countries, groundnut straw is also used as dried hay and
represents a major source for cattle feed during the dry season. As is the case with
most of the grain legumes, peanut has an important nutritional value for human con-
sumption. Several studies have reported a positive impact of peanut on human health,
and its nutritional value has been exploited for the elaboration of highly nutritious
food products used in the treatment of severe child malnutrition (Briend 2001 ).
Peanut breeding objectives are mainly focused at increasing yield and improving
resistance to foliar diseases and nematodes, tolerance to drought, quality of oil and
food and safety (resistance to afl atoxin contamination and reduced allergenicity).
Signifi cant progress has been achieved in developing elite cultivars using sources of
adaptive traits and disease resistance that exists in cultivated germplasm collections.
This was particularly the case for drought tolerance-related traits, oil quality and
resistance to rosette disease. However, for some other traits such as resistance to
early and late leaf spot, rust and nematode, only moderate levels of resistance are
observed in the cultivated germplasm (Holbrook and Stalker 2003 ).
J.-F. Rami et al.
255
Peanut breeding has also been slowed down by the diffi culties in making large
numbers of crosses and by the low number of progenies produced per cross. This has
limited the exploration and the utilisation of cultivated genetic resources. In addition
to these practical constraints, and in spite of the morphological variability that is
observed in the cultivated gene pool, there are limitations to genetic improvement
that can be achieved using only cultivated germplasm. A clear example of this is
disease resistance: wild species display much stronger disease resistances than are
found in cultivated peanut. There are also good theoretical reasons to believe that
genetic limits for more complex traits like yield and drought tolerance can be
overcome by using wild relatives of the crop as this has been the case in other crops
(Gur and Zamir 2004 ). For these reasons, peanut breeders have for many years been
interested in the introduction of new alleles from wild species.
12.2 Peanut Gene Pools and Genetic Resources
The genus Arachis consists of 80 described species (Krapovickas and Gregory
1994 , 2007 ; Valls and Simpson 2005 ) and is divided into nine taxonomic sections:
Trierectoides , Erectoides , Procumbentes , Rhizomatosae , Heteranthae , Caulorrhizae ,
Extranervosae , Triseminatae and Arachis (Fig. 12.1 ). These divisions were made
Fig. 12.1 Primary, secondary and tertiary gene pools of the genus Arachis
12 Groundnut
256
based on sexual compatibilities, morphological and cytogenetic features and
geographic distributions (Krapovickas and Gregory 1994 ). The sexual compatibility
data available from a large number of crossing experiments is very informative as
to the barriers between gene pools in the genus (Krapovickas and Gregory 1994 ).
The section Arachis contains the primary gene pool of cultivated peanut with
two tetraploids, A. hypogaea and A. monticola . (2 n = 4 x = 40; genome AB) and the
secondary gene pool with the most closely related wild species.
Arachis hypogaea presents considerable morphological variation, and two
subspecies, hypogaea and fastigiata , have been described (Krapovickas and
Gregory 1994 ). Subspecies hypogaea has spreading growth habit with side
branches procumbent to decumbent, a long growth cycle, no fl owers on the cen-
tral stem and regularly alternating vegetative and reproductive side stems. This
subspecies is divided into two botanical varieties hypogaea and hirsuta , the latter
being distinguished by more hirsute leafl ets and even longer cycle. These variet-
ies, respectively, exemplify “Runner” and “Peruvian Runner” agronomic classes.
The subspecies fastigiata Waldron has a more erect growth habit with side branches
erect to procumbent, a shorter cycle, fl owers on the central stem and reproductive
and vegetative stems distributed in a disorganised fashion. This subspecies is
divided into four botanical varieties, fastigiata , vulgaris , aequatoriana and
peruviana . The former two are by far the most economically important and exem-
plify the agronomic classes “Spanish” and “Valencia”, respectively (Krapovickas
and Gregory 1994 ).
Within the agronomic classes, modern cultivars are relatively uniform compared
to landraces. Especially in South America, but also in Africa and Asia, landraces are
spectacularly diverse. This diversity provides a source for constant study, such as
the recent interesting description of 62 distinct landraces in Bolivia (Krapovickas
et al. 2009 ). Also, new collections of landraces continue to be made. For instance,
in the Xingu Indigenous Park in the Central-West of Brazil, the Kayabi people cul-
tivate peanuts which are morphologically very diverse, displaying combinations of
unusual characters which make them unique. Some types form very large plants and
have a very long cycle; some have extremely large seeds. The different types also
display diverse seed colours and patterns, purple, brown, red or white, variegated or
uniform in colour (Freitas et al. 2007 ; Bertioli et al. 2011 ).
Morphological diversity is so high that a different origin for the two subspecies
was proposed. This hypothesis was supported by the partial reproductive isolation
of the two subspecies (Singh and Moss 1982 ; Lu and Pickersgill 1993 ). However,
molecular data has fi rmly contradicted this hypothesis. Genetic variability observed
among commercial cultivars and landraces of peanut is so low that it is generally
accepted that peanut is an allotetraploid of recent and single origin (Halward et al.
1993 ; Kochert et al. 1996 ; Raina et al. 2001 ; Milla et al. 2005 ).
The secondary gene pool includes A. hypogaea ’s most closely related wild
species that can be used for peanut crop improvement. Most of these species are
diploid (2 n = 2 x = 20) with metacentric chromosomes of similar size (genomes A, B,
F and K); one species ( A. glandulifera ) is diploid with an asymmetric karyotype
(genome D); three can be considered dysploid (2 n = 2 x = 18) (Krapovickas and Gregory
J.-F. Rami et al.
257
1994 ; Lavia 1998 ; Peñaloza and Valls 1997 ; Stalker 1991 ; Valls and Simpson 2005 ;
Robledo and Seijo 2010 ). The single wild tetraploid species, A. monticola , is very
closely related to A. hypogaea (Lu and Pickersgill 1993 ), probably sharing the
same origin, and it is considered A. hypogaea ’s immediate tetraploid ancestor
(Seijo et al. 2007 ; Grabiele et al. 2012 ). The ploidy barrier between cultivated peanut
and most of its wild relatives (with the single exception of A. monticola 2 n = 40)
effectively prevented the introgression of wild genes into cultivated peanut and cre-
ated a strong genetic bottleneck.
The most frequent of the genome types among the species is the A genome
(Fig. 12.1 ). It is characterised by the presence of a chromosome pair of reduced size
and by chromosomes with strongly condensed centromeric bands (Husted 1936 ;
Seijo et al. 2004 ). The next most frequent genome type is B, which is characterised
by the lack of a small chromosome pair and by chromosomes with a much lower
degree of centromeric DNA condensation. The genome types F and K were formerly
considered B genome species, and their recent classifi cation was based on rDNA loci
and the presence in most chromosomes of strongly condensed centromeric bands
(Robledo and Seijo 2010 ). Phylogenies based on DNA sequence data strongly sup-
port the validity of these genome divisions (Moretzsohn et al. 2004 , 2013 ; Milla et al.
2005 ; Tallury et al. 2005 ; Bravo et al. 2006 ; Bechara et al. 2010 ; Friend et al. 2010 ;
Grabiele et al. 2012 ).
12.3 Characterisation of Wild Species
Peanut wild relatives are considered as sources of agriculturally important traits that
can be tapped to improve the cultigen. Although a low number of peanut wild acces-
sions have been used in the breeding programmes, as compared to the high diversity
that exists in wild species, extensive phenotypic characterisation of peanut wild
relatives has been performed for many traits.
12.3.1 Resistance to Pests and Pathogens
Resistance to pests and pathogens have been identifi ed in several species belonging
to the genus Arachis (Upadhyaya et al. 2011b ). When crosses with the cultivated
species are possible, wild species can be used as a source of disease resistance for
cultivated peanut, thanks to their broad resistance spectrum and because they are
effective against a disease for which variability is not available in the cultivated
species. One good example of a source of resistance that fi ts these criteria is the
accession GKP10017 (PI 262141) of the wild species A. cardenasii that has been
used in the US breeding programmes to transfer resistances for both early and late
leaf spot, nematodes and insects into cultivated species. Moreover, Singh and
Oswalt (
1991 ) reported accessions of A. duranensis , A. stenosperma , A. cardenasii
12 Groundnut
258
and A. villosa combining immunity and/or resistance to rust and early or late leaf spot,
tomato spotted virus, thrips and/or aphids.
Resistance to disease might have complex inheritance that involves several
components including initial infection, lesion size and number, sporulation and
defoliation. Recently, Mallikarjuna et al. ( 2012a ) characterised several diploid spe-
cies, their hybrids and auto- and allotetraploid derivatives. They reported that they
combined several components of resistance to late leaf spot. Leal-Bertioli et al.
( 2009 ) phenotyped an F
2 population derived from the cross between two wild dip-
loid species A. duranensis and A. stenosperma for resistance to late leaf spot and
expressed the results as percentages of diseased leaf area (DLA). The susceptible
parent had an average of 4.53 % DLA, and the resistant parent had 0.15 % DLA.
Among the 93 F
2 plants, 73 had lower percentage DLA than the resistant parent, of
which 47 had no lesion attesting for important transgressive segregation. Finally,
fi ve QTLs of resistance to late leaf spot were detected. Moreover, resistance for
foliar diseases was characterised at the microscopic level, and it was found that in
A. stenosperma , resistance occurs at the pre-penetration level (Leal-Bertioli et al.
2010 ). The same species also harbours resistance against root-knot nematode, a
resistance that is manifest in at least two distinct levels: very few nematodes that
penetrate the roots and those that are unable to set up an infection because of a
hypersensitive-like response (Proite et al. 2008 ).
Despite the high level of disease resistance generally found in peanut wild rela-
tives, important variation can exist between accessions belonging to the same spe-
cies. Singh et al. ( 1996 ) conducted a detailed characterisation of 42 accessions
belonging to the species A. duranensis using principal component analysis and
showed that differences in reaction to rust between accessions of the same species
explained 15 % of the total variation. Variation between accessions for resistance to
pests and diseases has also been reported for nematodes (Sharma et al. 1999 ),
peanut bud necrosis virus (Reddy et al. 2000 ), late leaf spot and rust (Pande and
Rao 2001 ). These results indicated that clear identifi cation of most resistant wild
accessions is needed before their utilisation as source of disease resistance.
12.3.2 Tolerance to Abiotic Stresses
Unlike resistance to pests and diseases that is generally governed by one or a few
genes, tolerance to abiotic stress is often polygenic, subject to G × E interactions and
thus necessitates accurate phenotyping to better capture the genetic component of
trait variation. Field evaluation of peanut wild relatives over several years is diffi cult
because of their differences in generation time (annual to perennial life cycles) and
the diffi culty of harvesting seeds. Hence, only a limited number of studies have
reported the characterisation of peanut wild relatives for response to abiotic stress,
and most of them were based on the measurement of morphological and/or physi-
ological traits in greenhouse conditions. Nautiyal et al. (
2008 ) evaluated 38 accessions
of 12 Arachis species belonging to four sections for thermo-tolerance (heat and cold).
J.-F. Rami et al.
259
Several morphological and physiological traits, viz., leaf morphology, electrolyte
leakage, leaf water potential, specifi c leaf area (SLA) and leaf chemical constituents,
were recorded. Tolerance to heat and cold has been expressed as percentage of leaf
relative injury (RI). These authors reported important variation between species and
between accessions within a species. One accession of A. glabrata (section
Rhizomatosae ) and one accession of A. paraguariensis (section Erectoides ) were
identifi ed as heat resistant and cold resistant, respectively. One accession of A.
appressipila (section Procumbentes ) was found susceptible to both cold and heat.
Moreover, positive correlations were found between RI and SLA both for heat and
cold resistance, indicating that genotypes with thicker leaves also have higher toler-
ance. Upadhyaya et al. ( 2011a ) measured 41 morpho-agronomic traits over 269
accessions from 20 wild Arachis species belonging to six sections. A large range of
variation was observed for traits related to drought: earliness, SLA and SPAD chlo-
rophyll meter reading (SCMR). Finally, a set of 20 accessions with superior agro-
nomic and drought-related trait combinations were proposed to be used in breeding
programmes for introgression of wild favourable alleles in the genetic background
of cultivated varieties. Leal-Bertioli et al. ( 2012 ) investigated drought-related traits
such as leaf morphology, transpiration profi le, SCMR, SLA and transpiration
rate per leaf area of two wild diploid species ( A. duranensis and A. ipaënsis ) and
one synthetic tetraploid deriving from the cross between the same diploid species.
One interesting result that came from this study is that most drought- related traits
such as leaf area, stomata size and transpiration rate were substantially modifi ed when
evaluated in a wild tetraploid context attesting for effects of the ploidy level on trait
variations. These authors concluded that, for the introgression of drought-related traits
from wild species to cultivated species, evaluation of the synthetic tetraploid was
likely to be more informative than the evaluation of the diploids. Additionally, it
would also be interesting to investigate the effect of genetic background (cultivated
versus wild) on the modifi cation of drought-related trait variation.
12.3.3 Evaluation for Nutritional Value
As peanut is an important food and oil crop, improving protein content and oil quality
in seeds are important objectives of breeding programmes. The properties of peanut
oil are determined by the fatty acid content and particularly the oleic-to- linoleic
ratio (O/L). The analysis of the chemical composition of peanut wild species seeds has
been reported. The oil and protein content and the fatty acid and sterol composition
of the seeds of several wild accessions were studied by Stalker et al. ( 1989 ) in sec-
tions Arachis , Heteranthae , Caulorrhizae and Procumbentes and by Grosso et al.
( 2000 ) in sections Arachis , Extranervosae , Erectoides and Triseminatae . The high-
est oil content and O/L ratio were found in species belonging to section Arachis
( A. stenosperma and A. villosa , respectively). In both studies, none of the wild
species analysed overrode the cultivated species in terms of chemical quality and oil
stability. However one can expect that the cultivated species could benefi t from
12 Groundnut
260
positive alleles from the wild through transgressive segregation. Jiang et al. ( 2009 )
evaluated 87 wild Arachis accessions and 113 interspecifi c offspring for traits
related to fatty acid composition. These authors reported transgressive segregation
in progeny derived from the crosses between A. stenosperma and two Chinese cul-
tivated varieties and between A. glabrata and one cultivated line. Two progenies
involving A. stenosperma as wild donor had 12.8 to 29.7 % more oleic acid than
their parents. Similarly, four progenies from the cross between A. glabrata and one
cultivated line had higher content of oleic acid and lower content of palmitic acid than
the cultivated line. Moreover, in this study, high content of oleic acid was found in
accessions of A. duranensis and A. pusilla . Wang et al. ( 2010 ) evaluated 39 wild spe-
cies of different sections for oil content, fatty acid composition and D150N functional
mutation of the FAD2A gene. Signifi cant variability was found among species, but no
accession had high oleic/linoleic acid ratio. Finally, Upadhyaya et al. ( 2011a ) evalu-
ated the nutritional value (oil, protein and sugar) of 20 peanut wild accessions among
which seven belong to A. stenosperma , three each to A. monticola and A. pusilla ,
two to A. kuhlmannii and one each to A. villosa , A. batizocoi , A. duranensis , A.
dardani and A. paraguariensis . These authors reported for oil content a range of
variation (45–55 %) similar to that reported in cultivated varieties.
12.4 Molecular Markers and Maps: The Introgression
Toolbox
Plant breeding programmes generally use backcrossing for the introgression of wild
genes into elite materials for a specifi c trait. At each backcross generation, plants
with the wild target phenotype introgression are selected, while the background of
the cultivated parent is recovered through generations. Without the help of molecu-
lar markers, this process results in the introgression of a large portion of the donor
genome, which carries undesirable genes associated to the allele of interest (linkage
drag), and many backcross generations are necessary to eliminate the deleterious
genes. Molecular markers, ordered on a genetic map, provide a tool to monitor
the size and distribution of wild introgressions throughout the breeding process.
Their availability is a key step in the successful implementation of large-scale intro-
gression programmes.
12.4.1 Molecular Markers
The fi rst markers used in peanut were isozymes and proteins (Grieshammer and
Wynne 1990 ; Krishna and Mitra 1988 ; Lu and Pickersgill 1993 ), followed by
restriction fragment length polymorphisms—RFLPs (Kochert et al. 1991 , 1996 ;
Paik-Ro et al.
1992 ), random amplifi ed polymorphic DNA—RAPD (Dwivedi et al.
2001 ; Halward et al. 1991 , 1992 ; Hilu and Stalker 1995 ; Raina et al. 2001 ;
J.-F. Rami et al.
261
Subramanian et al. 2000 ) and amplifi ed fragment length polymorphism—AFLP
(Gimenes et al. 2002 ; He and Prakash 1997 , 2001 ; Herselman 2003 ; Milla et al.
2005 ; Tallury et al. 2005 ). However, none of these marker systems were very infor-
mative in cultivated germplasm. In recent years, microsatellite or simple sequence
repeat (SSR) markers have become the assay of choice for genetic studies in Arachis ,
since they are multiallelic, co-dominant, polymorphic, transferable among related
species, PCR based and usable in tetraploid genomes. In consequence, efforts have
been made by several research groups to develop microsatellite markers for peanut.
Up to 15,000 SSR markers have been published to date (Hopkins et al. 1999 ;
Palmieri et al. 2002 , 2005 ; He et al. 2003 , 2005 ; Ferguson et al. 2004 ; Moretzsohn
et al. 2004 , 2005 , 2009 ; Bravo et al. 2006 ; Budiman et al. 2006 ; Gimenes et al. 2007 ;
Proite et al. 2007 ; Wang et al. 2007 , 2012 ; Cuc et al. 2008 ; Gautami et al. 2009 ; Guo
et al. 2009 ; Liang et al. 2009 ; Nagy et al. 2010 ; Song et al. 2010 ; Yuan et al. 2010 ;
Koilkonda et al. 2012 ; Macedo et al. 2012 ; Shirasawa et al. 2012a ). The availability
of a great number of microsatellite markers has enabled access to the low genetic
variation available in cultivated peanut (Barkley et al. 2007 ; Krishna et al. 2004 ;
Macedo et al. 2012 ; Tang et al. 2007 ; Varshney et al. 2009b ). Recently, Shirasawa
et al. ( 2012b ) developed 535 markers derived from transposon-enriched genomic
libraries. These MITE markers showed great potential, as they detected higher poly-
morphism levels than genomic microsatellite markers. Finally, single- nucleotide
polymorphism (SNP) markers constitute the most abundant molecular markers in the
genome and can be carried out with higher throughput genotyping methods. SNP
markers have been widely used in many plant species. However, they have not been
used in peanut so far, as the implementation in polyploid plants is diffi cult.
12.4.2 Genetic Maps
Linkage maps are particularly useful for the study of the genome structure and
organisation and for marker-assisted selection in breeding programmes. Due to the
very low genetic variation in cultivated peanut, interspecifi c populations have fi rst
been used for the construction of linkage maps in Arachis .
The fi rst published map for Arachis was based on RFLP markers and developed
using an F
2 population of 87 individuals derived from a cross A. stenosperma × A.
cardenasii , both diploid species with A genome (Halward et al. 1993 ). One hundred
and seventeen loci were mapped into 11 linkage groups covering a total map dis-
tance of 1,063 cM. A diploid backcross population derived from the same parents
was also used to compute a linkage map ( Garcia et al. 2005 ). One hundred and
sixty-seven RAPD and 39 RFLP loci were mapped into 11 linkage groups, spanning
800 cM. The 39 RFLP markers were common to the F
2 -based map of Halward et al.
( 1993 ) and were used to establish correspondences between both maps. All com-
mon markers mapped to the same linkage groups and mostly in the same order.
The fi rst genetic map for the tetraploid genome of Arachis was based on a
backcross population (BC
1 ) having the amphidiploid TxAG-6 [ A. batizocoi ×
12 Groundnut
262
( A. cardenasii × A. diogoi )] 4 x
as donor parent and A. hypogaea cv. Florunner as recur-
rent parent (Burow et al. 2001 ). A total of 370 RFLP markers were mapped into 23
linkage groups covering 2,210 cM. The pairing of homoeologous linkage groups
was consistent with the disomic nature of the allotetraploid peanut.
The fi rst peanut SSR-based map was constructed for an F
2 population derived from
a cross of two diploid species with A genome, A. duranensis and A. stenosperma
(Moretzsohn et al. 2005 ). One hundred and seventy loci were mapped into 11 linkage
groups covering 1,231 cM of total map distance. New markers were added to this
map, resulting in 369 loci, including 188 microsatellites, 80 anchors and 35 resis-
tance gene analogue (RGA) markers, mapped into ten linkage groups, as expected
for diploid species of Arachis (Leal-Bertioli et al. 2009 ). The same authors devel-
oped a diploid F
2 population derived from the cross A. ipaënsis × A. magna to build a
map for the B genome of Arachis (Moretzsohn et al. 2009 ). A total of 149 co-dominant
markers, mostly microsatellites, were mapped into ten linkage groups spanning a
distance of 1,294.4 cM. Fifty-one common markers evidenced the high synteny of
the B genome map and the A map and revealed the translocation of chromosomal
segments from the group A7 to the group A8.
A synthetic amphidiploid ( A. ipaënsis × A. duranensis ) was crossed and back-
crossed to A. hypogaea cv. Fleur 11, resulting in 88 BC
1 F 1 individuals (Fonceka
et al. 2009 ). This population was used to develop an SSR-based linkage map for the
tetraploid genome, composed of 298 markers and 21 linkage groups, covering a total
distance of 1,843.7 cM. The segregation analysis indicated a disomic inheritance of
all loci and chromosome pairing occurring between homologous genome confi rm-
ing the close relationship between the wild diploids A. duranensis , A. ipaënsis and
the cultivated peanut and highlighted structural rearrangements, such as chromo-
somal segment inversions and a major translocation event, between the A and B
genome species. A comparative analysis of this map with the diploid genome maps
of Moretzsohn et al. ( 2005 , 2009 ) suggested the occurrence of this event prior to the
peanut’s tetraploidisation.
An intraspecifi c map was published in 2008, using 142 individuals of a recombi-
nant inbred line (RIL) population derived from a cross between one accession of A.
hypogaea subsp. hypogaea and one accession of the fastigiata subspecies (Hong et al.
2008 ). New markers were added to this map, and two additional maps were constructed
based on RIL populations having accessions of the subspecies fastigiata as parents
(Hong et al. 2010 ). Of the 901 screened, 132, 109 and 46 SSR markers were mapped
on each of the three linkage maps. A reference map was developed, with 175 loci
and 22 linkage groups, covering a total distance of 885.4 cM. The marker order was
in general collinear to the A genome map of Moretzsohn et al. ( 2005 ).
Another intraspecifi c map for peanut was developed using a RIL population
composed of 318 F
8 /F 9 plants (Varshney et al. 2009a ). Corroborating the known low
genetic variation of peanut, only 135 microsatellite markers, of the 1,145 screened,
mapped in 22 linkage groups spanning 1,270.5 cM. This map enabled the mapping
of QTLs controlling drought tolerance-related traits as well as establishing relation-
ships with diploid A genome of groundnut and model legume genome species.
In 2012, several moderately saturated maps and two proposed reference maps
were published. Wang et al. ( 2012 ) reported a linkage map, based on an F
2
J.-F. Rami et al.
263
population of 94 individuals derived from A. hypogaea subsp. hypogaea × A.
hypogaea subsp. fastigiata cross. The map consisted of 318 loci, mostly SSRs, onto
21 linkage groups covering a total distance of 1,674.4 cM. In this study, resistance
gene homolog (RGH)-containing BAC clones were sequenced to develop SSR
markers. Two of these markers were mapped into two different linkage groups,
anchoring one RGH-BAC contig and one singleton, which can facilitate marker-
assisted selection for disease resistance breeding and map-based cloning of resis-
tance genes. Shirasawa et al. ( 2012a ) developed a great number of microsatellite
and transposon markers by in silico analysis and published the most saturated indi-
vidual map for Arachis to date. A total of 1,114 markers were mapped into 21 link-
age groups covering 2,166.4 cM based on an F
2 population ( n = 94) derived from an
A. hypogaea subsp. hypogaea × A. hypogaea subsp. fastigiata cross. The authors also
published an intra-subspecifi c A. hypogaea subsp. hypogaea × A. hypogaea subsp.
hypogaea map, with 326 markers and 19 linkage groups, spanning 1,332.9 cM.
An integrated map was constructed from two RIL populations (Qin et al. 2012 ).
This map contained 324 markers covering 1,352.1 cM with 21 linkage groups. The
translocation event that seems to have occurred between linkage groups A7 and A8
or B7 and B8 was also evident in comparison of this map to previously published
diploid and tetraploid maps (Moretzsohn et al. 2005 , 2009 ; Fonceka et al. 2009 ).
Two reference consensus linkage maps were published very recently for peanut
(Gautami et al. 2012 ; Shirasawa et al. 2013 ). The fi rst map (Gautami et al. 2012 ) was
based on ten intraspecifi c RILs and one interspecifi c backcross population and com-
prised 895 microsatellite markers. Linkage groups were identifi ed and named by com-
parisons with the diploid maps previously published for the A and B genomes of
Arachis (Moretzsohn et al. 2005 , 2009 ; Leal-Bertioli et al. 2009 ). The reference map
was divided into 20 cM long 203 BINs having microsatellite markers with known
polymorphism information content (PIC) values. The second map (Shirasawa et al.
2013 ) was based on three wild-derived RIL populations, integrated with another 13
maps already published and with sequences of other legume species. All this information
will be useful for selecting highly polymorphic and uniformly distributed markers for
further genetic studies and marker-assisted selection in peanut.
12.5 Achievements
12.5.1 The Different Routes for Interspecifi c Population
Development: How to Access Wild Gene Reservoir
in the Context of Ploidy Reproductive Barrier
One of the main constraints to hybridisation between cultivated peanut A. hypogaea
and its wild relatives is the reproductive barrier caused by the difference in ploidy
level. In order to access and use the large genetic diversity available in diploid
species in a tetraploid context, one has to turn to bridging strategies allowing the
crossability of wild species and the cultivated. Four different routes have been
12 Groundnut
264
described by Simpson ( 2001 ): the hexaploid pathway, two different diploid/tetraploid
pathways and genetic engineering-based methods.
The hexaploid pathway consists in the direct cross of a given diploid species
with A. hypogaea. The resulting hybrid is triploid and sterile and can be doubled
to the hexaploid level after treatment by colchicine. In general, the hexaploid is
cytologically unstable, and the tetraploid state needs to be recovered following
chromosome loss through successive selfi ng or backcrossing to A. hypogaea.
The fi rst diploid/tetraploid route consists of reconstructing a tetraploid from a
two- or a multiple-way cross of different Arachis diploid species having different
genome types. The hybrid is treated by colchicine to double the chromosome num-
ber. The resulting allotetraploid is cross compatible with cultivated peanut and can
be used as a parent for an introgression programme. Alternatively, in the second
diploid/tetraploid route, a single Arachis diploid species representative or hybrids
between diploid species having the same genome can be colchicine doubled to form
an autotetraploid that is cross compatible with cultivated peanut. Autotetraploids
have however been described as weak plants and crossing with A. hypogaea reported
as diffi cult (Holbrook and Stalker 2003 ).
As a fourth strategy, transformation technologies can be used to access genes
from species of the tertiary gene pools or from outside the genus.
12.5.2 Wild Introgressions in Peanut: A Historical View
Several long-term programmes have been conducted to introgress valuable genes
from wild Arachis species into cultivated peanut since the fi rst interspecifi c hybridi-
sations realised by Krapovickas and Gregory in the 1940s.
Using the hexaploid pathway, Stalker et al. ( 1979 ) generated a tetraploid inter-
specifi c population from a cross produced earlier by Smartt and Gregory ( 1967 )
between a cultivated peanut line (PI 261942-3), collected from Paraguay, and the A
genome diploid species A. cardenasii (10017 GKP, PI 262141). The population was
obtained after fi ve generations of selfi ng from the colchicine-doubled triploid hybrid
that allowed to recover tetraploid individuals with 40 chromosomes. The pheno-
typic characterisation of this population allowed the identifi cation and selection of
several lines for higher yield, resistance to leaf spots ( Cercospora arachidicola and
Cercosporidium personatum ) as well as resistance to several insects. Using the ten
highest yielding families of this population, a recurrent selection programme was
conducted (Guok et al. 1986 ) and resulted in a signifi cant increase in fruit yield and
kernel yield components after two cycles of recurrent selection, providing an early
evidence that favourable alleles for grain production can be gained from a wild
Arachis diploid species. From the same population, several hybrid selections were
identifi ed as having signifi cantly higher level of resistance to early leaf spot (Stalker
1984 ) than the most resistant cultivar evaluated at the same time. However, these
hybrid derivatives had poor agronomic performance and could not be used directly
as improved variety.
J.-F. Rami et al.
265
With the development of molecular markers, the same group of researchers
characterised a set of lines from the same interspecifi c population with RFLP and
RAPD markers (Garcia et al. 1995 ). Based on an existing RFLP linkage map
(Halward et al. 1993 ), the analysis revealed the distribution of introgressed segments
from A. cardenasii in the cultivated genetic background attesting of recombination
events between the diploid genome and both genomes of the cultivated (88 % of the
A. cardenasii introgression events were located in the A genome and 12 % were
located in the B genome). One of the lines, identifi ed as resistant to nematode
( Meloidogyne arenaria ), was crossed again to the cultivated parent to generate a
segregating population from which two linked dominant resistance genes could be
identifi ed and designated as Mae , a dominant gene restricting egg number, and Mag ,
a dominant gene restricting galling. Using bulked segregant analysis (BSA), one
RAPD marker was linked at 10 and 14 cM from Mag and Mae , respectively (Garcia
et al. 1996 ). Two root-knot nematode-resistant varieties have been released following
this research (Stalker et al. 2002a ). In addition, late leaf spot resistance lines deriving
from the same population were also registered (Stalker and Beute 1993 ; Stalker
et al. 2002b ) as well as insect resistant lines (Stalker and Lynch 2002 ).
More recently, the variety GPBD4 has been developed through pedigree selection
from the cross between KRG1, an early maturing line from Argentina, and ICGV
86855 (Gowda et al. 2002 ), also referred to as CS16 (Vishnuvardhan et al. 2011 ), an
interspecifi c derivative from A. cardenasii . GPBD4 is resistant to late leaf spot and
rust and has spread over large area in the state of Karnataka in south of India (Gowda
et al. 2002 ). A QTL mapping study involving a RIL population from the cross
between GPBD4 and TAG24 allowed the identifi cation of late leaf spot and rust
resistance QTLs that could be related to early introgressions from A. cardenasii
into the cultivated genome (Khedikar et al. 2010 ). Another case of utilisation of
A. cardenasii was the development of a foliar disease-resistant variety using the
hexaploid pathway from a primary cross between the variety CO1 and A. cardena-
sii. After three successive backcrosses with the cultivated parent and four genera-
tions of selfi ng, the variety VG9514 was selected (Varman 1999 ), and it showed
good resistance to rust and late leaf spot. The rust resistance QTL identifi ed by
Khedikar et al. ( 2010 ) from GPBD4 was confi rmed in a similar RIL population
involving VG9514 and TAG24 as parents (Mondal et al. 2012 ).
Following the work with A. cardenasii , another landmark in the use of wild species
occurred with the use of the tetraploid route. Simpson et al. ( 1993 ) created the fi rst
amphidiploid from a three-way cross between A. cardenasii and A. diogoi on the A
genome side and A. batizocoi on the B genome side. The AB sterile hybrid was
treated with colchicine to produce TxAG-6, a fertile amphidiploid that has been at
the root of major genetic studies and breeding applications. The fi rst tetraploid
RFLP-based genetic map was constructed from an interspecifi c BC
1 population
involving TxAG-6 as donor parent into the cultivated background of Florunner
(Burow et al. 2001 ). The genetic map obtained was the fi rst nearly saturated tetra-
ploid map and allowed the genome-wide analysis of the transmission of chromatin
between wild and cultivated species attesting of a similar recombination pattern as
chromosome pairing reported for A. hypogaea . The RFLP nature of the markers
12 Groundnut
266
used in this study also made it possible to analyse the synteny conservation and
colinearity between the two subgenomes of A. hypogaea showing a globally high
level of conservation and some chromosomal rearrangements. TxAG-6 and TxAG- 7,
a backcross derivative (BC
1 ) of TxAG-6 with the variety Florunner, were released
for their breeding potential for resistance to root-knot nematode and leaf spot
(Simpson et al. 1993 ). TxAG-7 was further used as parent of a backcross population
(BC
4 F 2 ) from which genetic markers linked to root-knot nematode have been identi-
fi ed by bulk segregant analysis. This single gene, identifi ed in A. cardenasii and
transferred to peanut through TxAG-6, is currently the only dominant root-knot
nematode resistance gene deployed in modern cultivars (Holbrook et al. 2008 ). By
comparative genetic mapping in diploid and tetraploid peanut populations, this
gene, called Rma , was found to have been introduced in a chromosome segment
spanning one-third to one-half of chromosome 9A (Nagy et al. 2010 ). In the latter
study, numerous codominant markers were identifi ed for fi ner mapping of Rma and
for marker-assisted selection for nematode resistance, by using two tetraploid RIL
populations of A. hypogaea and an intraspecifi c F
2 diploid population from a cross
between two A. duranensis accessions. Initially, two varieties were released from
backcross derivatives of TxAG6 with Florunner: COAN and NemaTAM (Simpson
and Starr 2001 ; Simpson et al. 2003 ). NemaTAM was almost immune to root-knot
nematode but sensitive to tomato spotted wilt tospovirus (TSWV). Further improved
varieties were developed starting either from NemaTAM or COAN and using either
conventional methods or marker-assisted selection to develop varieties combining
resistance to nematode and TSWV, like Tifguard (Timper et al. 2008 ) or Tifguard
high O/L (Holbrook et al. 2011 ).
Another route, involving in vitro techniques, has also been described that allowed
to tap wild species from tertiary gene pool of Arachis genus. Hybrids have been
obtained between A. hypogaea and two diploid wild species from section
Procumbentes , A. chiquitana and A. kretschmeri (Mallikarjuna and Hoisington
2009 ; Mallikarjuna and Tandra 2006 ). Arachis glabrata from section Rhizomatosae
has also been successfully crossed with A. hypogaea (Mallikarjuna and Sastri 2002 ).
The method includes embryo rescue from immature pods resulting from the inter-
specifi c cross between A. hypogaea and the diploid wild. To recover tetraploid state
the authors benefi ted from numerically unreduced gametes or 2 n pollen that are
produced at low frequency from F
1 hybrids (Mallikarjuna and Tandra 2006 ). The
same authors have also used the tetraploid route to produce a collection of 17 new
allotetraploids and autotetraploids between different species of the secondary gene
pool (Mallikarjuna et al. 2011 ). The different diploid species involved were A. bati-
zocoi , A. cardenasii , A. diogoi , A. duranensis , A. hoehnei , A. ipaënsis , A. kempff-
mercadoi , A. magna , A. stenosperma and A. valida . One allotetraploid (ISATGR
1212) and its reciprocal form (ISATGR-40A) had the same genomic composition of
A. hypogaea originating from the cross of A. duranensis with A. ipaënsis. This
collection of synthetics representing a wide coverage of diversity of the second-
ary gene pool of Arachis are a valuable resource for introgression of positive wild
alleles into cultivated gene pool, and the crossability with cultivated peanut has been
analysed for fi ve of them (Mallikarjuna et al.
2012b ). The use of these synthetics as
J.-F. Rami et al.
267
progenitors to conduct introgression programmes in cultivated peanut is in progress
in breeding programmes in Senegal and in India.
Also using the tetraploid route, a synthetic amphidiploid has been developed
in Brazil from the proposed ancestors of cultivated peanut ( A. ipaënsis and A.
duranensis ) (Fávero et al. 2006 ). This amphidiploid donor has been crossed with
Runner IAC 886 (a selection of Florunner), and 12 lines that combine agronomi-
cally adapted phenotype with resistance to late leaf spot have been selected using a
combination of genotyping and phenotyping (Fig. 12.2 ) (Leal-Bertioli et al. 2010 ;
Leal- Bertioli SCM, Moretzsohn MC, Guimaraes PM, Godoy I and Bertioli DJ
unpublished results).
An introgression programme has been conducted using the same amphidiploid
and Fleur 11, a popular variety from Senegal, as cultivated recipient. The whole
process involved the construction of an interspecifi c SSR genetic map at the BC
1 F 1
generation (Fonceka et al. 2009 ), followed by a large marker-assisted backcross
scheme to monitor wild introgression distribution in the genome of the cultivated
parent at each generation. The programme was conducted up to the BC
4 F 3 genera-
tion to produce a set of chromosome segment substitution lines (CSSLs) that glob-
ally incorporate the whole genome of the wild ancestors as overlapping segments
Fig. 12.2 Introgression of resistance for late leaf spot into the cultivated variety Runner IAC 886.
After one backcross and fi eld selection of backcross, lines combining resistance to LLS and good
agronomic performance were selected
12 Groundnut
268
introgressed in the recipient cultivar. The whole programme that represents seven
generations was conducted over a period of 4 years (Fig. 12.3 ) thanks to off-season
generations and the ability to successfully genotype progenies as part of the breeding
process during the short time frame between seedling and fl owering.
As part of this introgression programme, an advanced backcross (AB-QTL) pop-
ulation was derived from the plants that were not selected to be advanced to CSSLs
at the BC
2 F 1 generation (Fonceka et al. 2012a ). The population was composed of a
mix of BC
3 F 1 and BC
2 F 2 individuals that were allowed to self-pollinate to produce
BC
3 F 2 and BC
2 F 3 families used for the phenotyping and QTL detection. Several
traits concerning days to fl owering, plant architecture, pod and seed morphology
and yield components were analysed in this population leading to the identifi cation
of 95 QTLs in two different water regimes. As a fi rst conclusion, it could be shown
Fig. 12.3 Breeding scheme followed for the development of the CSSL population (Fonceka et al.
2012b )
J.-F. Rami et al.
269
that wild alleles contributed positive variation to many valuable agronomic traits
such as fl owering precocity, seed and pod number per plant, length and size as well
as pod maturity. About half of the positive QTL effects were associated to the allele
of the amphidiploid parent. In some cases, these QTLs, such as QTLs for seed
length on chromosome a09, were associated to undesirable morphological traits like
pod constriction or pod beak, probably requiring further backcrosses to reduce
linkage drag. However, in several cases favourable wild QTLs had no detrimental
association and could be directly used to improve the cultivated variety: QTLs for
pod number and weight on chromosome a01, QTLs for seed number, total biomass
and stress tolerance indices on chromosome a05 and QTLs for seed diameter on chro-
mosome b06. Moreover, the comparison of QTLs obtained under well-watered and
water-limited conditions revealed that QTLs for stress tolerance indices for pod and
seed numbers with favourable alleles attributed to the wild parents could be involved
in the trade-off between maintaining large-sized seed and producing more seeds under
water stress. In addition, QTL clusters related to domestication syndrome, i.e. involved
in plant and pod morphology as well as pod and seed size, were also mapped in the
same study. QTLs that greatly affected pod and seed size appeared to be clustered
in three genomic regions while those affecting the plant and pod morphology were
dispersed across the genome. It was proposed from these fi ndings that the main
focus of human selection at the incipient stage of domestication could have been
concentrated on pod and seed size, given the primitive growth habits and constriction
depths that still exist in peanut cultivated species (Fonceka et al. 2012a ).
The fi nal CSSL population (Fonceka et al. 2012b ) was composed of 122 lines
offering a wide coverage of the peanut genome especially in the context of the large
peanut genome size (c. 2,800 Mb/1C and 20 linkage groups) with target wild chro-
mosome segments of 39.2 cM on average. Most of the CSSLs (62 %) contained a
single wild fragment in a homogeneous cultivated genetic background (Fig. 12.4 ).
For the lines that contained more than one fragment, additional backcrossing efforts
are ongoing for deriving lines harbouring a unique wild chromosome segment.
Using simple high-heritability traits like plant growth habit or pod constriction as a
proof of concept, the value of the CSSL population could be illustrated. For example,
an introgression line harbouring a single wild donor fragment corresponding to the
location of a QTL for pod constriction identifi ed in the AB-QTL population showed
deeply constricted pods as compared to the moderate constriction observed with the
cultivated parent, confi rming the QTL previously identifi ed. Similarly, two lines
harbouring single overlapping donor fragments in the region of a QTL for plant
growth habit showed contrasting phenotypes, allowing to confi rm and refi ne the
position of this QTL (Fig. 12.5 ).
12.6 Conclusion and Further Prospects
As described in the previous sections, wild introgressions in peanut have now been
carried out for many years, particularly because of the specifi c interest this approach
represents for the improvement of this crop. However, in spite of those important
12 Groundnut
271
achievements, and mainly due to the limitations of the plant itself in terms of
crossability, multiplication rate, and, until recently, lack of appropriate molecular
tools, the extent of utilisation of the useful allele reservoir of the wild species and
its impact on peanut breeding have been limited. For now, successful introgression
of wild genes into cultivated peanut concerns few wild species. Arachis cardenasii
has probably been one of the most used sources of useful genes to date even if
crosses involving other species have also been used. The recent use of the two most
probable ancestors of peanut A. duranensis and A. ipaënsis in a systematic
Fig. 12.5 Relation between introgression and phenotype for pod constriction and plant growth
habit for three CSSL lines. ( a ) QTLs detected in AB-QTL population for pod constriction (PC)
on linkage group a02 and for plant growth habit (GH) on linkage group a03. ( b ) Graphical geno-
type of three CSSL lines corresponding to the same QTLs. ( c ) Phenotype of the CSSL line
12CS_052 for pod constriction. ( d ) Phenotype of the CSSL line 12CS_004 for plant growth habit.
( e ) Phenotype of the CSSL line 12CS_072 for plant growth habit
12 Groundnut
272
introgression programme opens the way for extensive and detailed characterisation
of genetic determinism and wild alleles’ effects on a wide range of traits. However
this resource only involves two representatives of two wild species, and the poten-
tial in generalising introgression programmes to other accessions of the same spe-
cies and to other species of the secondary gene pool is immense.
A general strategy to harness this potential is proposed in Fig.
12.6 . One of the
major lessons learned through the utilisation of wild species in crop improvement is
that cryptic valuable alleles can be found in wilds that can be identifi ed and charac-
terised only once it is incorporated in a cultivated genetic background. As proposed
by Tanksley and Nelson (
1996 ), advanced backcross QTL analysis has the potential
to simultaneously identify wild QTL alleles while delivering genetic material
directly applicable to breeding. One extension of this approach is to construct a
CSSL library through more backcross generations and a higher control of introgres-
sion sizes and distribution. However, this last approach requires a large investment
in terms of crossing and genotyping and cannot be generalised to a wide range of
wild donors. Nevertheless, single-fragment introgression lines can be derived from
AB-QTL populations on a QTL-by-QTL basis. Such lines, once the wild effect has
been validated and characterised, can be crossed to accumulate favourable alleles
for different traits toward variety release. They can also be used for deriving near-
isogenic lines through further backcrossing providing experimental material for
map-based gene cloning. The implementation of this strategy requires a close inte-
gration of genotyping in the breeding process, which can now be widely achieved,
thanks to the development of molecular markers and genetic maps in peanut and the
availability of genotyping platforms offering fast and reliable genotyping services.
Fig. 12.6 A general strategy for harnessing the potential of peanut wild relatives using AB-QTL
and CSSL populations
J.-F. Rami et al.
273
Such a large-scale generalised introgression programme would require a concerted
effort of the peanut international community. Taking into account the number of wild
accessions available in gene banks, a rational sampling of target donors would have
to be achieved, regarding peanut breeding objectives, based on the characterisation
knowledge base that already exists on wild diseases resistance, ecological adapta-
tion, fertility and crossability. A concerted strategy would also be required on the
choice of cultivated backgrounds for introgression. A fi rst option (the one that has
been used in tomato) would be to use a common cultivated background allowing the
direct comparison of the effects of introgressions from different species and the opti-
misation of the introgression effort among the community. However, the disadvan-
tage of this option resides in the fact that a common cultivated background may not
be adapted to some of the target environments compromising the potential of direct
breeding application of introgressed material. As an alternative, the choice of spe-
cifi c targeted elite cultivars by improving wild crosses seems to offer a better trade-
off between breeding opportunities and genetic analysis.
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