Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid
© Foncéka et al; licensee BioMed Central Ltd. 2009
Received: 20 February 2009
Accepted: 3 August 2009
Published: 3 August 2009
Peanut (Arachis hypogaea L.) is widely used as a food and cash crop around the world. It is considered to be an allotetraploid (2n = 4x = 40) originated from a single hybridization event between two wild diploids. The most probable hypothesis gave A. duranensis as the wild donor of the A genome and A. ipaënsis as the wild donor of the B genome. A low level of molecular polymorphism is found in cultivated germplasm and up to date few genetic linkage maps have been published. The utilization of wild germplasm in breeding programs has received little attention due to the reproductive barriers between wild and cultivated species and to the technical difficulties encountered in making large number of crosses. We report here the development of a SSR based genetic map and the analysis of genome-wide segment introgressions into the background of a cultivated variety through the utilization of a synthetic amphidiploid between A. duranensis and A. ipaënsis.
Two hundred ninety eight (298) loci were mapped in 21 linkage groups (LGs), spanning a total map distance of 1843.7 cM with an average distance of 6.1 cM between adjacent markers. The level of polymorphism observed between the parent of the amphidiploid and the cultivated variety is consistent with A. duranensis and A. ipaënsis being the most probable donor of the A and B genomes respectively. The synteny analysis between the A and B genomes revealed an overall good collinearity of the homeologous LGs. The comparison with the diploid and tetraploid maps shed new light on the evolutionary forces that contributed to the divergence of the A and B genome species and raised the question of the classification of the B genome species. Structural modifications such as chromosomal segment inversions and a major translocation event prior to the tetraploidisation of the cultivated species were revealed. Marker assisted selection of BC1F1 and then BC2F1 lines carrying the desirable donor segment with the best possible return to the background of the cultivated variety provided a set of lines offering an optimal distribution of the wild introgressions.
The genetic map developed, allowed the synteny analysis of the A and B genomes, the comparison with diploid and tetraploid maps and the analysis of the introgression segments from the wild synthetic into the background of a cultivated variety. The material we have produced in this study should facilitate the development of advanced backcross and CSSL breeding populations for the improvement of cultivated peanut.
Peanut (Arachis hypogaea L.) is widely used as a food and cash crop around the world. It is mainly grown by resource-poor farmers in Africa and Asia to produce edible oil, and for human and animal consumption. Peanut is a member of the Fabaceae, tribe Aeschynomeneae, subtribe Stylosanthinae, genus Arachis. In this genus, 69 diploid and tetraploid species have been described . A. hypogaea is the only species that has been truly domesticated although several species have been cultivated for their seed or forage . Cultivated peanut is considered to be an allotetraploid (2n = 4x = 40) originated from a single hybridization event between two wild diploids with A and B genome . Several studies aimed at identifying the wild diploid ancestors of A. hypogaea. The wild species A. duranensis and A. ipaënsis appeared to be the best candidates for the A and B genome donors, respectively [4–6].
Polyploidy is a widespread process that played a major role in higher plants' speciation and adaptation. The stages of polyploid formation usually include reproductive isolation from the progenitors [7, 8]. As for many polyploid species, cultivated peanut has experienced a genetic bottleneck which, superimposed with the effects of the domestication, has greatly narrowed the genetic diversity. The low level of DNA polymorphism between cultivated genotypes has been described by many authors [9–12]. More recently, a rate of polymorphism of 12.6% has been reported between two cultivated varieties, used as parents of a RIL population, surveyed with 1145 SSR markers . The low level of polymorphism within cultivated peanut has greatly hampered the application of molecular breeding approaches for the genetic improvement of cultivated peanut. Up to date, few genetic linkage maps have been published in Arachis. At the diploid level, three genetic maps involving species with A and B genomes, one based on RFLP markers  and the other ones on SSR markers [15, 16], have been produced. The A genome SSR based map has been recently extended using legume anchor markers and aligned with Medicago and Lotus genomic sequences . At the tetraploid level, two genetic maps were also reported. Varshney et al.  reported the detection of drought tolerance QTLs based on a cultivated × cultivated SSR genetic map. Although the genetic map remained unsaturated, due to the low level of polymorphism between cultivated peanut varieties, QTLs have been detected attesting of the interest of molecular breeding tools in genetic improvement of peanut. Burow et al.  reported the construction of a RFLP map, based on a BC1 population deriving from a cross between a wild synthetic amphidiploid (TxAG6) and a cultivated peanut variety (Florunner). The synthetic amphidiploid, used to overcome the reproductive barriers between the wild diploids and the cultivated species, allowed the genome-wide analysis of the transmission of chromatin between wild and cultivated species of the genus Arachis. However, the wild parents used to create the amphidiploid (A. batizocoi, A. cardenasii and A. diogoii) are unlikely to be the ancestors of A. hypogaea [12, 19–21]. The genetic mapping of populations derived from the cross between the most probable wild progenitors of A. hypogaea and a cultivated peanut variety has, to our knowledge, never been reported.
Genome-wide introgression of a small fraction of the wild genome species while keeping the genetic background of the cultivated is a good mean to explore the largely untapped reservoir of useful alleles of interest that remain in the wild species. This is especially interesting for species with narrow genetic basis. This approach has been widely utilized for the introgression of favourable QTL(s) for various traits in tomato [22–26], in rice [27–32], in wheat  and in barley [34, 35]. In peanut, the reproductive barriers between wild and cultivated species, the technical difficulties encountered in making large number of crosses as well as the short period between sowing and flowering have impeded the efforts to apply a Marker Assisted Backcross (MABC) approach for the development of interspecific introgression line populations.
In this study, we report for the first time the development and the analysis of the genome-wide segment introgressions of the most probable wild progenitors of the cultivated peanut species (A. duranensis and A. ipaënsis) into the background of the cultivated Fleur 11 variety through the construction of a SSR genetic map as well as the evaluation of the coverage and the length of the wild genome segments in a BC1F1 and BC2F1 populations. This work benefits from the recently developed synthetic amphidiploid (A. ipaënsis × A. duranensis)4X  that made possible the interspecific introgressions.
Young leaves were harvested from 15 day old plants and immediately stored at 4°C in ice before DNA extraction. DNA was extracted from 100 mg of fresh leaves following a slightly modified MATAB protocol . Briefly, leaves were ground in liquid nitrogen using a mortal and pestle and dissolved in 750 μL of MATAB buffer at 74°C. The samples were incubated 20 minutes at 74°C and cooled during 5 minutes at room temperature. A volume of 750 μL of CIA (24:1) was added in each sample and all samples were shaken gently until homogenization before centrifugation at 12000 rpm during 20 minutes. The supernatant was harvested and the DNA was precipitated with 600 μL of 2-propanol. After centrifugation, pellets were washed with 300 μL of 70% ethanol, air dried and dissolved in 500 μL of TE.
Four hundred twenty three already-published SSR markers [12, 15, 21, 37–45] plus 135 unpublished long size SSR markers from EMBRAPA and the Universidade Católica de Brasília were used in this study. A total of 558 SSR markers have been screened for polymorphism on the amphidiploid and its two wild diploid parents, and on the cultivated Fleur 11 variety. For a given SSR locus, the forward primer was designed with a 5'-end M13 tail (5'-CACGACGTTGTAAAACGAC-3'). PCR amplifications were performed in a MJ Research PTC-100™ thermocycler (Waltham, MA, USA) or in an Eppendorf Mastercycler on 25 ng of DNA in a 10 μl final volume of buffer (10 mM Tris-HCl (pH 8), 100 mM KCl, 0.05% w/v gelatin, and 2.0 mM MgCl2) containing 0.1 μM of the M13-tailed primer, 0.1 μM of the other primer, 160 μM of dNTP, 1 U of Taq DNA polymerase (Life Technologies, USA.) and 0.1 μM of M13 primer-fluorescent dye IR700 or IR800 (MWG, Germany). The touchdown PCR programme used was as follow: initial denaturation at 95°C for 1 min; following by 10 cycles of 94°C for 30 s, Tm (+5°C, -0.5°C/cycle) for 1 min, and 72°C for 1 min. After these cycles, an additional round of 25 cycles of 94°C for 30 s, Tm for 1 min, and 72°C for 1 mn and a final elongation step at 72°C for 8 min was performed. IR700 or IR800-labeled PCR products were diluted 7-fold and 5-fold respectively, subjected to electrophoresis in a 6.5% polyacrylamide gel and then sized by the IR fluorescence scanning system of the sequencer (LI-COR, USA). Migration images were analysed using Jelly 0.1 (Rami, unpublished) and exported as a data table. Segregations were checked for distortion to the expected 1:1 ratio using a Chi2 test at a significance level of 0.05.
Genetic map construction
The polymorphic markers were used to genotype 88 individuals of the BC1F1 population. The linkage analysis was performed using Mapdisto software version 18.104.22.168  and CarthaGene software version 1.0 . The origins of the alleles (A or B genomes) were determined by comparison to the alleles coming from the diploid progenitors of the amphidiploid. Mapdisto software was used in a first step, for the linkage group determination and marker ordering within each linkage group. A minimum LOD of 4 and maximum recombination fraction of 0.3 were fixed for the linkage group determination using the "find groups" command. The order of the markers within each linkage group was estimated using the "order" command. The markers that had not been placed at LOD 4 were tried at decreasing LOD, down to a LOD of 2 and a maximum recombination fraction of 0.3. These markers are indicated in italic on the map (Figure 2). The quality of the genotyping data at a specific marker was controlled using the "drop locus" command. The few markers having bad quality genotyping data were discarded from the linkage analysis. In a second step, CarthaGene software was used for the optimization of the best marker order determined by Mapdisto. This was done applying the simulated "annealing" and "greedy" algorithms. The best maps obtained were improved using the "Flips" and the "Polish" commands. Genetic distances between markers were computed using Kosambi mapping function.
From the map of 298 SSR markers previously developed on the BC1F1 generation, a framework map comprising 115 SSR markers was derived. Compared to the initial map, this framework offered a regular coverage of all the linkage groups. These 115 SSR markers were used to genotype 123 BC2F1 individuals.
Introgression analysis of the BC1F1 and BC2F1 populations was performed using the CSSL Finder software version 0.8b4 . To select a subset of BC1F1 and BC2F1 lines providing an optimal coverage of donor genome into the recurrent background, we imposed a target length of the introgressed wild segments of 20 cM, an overlapping of adjacent segments for a given LG and the best possible return to the background of the cultivated variety.
The percentage of wild genome in the BC1F1 and BC2F1 generations and its relative diminution between the two generations, the mean size of wild introgression segments per LG and per generation, as well as the distribution of the wild segment lengths were estimated using the genotyping data available for each generation. The analysis was conducted on LGs longer than 75 cM. The lengths of the introgressed segments were calculated as the sum of consecutive intervals having a heterozygous genotype plus half the size of each flanking interval having a recurrent homozygous genotype.
SSR polymorphism and origin of the markers
Among the 558 SSR markers screened, 333 (59.6%) were polymorphic between Fleur 11 and AiAd. At a given SSR locus, the sub-genomic origin of the alleles was determined by comparison with the alleles of the diploid parents of the amphidiploid A. ipaënsis and A. duranensis that were included on each gel. This allowed distinguishing three categories of markers among the 333 polymorphic markers: 174 SSRs that were polymorphic for the A genome (52.0%), 77 SSRs that were polymorphic for the B genome (23.0%) and 82 SSRs that were polymorphic for the two genomes (24.5%). The largest proportion of polymorphic markers originated from the A genome donor A. duranensis (76.6%), the B genome donor A. ipaënsis generating 47.6% of polymorphic markers.
Genetic map construction
The comparison of the A and B genomes was undertaken using 53 SSR markers that mapped on both A and B LGs. The A and B LGs were considered to be homeologous when they shared at least 2 common markers. This allowed distinguishing 8 pairs of homeologous LGs (a01/b01, a02/b02, a03/b03, a04/b04, a05/b05, a06/b06, a09/b09 and a10/b10) and one quadruplet involving the LGs a07, b07, a08 and b08. LG a07 shared three markers with the upper part of LG b07 corresponding to at least the half of this LG. The lower part of LG b07 shared three markers with the upper part of LG a08. Furthermore, the lower part of LG a08 shared three markers with LG b08 (Figure 2). The small LG b11 shared 1 marker with LG a03. An overall good collinearity was observed between homeologous LGs. However, three inversions of chromosomal segments were observed on the homeologous LGs a01/b01, a03/b03, and a09/b09. Small inversions were also observed on the homeologous LGs a08/b08. These inversions might result from artefacts as they concerned closely linked markers with more than one possible order having similar LOD values. No mosaic composition of linkage groups, where A genome markers would map together with B genome markers, was observed.
A total of 32 SSR markers (10.7%) showed significant segregation distortion at P < 0.05. Apart from 4 markers mapped on LGs b01 (IPAHM037), b04 (TC12A01), b06 (AC2C02), and LG a08 (TC3B05) all the distorted markers were concentrated in specific zones of 6 different LGs (a02, b02, a03, b03, b07 and b10). Differences between the A and B genomes were also observed. For the A genome, only 8 markers (4.4%) showed segregation distortions compared to 24 (20.3%) for the B genome. For the A genome, in the zones of distortion of LGs a02 and a03, all the distorted markers were skewed toward the alleles of the cultivated parent. For the B genome, the zones of distorted markers of LGs b02 and b07 were skewed toward the allele of the wild parent while those of b03 and b10 were skewed toward the allele of the cultivated parent.
Fifteen primer pairs (AC2C02, Ah-594, PM042, Seq14D11, Seq18A03, Seq18G09, Seq19H03, Seq3C02, Seq4H11, Seq9E08, TC11B04, TC9E08, TC19E01, TC23F04 and TC40C03) amplified consistently more than one locus on the same genome. We were able to map the duplicated loci for the markers Ah-594, PM042, Seq18A03, Seq18G09, Seq19H03, TC11B04 and TC9E08. Apart from the loci amplified by TC9E08 that mapped on the same LG (a04), the loci amplified by AC2C02, Ah-594, PM042, Seq14D11, Seq18A03, Seq18G09, Seq19H03, Seq3C02, Seq4H11, Seq9E08, TC11B04, TC19E01, TC23F04 and TC40C03 mapped on different LGs suggesting possible segmental duplications. These markers were identified by the number 1, 2 and 3 on the map (Figure 2).
Comparison with peanut published genetic maps
Conserved structural features between tetraploid maps
The present tetraploid map was compared to the RFLP based tetraploid BC1F1 map published by Burow et al. , further called "Burow's map" involving a cross between A. hypogaea variety Florunner and the synthetic amphidiploid TxAG6 ([(A. batizocoi × (A. cardenasii × A. diogoii)]4X). A. batizocoi was considered to be the B genome donor and A. cardenasii and A diogoi were the donors of the A genome. In that cross, 23 LGs spanning a total genetic distance of 2210 cM (Kosambi mapping function) were obtained. This map size was slightly larger than our map. A similar number of loci had been mapped on the A genome (156 for Burow's map versus 181 for our map) but the number of loci mapped on the B genome of the Burow's map was about 2 fold larger than on the present map (206 versus 117 respectively). The mean length of the A genome LGs was similar between the 2 maps (93.7 cM for the Burow's map vs 100.5 cM for our map) while the mean length of the B genome LGs of the Burow's map was 1.2 larger than that of the present map (94.1 cM for the Burow's map versus 76.2 cM for our map). The difference in map size between the two studies seems related to the difference of the number of mapped markers on the B genome. Interestingly, conservation of synteny between one B genome LG and two A genome LGs was observed in the two maps. On our map, LG b07 shared common markers with LG a07 and a08 while on Burow's map, LG 19 shared common markers with LG 9.1 and 9.2. Moreover, Burow et al.  has reported structural differences, mainly chromosome segment inversion, between four pairs of homeologous LGs (LG1/LG11, LG7/LG17, LG4/LG14 and LG5/LG15). Inversions of chromosomal segments have been observed for at least 3 LGs in our map (a01/b01, a03/b03 and a09/b09).
Comparison with diploid map
The results from the present tetraploid map were compared to the SSR based diploid F2 map , involving a cross between two wild diploids with A genome, A. duranensis and A. stenosperma. In that population, 11 LGs covering a total map length of 1230.8 cM (Kosambi mapping function) have been described. The total map length was slightly longer than what we obtained in our map when considering the total size of the LGs of the A genome (1005.2 cM). The proportion of distorted markers found in the study of Moretzsohn et al.  was higher than what we recorded for our A genome map (50% versus 4%). Given that a similar number of individuals were used for the map construction in the two studies, the length difference between the 2 maps might be related to the higher proportion of distorted markers on the Moretzsohn's map.
In this study, the construction of a tetraploid molecular genetic map using a BC1F1 population and the development of a BC2F1 population allowed the analysis of the introgression of wild alleles in the background of a cultivated peanut variety. Several points have been highlighted including (1) the low level of polymorphism of the SSR markers especially between the B wild genome A. ipaënsis and the B genome of the cultivated, (2) the collinearity between the A and B genomes, the synteny between tetraploid and diploid maps, and the similarity between tetraploid maps, (3) the good level of introgression of the wild genome segments in the background of the cultivated variety.
SSR polymorphism data is consistent with A. duranensis and A. ipaënsisbeing the most probable progenitors of the cultivated species
Cultivated peanut Arachis hypogaea is considered to be an allotetraploid (2n = 4x = 40) originated from a single hybridization event between two wild diploids with A and B genomes , followed by spontaneous duplication of the chromosomes. The identification of the wild progenitors of the cultivated peanut has been the object of numerous investigations using various approaches including cross-compatibility , molecular markers [4, 12, 20, 21, 49, 50], biogeography , gene sequence comparison , physical mapping of rRNA genes  and Genome In Situ Hybridization (GISH) . The most probable hypothesis gave A. duranensis as the wild donor of the A genome and A. ipaënsis as the wild donor of the B genome. In our study, a close relationship has been observed between the putative wild progenitor's A. duranensis and A. ipaënsis and the cultivated A. hypogaea var. Fleur 11 based on 558 SSR markers. A. duranensis and A. ipaënsis shared 54.1% and 72.6% of common SSR alleles with the A genome and the B genome of A hypogaea respectively. Moreover, 59.8% polymorphism was observed between the synthetic amphidiploid AiAd and the cultivated Fleur 11 variety. This is lower than the 83% of polymorphism that has been observed between the synthetic polyploid TxAG6 ([(A. batizocoi × (A. cardenasii × A. diogoii)]4X) and the cultivated Florunner variety based on RFLP markers . This result indicates that A. duranensis and A. ipaiensis are more closely related to the A and the B genomes of the cultivated species than are A. cardenasii and A. diogoi for the A and A. batizocoi for the B genomes respectively. Moreover, the BC1 tetraploid map obtained by crossing the synthetic amphidiploid AiAd and Fleur 11 indicated a disomic inheritance of all loci. For all the LGs obtained, the markers that were polymorphic for the A genome mapped on A LGs and those polymorphic for the B genome mapped on B LGs. The chromosome pairing seems to happen between "homologous genome" attesting the high affinity between A. duranensis and the A genome of the cultivated species, and between A. ipaënsis and the B genome of the cultivated species. The same results have also been reported by Seijo et al. . Our data fit well with the earlier reports indicating A. duranensis and A. ipaënsis as the most probable diploid progenitors of the cultivated peanut.
In this study, the synteny analysis between the A and B genomes revealed inversion of chromosomal segments for at least three LGs, and a particular feature of synteny involving the LGs a07, b07, a08 and b08 (Figure 2). Conservation of synteny between the upper region of LGs a07 and b07, and between LG b08 and the lower region of LG a08 has been pointed out. Furthermore, the upper region of LG a08 shared also three markers with the lower region of LG a07 while LG b08 lacked a large chromosomal segment that could correspond to the region of conserved synteny between LGs b07 and a08. These observations are consistent with a major translocation event that has occurred between LGs b07 and b08. Similar feature of synteny conservation between two LGs of the B genome and two LGs of the A genome have also been reported at the diploid level when comparing the A. duranensis × A. stenosperma diploid AA map  and the A. ipaënsis × A. magna diploid BB map . Interestingly, the quadruplet of syntenic LGs in the diploid maps was also found to be syntenic with those in our map (data not shown). These observations suggest that the rearrangement between LGs b07 and b08 is an ancient translocation event that happened prior to the tetraploidisation of the cultivated peanut.
Chromosome rearrangements, including the inversion of chromosomal segments within pairs of homeologous linkage groups and the conservation of synteny between a triplet of LGs (one LG of the B genome sharing common markers with two LGs of the A genome) have also been reported by Burow et al. . We were not able to identify which LGs of our map are in synteny with those of the Burow's map due to the difference of the marker types used in the two studies.
The similarity of the rearrangement events observed in the diploid and the tetraploid maps, which involve different species for A and B genomes, suggests that these evolutionary mechanisms have contributed to the divergence of the A and B genomes of the section Arachis. It also raises the question of the classification of the B genome species. The relationships between species with B genome remain controversial. Using RFLP makers, Gimenes et al.  reported a clustering of A. batizocoi and A. magna which were less related to A. ipaënsis, while with SSR markers, Moretzsohn et al.  reported a clustering of the species with B genome including A. batizocoi, A. magna and A. ipaënsis. Seijo et al.  reported, based on GISH, the distinction of A. batizocoi from the other B genome species and concluded that species with B genome do not seem to constitute a natural group.
The results obtained from the comparison of the diploid and tetraploid maps suggest that, based on the similarities of the rearrangement event, the species with B genome A. ipaënsis, A. magna and A. batizocoi could have derived from a common B genome ancestor and could be more closely related than what was previously reported based on molecular makers and on GISH. The construction of a consensus molecular genetic map involving the available diploid AA and BB maps and the tetraploid AABB maps as well as the study of crossability between species with B genome should shed new light on this issue.
Modifications of parental diploid genome following polyploidization, have been reported (for review see, [54, 55]). The modifications include structural rearrangements, transposable element activation, difference in gene expression and epigenetic changes. These changes were observed in old polyploid [56–59] as well as in newly synthesized amphidiploids [60–62]. Rapid and dynamic changes in genome structure, including non additive inheritance of genomic fragments and genome-specific sequence deletion have been described in some taxa including Brassica  and wheat synthetic allotetraploids , but not in others including cotton  and sugarcane . In peanut, Burow et al.  reported a possible genomic restructuring in the synthetic amphidiploid TxAG6 characterized by 5% of mapped alleles having unknown parental origins. In our study, we utilized a synthetic amphidiploid which had undergone several cycles of self-pollination before crossing with the cultivated allotetraploid. However, to the level of resolution afforded by our experiment, no change in genome structure has been pointed out. Further studies are needed to confirm the effectiveness and the level of genomic restructuring in peanut synthetic allotetraploid.
Wild segment introgressions and perspectives for the development of interspecific breeding populations
Few studies have been reported in the literature regarding the genetic mapping of introgressions from wild to the cultivated peanut. Apart from the study of Burow et al. , introgression mapping of wild segments in the background of a cultivated variety has been reported in 46 introgression lines originated from the hybridization between A. cardenasii × A. hypogaea . Considering all the lines together, introgressed segments could be found on 10 of the 11 LGs of the A. stenosperma × A. cardenasii diploid AA map , and represented 30% of the diploid peanut genome. The mapping of a wild segment from A. cardenasii conferring resistance to root-knot nematode  and the registration of two varieties of peanut 'COAN'  and 'NemaTAM' , having identifiable alleles conferring resistance to root-knot nematode transferred from wild species, have also been reported.
In our study, we used a synthetic wild amphidiploid as a mean for the introgression of alien alleles in the genetic background of a cultivated variety and, consequently, enlarging the genetic basis of the cultivated peanut. Genetic mapping of the wild introgressed segments gave a clear picture of the amount and the level of coverage of the wild donor genome in the background of the cultivated, and of the segment lengths and their relative decrease from BC1F1 to BC2F1 generation. The mean length of the wild segments was 51.8 cM in BC1F1 and 34.8 cM in BC2F1, and the decrease of segment size from BC1F1 to BC2F1 was about -33%. These values were similar to what was obtained in Lycopersicon wild × cultivated backcross populations . Marker assisted selection of BC1F1 and then BC2F1 lines carrying the desirable donor segment with the best possible return to the background of the cultivated variety allowed the selection of a limited set of lines that offer an optimal coverage of the wild genome with an overlapping regions between neighbouring lines and an average segment lengths of 34.8 cM in BC1F1 and 24.5 cM in BC2F1, as well as a 79% return to the background of the cultivated variety in BC2F1. The rapid decrease of wild segment lengths observed between the BC1F1 and BC2F1 generations as well as the good level of recovery of the genetic background of the cultivated variety in BC2F1 generation is of great interest for the genetic mapping of QTLs and the development of Introgression Line (IL) libraries. ILs carrying small wild segments in a constant cultivated genetic background have the advantages of reducing epistatic and linkage drag effects and of improving the resolution of QTL mapping [23, 70]. Furthermore, ILs are reliable and stable genetic resources that can be multiplied and evaluated in various environments. Many valuable sources of resistance to biotic stresses including resistance to Cercospora leafspot , to root-Knot nematode [67, 72], to Peanut Bud Necrosis virus (PBNV) , to late leaf spot disease  and sources of tolerance to abiotic stresses including tolerance to thermal stress  and to drought (Soraya Bertioli, Vincent Vadez personal communication) were identified in peanut wild relatives. These sources can be used for genetic improvement in peanut.
The BC1F1 and BC2F1 populations that we developed are excellent starting points for the development of new breeding populations such as Advanced Backcross (AB) and Chromosome Segment Substitution Lines (CSSL) populations for analysis of the wild alleles contribution to the improvement of cultivated peanut varieties.
In this study, a nearly saturated genetic map has been developed from a cross between the synthetic amphidiploid AiAd and the cultivated Fleur 11 variety. This allowed the synteny analysis of the A and B genomes, the comparison with diploid and tetraploid maps and the analysis of the introgression segments from the most probable wild progenitors of the cultivated peanut into the background of the cultivated Fleur 11 variety. The results of this study confirmed the close relationship between the wild diploids A. duranensis, A. ipaënsis and the cultivated peanut and highlighted structural rearrangements, such as chromosomal segment inversions and a major translocation event, between the A and B genome species. Finally, we showed that the low level of polymorphism reported between cultivated peanut can be overcome by using the wild species. The material we have produced in this study should facilitate the development of AB and CSSL breeding populations for the identification and utilization of valuable genes from the largely untapped reservoir of useful alleles that remained in the wild peanut species.
The authors gratefully acknowledge Angelique D'Hont, Jean-Marc Lacape and Nabila Yahiaoui for the critical review of the manuscript. This study was funded by the Cirad and the Generation Challenge Programme.
- Krapovickas A, Gregory WC: Taxonomía del género Arachis (Leguminosae). Bonplandia. 1994, 8: 1-186.Google Scholar
- Holbrook CC, Stalker HT: Peanut breeding and genetic resources. Plant Breeding Reviews. 2003, 22: 297-355.Google Scholar
- Kochert G, Stalker HT, Gimenes MA, Galgaro ML, Lopes CR, Moore K: RFLP and cytogenetic evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae). Am J Bot. 1996, 83 (10): 1282-1291. 10.2307/2446112.View ArticleGoogle Scholar
- Milla SR, Isleib TG, Stalker HT: Taxonomic relationships among Arachis sect. Arachis species as revealed by AFLP markers. Genome. 2005, 48 (1): 1-11. 10.1139/g04-089.PubMedView ArticleGoogle Scholar
- Favero AP, Simpson CE, Valls JF, Vello NA: Study of the evolution of cultivated peanut through crossability studies among Arachis ipaensis, A. duranensis, and A. hypogaea. Crop Sci. 2006, 46 (4): 1546-1552. 10.2135/cropsci2005.09-0331.View ArticleGoogle Scholar
- Seijo G, Lavia GI, Fernandez A, Krapovickas A, Ducasse DA, Bertioli DJ, Moscone EA: Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH. Am J Bot. 2007, 94 (12): 1963-1971. 10.3732/ajb.94.12.1963.PubMedView ArticleGoogle Scholar
- Ramsey J, Schemske DW: Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annual Review of Ecology and Systematics. 1998, 29 (1): 467-501. 10.1146/annurev.ecolsys.29.1.467.View ArticleGoogle Scholar
- Soltis PS, Soltis DE: The role of genetic and genomic attributes in the success of polyploids. Proc Natl Acad Sci USA. 2000, 97 (13): 7051-7057. 10.1073/pnas.97.13.7051.PubMedPubMed CentralView ArticleGoogle Scholar
- Kochert G, Halward T, Branch WD, Simpson CE: RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theor Appl Genet. 1991, 81 (5): 565-570. 10.1007/BF00226719.PubMedView ArticleGoogle Scholar
- Halward T, Stalker T, LaRue E, Kochert G: Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). Plant Mol Biol. 1992, 18 (2): 315-325. 10.1007/BF00034958.PubMedView ArticleGoogle Scholar
- He G, Prakash CS: Identification of polymorphic DNA markers in cultivated peanut (Arachis hypogaea L.). Euphytica. 1997, 97: 143-149. 10.1023/A:1002949813052.View ArticleGoogle Scholar
- Hopkins MS, Casa AM, Wang T, Mitchell SE, Dean RE, Kochert GD, Kresovich S: Discovery and characterization of polymorphic simple sequence repeats (SSRs) in peanut. Crop Science. 1999, 39: 1243-1247.View ArticleGoogle Scholar
- Varshney R, Bertioli D, Moretzsohn M, Vadez V, Krishnamurthy L, Aruna R, Nigam S, Moss B, Seetha K, Ravi K, et al: The first SSR-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theor Appl Genet. 2008, 118 (4): 729-739. 10.1007/s00122-008-0933-x.PubMedView ArticleGoogle Scholar
- Halward T, Stalker HT, Kochert G: Development of an RFLP linkage map in diploid peanut species. Theor Appl Genet. 1993, 87 (3): 379-384. 10.1007/BF01184927.PubMedView ArticleGoogle Scholar
- Moretzsohn M, Leoi L, Proite K, Guimarães P, Leal-Bertioli S, Gimenes M, Martins W, Valls J, Grattapaglia D, Bertioli D: A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet. 2005, 111: 1060-1071. 10.1007/s00122-005-0028-x.PubMedView ArticleGoogle Scholar
- Moretzsohn MC, Barbosa AV, Alves-Freitas DM, Teixeira C, Leal-Bertioli SC, Guimaraes PM, Pereira RW, Lopes CR, Cavallari MM, Valls JF, et al: A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome. BMC Plant Biol. 2009, 9: 40-10.1186/1471-2229-9-40.PubMedPubMed CentralView ArticleGoogle Scholar
- Bertioli D, Moretzsohn M, Madsen L, Sandal N, Leal-Bertioli S, Guimaraes P, Hougaard B, Fredslund J, Schauser L, Nielsen A, et al: An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics. 2009, 10 (1): 45-45. 10.1186/1471-2164-10-45.PubMedPubMed CentralView ArticleGoogle Scholar
- Burow MD, Simpson CE, Starr JL, Paterson AH: Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.). broadening the gene pool of a monophyletic polyploid species. Genetics. 2001, 159 (2): 823-837.PubMedPubMed CentralGoogle Scholar
- Raina SN, Mukai Y: Genomic in situ hybridization in Arachis (Fabaceae) identifies the diploid wild progenitors of cultivated (A. hypogaea) and related wild (A. monticola) peanut species. Plant Systematics and Evolution. 1999, 214 (1): 251-262. 10.1007/BF00985743.View ArticleGoogle Scholar
- Gimenes MA, Lopes CR, Galgaro ML, Valls JF, Kochert G: RFLP analysis of genetic variation in species of section Arachis, genus Arachis (Leguminosae). Euphytica. 2002, 123: 421-429. 10.1023/A:1015033700110.View ArticleGoogle Scholar
- Moretzsohn M, Hopkins M, Mitchell S, Kresovich S, Valls J, Ferreira M: Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol. 2004, 4: 11-11. 10.1186/1471-2229-4-11.PubMed CentralView ArticleGoogle Scholar
- Eshed Y, Zamir D: An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics. 1995, 141 (3): 1147-1162.PubMedPubMed CentralGoogle Scholar
- Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T: Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet. 1996, 92 (2): 213-224. 10.1007/BF00223378.PubMedView ArticleGoogle Scholar
- Fulton TM, Beck-Bunn T, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD: QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet. 1997, 95 (5): 881-894. 10.1007/s001220050639.View ArticleGoogle Scholar
- Fridman E, Carrari F, Liu Y-S, Fernie AR, Zamir D: Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science. 2004, 305 (5691): 1786-1789. 10.1126/science.1101666.PubMedView ArticleGoogle Scholar
- Lippman ZB, Semel Y, Zamir D: An integrated view of quantitative trait variation using tomato interspecific introgression lines. Current Opinion in Genetics & Development. 2007, 17 (6): 545-552. 10.1016/j.gde.2007.07.007.View ArticleGoogle Scholar
- Wan XY, Su JM, Wang CC, Shen CM, Li JM, Wang HL, Jiang L, Liu SJ, Chen LM, Yasui H, Yoshimura A: QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines. Theor Appl Genet. 2004, 110 (1): 71-79. 10.1007/s00122-004-1744-3.PubMedView ArticleGoogle Scholar
- Wang YM, Dong ZY, Zhang ZJ, Lin XY, Shen Y, Zhou D, Liu B: Extensive de novo genomic variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). Genetics. 2005, 170 (4): 1945-1956. 10.1534/genetics.105.040964.PubMedPubMed CentralView ArticleGoogle Scholar
- Li JZ, Huang HQ, Heinrichs F, Ganal MW, Röder RS: Analysis of QTLs for yield, yield components, and malting quality in a BC 3-DH population of spring barley. Theor Appl Genet. 2005, 110 (2): 356-363. 10.1007/s00122-004-1847-x.PubMedView ArticleGoogle Scholar
- Xu JL, Lafitte HR, Gao YM, Fu BY, Torres R, Li ZK: QTLs for drought escape and tolerance identified in a set of random introgression lines of rice. Theor Appl Genet. 2005, 111 (8): 1642-1650. 10.1007/s00122-005-0099-8.PubMedView ArticleGoogle Scholar
- Zhang X, Zhou S, Fu Y, Su Z, Wang X, Sun C: Identification of a drought tolerant introgression line derived from dongxiang common wild rice (O. rufipogon Griff.). Plant Mol Biol. 2006, 62 (1): 247-259. 10.1007/s11103-006-9018-x.PubMedView ArticleGoogle Scholar
- Zhao XQ, Xu JL, Zhao M, Lafitte R, Zhu LH, Fu BY, Gao YM, Li ZK: QTLs affecting morph-physiological traits related to drought tolerance detected in overlapping introgression lines of rice (Oryza sativa L.). Plant Science. 2008, 174 (6): 618-625. 10.1016/j.plantsci.2008.03.009.View ArticleGoogle Scholar
- Liu S, Zhou R, Dong Y, Li P, Jia J: Development, utilization of introgression lines using a synthetic wheat as donor. Theor Appl Genet. 2006, 112 (7): 1360-1373. 10.1007/s00122-006-0238-x.PubMedView ArticleGoogle Scholar
- von Korff M, Wang H, Léon J, Pillen K: AB-QTL analysis in spring barley: III. Identification of exotic alleles for the improvement of malting quality in spring barley (H. vulgare ssp. spontaneum). Molecular Breeding . 2007, 21 (1): 81-93. 10.1007/s11032-007-9110-1.View ArticleGoogle Scholar
- Schmalenbach I, Léon J, Pillen K: Identification and verification of QTLs for agronomic traits using wild barley introgression lines. Theor Appl Genet. 2009, 118 (3): 483-497. 10.1007/s00122-008-0915-z.PubMedView ArticleGoogle Scholar
- Risterucci AM, Grivet L, N'Goran JA, Pieretti I, Flament MH, Lanaud C: A high-density linkage map of Theobroma cacao L. Theor Appl Genet. 2000, 101 (5): 948-955. 10.1007/s001220051566.View ArticleGoogle Scholar
- Palmieri DA, Hoshino AA, Bravo JP, Lopes CR, Gimenes MA: Isolation and characterization of microsatellite loci from the forage species Arachis pintoi (Genus Arachis). Molecular Ecology Notes. 2002, 2: 551-553. 10.1046/j.1471-8286.2002.00317.x.View ArticleGoogle Scholar
- He G, Meng R, Newman M, Gao G, Pittman RN, Prakash C: Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC Plant Biol. 2003, 3: 3-3. 10.1186/1471-2229-3-3.PubMedPubMed CentralView ArticleGoogle Scholar
- Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S: Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet. 2004, 108: 1064-1070. 10.1007/s00122-003-1535-2.PubMedView ArticleGoogle Scholar
- Palmieri DA, Bechara MD, Curi RA, Gimenes MA, Lopes CR: Novel polymorphic microsatellite markers in section Caulorrhizae (Arachis, Fabaceae). Molecular Ecology Notes. 2005, 5: 77-79. 10.1111/j.1471-8286.2004.00838.x.View ArticleGoogle Scholar
- Bravo JP, Hoshino AA, Angelici CMLCD, Lopes CR, Gimenes MA: Transferability and use of microsatellite markers for the genetic analysis of the germplasm of some Arachis section species of the genus Arachis. Genetics and Molecular Biology. 2006, 29: 516-524. 10.1590/S1415-47572006000300021.View ArticleGoogle Scholar
- Hoshino AA, Bravo JP, Angelici CMLCD, Barbosa AaVG, Lopes CR, Gimenes MA: Heterologous microsatellite primer pairs informative for the whole genus Arachis. Genetics and Molecular Biology. 2006, 29: 665-675. 10.1590/S1415-47572006000400016.View ArticleGoogle Scholar
- Proite K, Leal-Bertioli SCM, Bertioli DJ, Moretzsohn MC, Silva FRd, Martins NF, Guimarães PM: ESTs from a wild Arachis species for gene discovery and marker development. BMC Plant Biol. 2007, 7: 7-7. 10.1186/1471-2229-7-7.PubMedPubMed CentralView ArticleGoogle Scholar
- Gimenes M, Hoshino A, Barbosa A, Palmieri D, Lopes C: Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea). BMC Plant Biol. 2007, 7 (9).Google Scholar
- Cuc L, Mace E, Crouch J, Quang V, Long T, Varshney R: Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol. 2008, 8 (1): 55-55. 10.1186/1471-2229-8-55.PubMedPubMed CentralView ArticleGoogle Scholar
- Lorieux M: MapDisto, A Free User-Friendly Program For Computing Genetic Maps. Plant and Animal Genome XV conference. San Diego, CA. 2007, P958.Google Scholar
- De Givry S, Bouchez M, Chabrier P, Milan D, Schiex T: CARTHAGENE: multipopulation integrated genetic and radiated hybrid mapping. Bioinformatics. 2005, 21 (8): 1703-1704. 10.1093/bioinformatics/bti222.PubMedView ArticleGoogle Scholar
- MapDisto Genetics Software: CSSL Finder. [http://mapdisto.free.fr/CSSLFinder/]
- Singh AK, Smartt J: The genome donors of the groundnut/peanut (Arachis hypogaea L.) revisited. Genetic Resources and Crop Evolution. 1998, 45 (2): 113-116. 10.1023/A:1008640631719.View ArticleGoogle Scholar
- Raina SN, Rani V, Kojima T, Ogihara Y, Singh KP, Devarumath RM: RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species. Genome. 2001, 44: 763-772. 10.1139/gen-44-5-763.PubMedView ArticleGoogle Scholar
- Ferguson ME, Jarvis A, Stalker HT, Williams DE, Guarino L, Valls JFM, Pittman RN, Simpson CE, Bramel PJ: Biogeography of wild Arachis (Leguminosae):distribution and environmental characterisation. Biodiversity and Conservation. 2005, 14 (7): 1777-1798. 10.1007/s10531-004-0699-7.View ArticleGoogle Scholar
- Jung S, Tate PL, Horn R, Kochert G, Moore K, Abbott AG: The phylogenetic relationship of possible progenitors of the cultivated peanut. J Hered. 2003, 94 (4): 334-340. 10.1093/jhered/esg061.PubMedView ArticleGoogle Scholar
- Seijo JG, Lavia GI, Fernandez A, Krapovickas A, Ducasse D, Moscone EA: Physical mapping of the 5S and 18S-25S rRNA genes by FISH as evidence that Arachis duranensis and A. ipaensis are the wild diploid progenitors of A. hypogaea (Leguminosae). Am J Bot. 2004, 91: 1294-1303. 10.3732/ajb.91.9.1294.PubMedView ArticleGoogle Scholar
- Soltis DE, Soltis PS: Polyploidy: recurrent formation and genome evolution. Trends in Ecology & Evolution. 1999, 14 (9): 348-352. 10.1016/S0169-5347(99)01638-9.View ArticleGoogle Scholar
- Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS, Wendel JF: Evolutionary genetics of genome merger and doubling in plants. Annual Review of Genetics. 2008, 42 (1): 443-461. 10.1146/annurev.genet.42.110807.091524.PubMedView ArticleGoogle Scholar
- Wendel JF: Genome evolution in polyploids. Plant Mol Biol. 2000, 42 (1): 225-249. 10.1023/A:1006392424384.PubMedView ArticleGoogle Scholar
- Rieseberg LH: Chromosomal rearrangements and speciation. Trends in Ecology & Evolution. 2001, 16 (7): 351-358. 10.1016/S0169-5347(01)02187-5.View ArticleGoogle Scholar
- Liu B, Wendel JF: Epigenetic phenomena and the evolution of plant allopolyploids. Molecular Phylogenetics and Evolution. 2003, 29 (3): 365-379. 10.1016/S1055-7903(03)00213-6.PubMedView ArticleGoogle Scholar
- Clarkson JJ, Lim KY, Kovarik A, Chase MW, Knapp S, Leitch AR: Long-term genome diploidization in allopolyploid Nicotiana section Repandae (Solanaceae). New Phytologist. 2005, 168 (1): 241-252. 10.1111/j.1469-8137.2005.01480.x.PubMedView ArticleGoogle Scholar
- Adams KL, Wendel JF: Polyploidy and genome evolution in plants. Current Opinion in Plant Biology. 2005, 8 (2): 135-141. 10.1016/j.pbi.2005.01.001.PubMedView ArticleGoogle Scholar
- Chen ZJ, Ni Z: Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays. 2006, 28 (3): 240-252. 10.1002/bies.20374.PubMedView ArticleGoogle Scholar
- Nicolas SD, Mignon GL, Eber F, Coriton O, Monod H, Clouet V, Huteau V, Lostanlen A, Delourme R, Chalhoub B, et al: Homeologous recombination plays a major role in chromosome rearrangements that occur during meiosis of Brassica napus haploids. Genetics. 2007, 175 (2): 487-503. 10.1534/genetics.106.062968.PubMedPubMed CentralView ArticleGoogle Scholar
- Liu B, Vega JM, Feldman M: Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome. 1998, 41 (4): 535-542. 10.1139/gen-41-4-535.PubMedView ArticleGoogle Scholar
- Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF: Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome. 2001, 44 (3): 321-330. 10.1139/gen-44-3-321.PubMedView ArticleGoogle Scholar
- Jannoo N, Grivet L, Chantret N, Garsmeur O, Glaszmann JC, Arruda P, D'Hont Al: Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. The Plant Journal. 2007, 50 (4): 574-585. 10.1111/j.1365-313X.2007.03082.x.PubMedView ArticleGoogle Scholar
- Garcia GM, Stalker HT, Kochert G: Introgression analysis of an interspecific hybrid population in peanuts (Arachis hypogaea L.) using RFLP and RAPD markers. Genome. 1995, 38 (1): 166-176.PubMedView ArticleGoogle Scholar
- Garcia GM, Stalker HT, Shroeder E, Kochert G: Identification of RAPD, SCAR, and RFLP markers tightly linked to nematode resistance genes introgressed from Arachis cardenasii into Arachis hypogaea. 1996, 836-845.Google Scholar
- Simpson CE, Starr JL: Registration of 'COAN' Peanut. Crop Science. 2001, 41: 918-918.View ArticleGoogle Scholar
- Simpson CE, Starr JL, Church GT, Burow MD, Paterson AH: Registration of 'NemaTAM' Peanut. Crop Science. 2003, 43: 1561-1561.View ArticleGoogle Scholar
- Zamir D: Improving plant breeding with exotic genetic libraries. Nat Rev Genet. 2001, 2 (12): 983-989. 10.1038/35103589.PubMedView ArticleGoogle Scholar
- Stalker : Utilizing Arachis cardenasii as a source of Cercospora leafspot resistance for peanut improvement. Euphytica. 1984, 33 (2): 529-538. 10.1007/BF00021154.View ArticleGoogle Scholar
- Sharma SB, Ansari MA, Varaprasad KS, Singh AK, Reddy LJ: Resistance to Meloidogyne javanica in wild Arachis species. Genetic Resources and Crop Evolution. 1999, 46 (6): 557-568. 10.1023/A:1008754812257.View ArticleGoogle Scholar
- Reddy AS, Reddy LJ, Mallikarjuna N, Abdurahman MD, Reddy YV, Bramel PJ, Reddy DV: Identification of resistance to Peanut bud necrosis virus (PBNV) in wild Arachis germplasm. Annals of Applied Biology. 2000, 137: 135-139. 10.1111/j.1744-7348.2000.tb00045.x.View ArticleGoogle Scholar
- Pande S, Rao JN: Resistance of wild Arachis species to late leaf spot and rust in greenhouse trials. Plant Disease. 2001, 85: 851-855. 10.1094/PDIS.2001.85.8.851.View ArticleGoogle Scholar
- Nautiyal PC, Rajgopal K, Zala PV, Pujari DS, Basu M, Dhadhal BA, Nandre BM: Evaluation of wild Arachis species for abiotic stress tolerance: I. Thermal stress and leaf water relations. Euphytica. 2008, 159 (1–2): 43-57.Google Scholar
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