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Peanut improvement is limited by a narrow genetic base. However, this obstacle can be circumvented by incorporating phenotypic variability from wild, diploid Arachis species through interspecific hybridizations. In this study, four allotetraploid interspecific hybrids IpaCor4x (A. ipaensis × A. correntina), IpaDur4x (A. ipaensis × A. duranensis), IpaSten4x (A. ipaensis × A. stenosperma), and ValSten4x (A. valida × A. stenosperma) were created and morphologically characterized through the following parameters: flower count, flower size, flower banner pigmentation, leaf area and weight, leaf hairiness, main stem height, internode length, percent of reproductive nodes, biomass, 100 pod weight, and 100 seed weight. For every trait, except for flower banner absorption at 380 nm, at least one or more allotetraploids differed from the cultivated peanut control. In general, these allotetraploids had a greater production of flowers during the growing season, larger flowers, larger and hairier leaves, taller main stems, longer primary laterals, longer internodes, lower percentage of reproductive nodes, heavier plant body masses, and smaller seeds and pods. This phenotypic diversity can be utilized directly in ornamental and forage breeding, while for oil and food crop breeding, this diversity will likely need to be selected against while desirable traits such as disease and insect resistance and abiotic stress tolerances derived from the wild diploid species are maintained.

Peanut is an important global food crop with a narrow genetic base due to its domestication bottleneck and the ploidy barrier between it and almost all of its wild diploid relatives. Increasingly, peanut breeders have been introgressing beneficial alleles from its diploid relatives into the cultigen to improve agronomic traits along with its pathogen and pest resistances. To overcome the ploidy barrier, the process of introgression can be initiated by making hybrids between A- and B/K-genome Arachis diploid species and then doubling their chromosomes to induce tetraploidy. These allotetraploids are generally cross-compatible with peanut. Previously, true allotetraploids were distinguished from selfed progeny by infertile pollen grain counts; however, markers that can distinguish allele dosage between A- and B/K-genomes allow allotetraploids to be confirmed before flowering or even planting and can be more reliable than infertile pollen grain counts. These markers also can be used to confirm and track the inheritance of previously discovered homoeologous recombination events, which commonly occur in synthetic allotetraploid-derived materials. In this study, 105 KASP markers distinguishing A- and B/K-genomes were designed to span the entire peanut genome. These markers can be used as a time and cost-efficient alternative to using the Axiom_Arachis SNP arrays where high-resolution is not required.

High oleate is an important seed quality trait frequently incorporated in peanut varieties. Crop wild relatives (CWR) are potentially useful genetic resources for cultivar improvement through genetic introgression; but for wild peanut species, many chemical or nutritional traits are not well characterized. A mutant from Arachis veigae S. H. Santana & Valls (2n = 2x = 20), with increased oleic and very long chain (C ≥ 22) fatty acid content was identified from screening 209 accessions of 45 species using gas chromatography (GC). The A. veigae (formerly A. sylvestris) accession, VVeSv 8373 (PI 688970) contained 55.5% oleic acid in seeds, significantly higher than the average (18.3%) of other accessions within the same species and also significantly higher than the average (37.0%) of all wild peanut accessions evaluated. A C37T substitution was identified by sequencing the coding region of FAD2H, resulting in the nonsense mutation of Q13* (a premature stop codon). This functional mutation may significantly reduce the fatty acid desaturase (FAD) activity and result in the enhanced oleate level. Arachis veigae also contained a high percentage of very long-chain (C ≥ 22) fatty acids, and their variation identified in this study is also discussed and compared with other species. The mutant with such an altered fatty acid composition may be useful for potentially improving seed or food nutrition quality.

Genome instability in newly synthesized allotetraploids of peanut has breeding implications that have not been fully appreciated. Synthesis of wild species-derived neo-tetraploids offers the opportunity to broaden the gene pool of peanut; however, the dynamics among the newly merged genomes creates predictable and unpredictable variation. Selfed progenies from the neo-tetraploid Arachis ipaënsis × Arachis correntina (A. ipaënsis × A. correntina)4x and F1 hybrids and F2 progenies from crosses between A. hypogaea × [A. ipaënsis × A. correntina]4x were genotyped by the Axiom Arachis 48 K SNP array. Homoeologous recombination between the A. ipaënsis and A. correntina derived subgenomes was observed in the S0 generation. Among the S1 progenies, these recombined segments segregated and new events of homoeologous recombination emerged. The genomic regions undergoing homoeologous recombination segregated mostly disomically in the F2 progenies from A. hypogaea × [A. ipaënsis × A. correntina]4x crosses. New homoeologous recombination events also occurred in the F2 population, mostly found on chromosomes 03, 04, 05, and 06. From the breeding perspective, these phenomena offer both possibilities and perils; recombination between genomes increases genetic diversity, but genome instability could lead to instability of traits or even loss of viability within lineages.

A diversity of pests can adversely affect peanut (Arachis hypogaea L.) yield, quality, and financial return. Farmers rely heavily on applied chemicals to suppress many of the economically important pests present in peanut. The effectiveness of this approach to pest management may not be sustainable, however, due to evolved resistance in pests to chemicals, reluctance of basic chemical manufacturers to invest in product development because of the relatively small market for peanut compared with other crops, cost to initially register or re‐register chemicals, and the desire for peanut buyers and processors to capture international markets that may have varying agrochemical residue restrictions for peanut. Heavy reliance on chemical control could leave peanut production systems vulnerable to yield loss; thus, a more concerted research effort is needed to increase the number and availability of nonchemical tools that protect peanut from pests in order to ensure long‐term sustainability of peanut production systems.

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid species with a very large and complex genome. This species is susceptible to numerous foliar and soil-borne diseases for which only moderate levels of resistance have been identified in the germplasm collection, but several of the 81 wild species are extremely resistant to many destructive peanut diseases. Peanut species were grouped into nine sections, but only taxa in section Arachis will hybridize with A. hypogaea. Most of these species are diploid, but two aneuploids and two tetraploids also exist in the section. The first peanut cultivars released after interspecific hybridization were ‘Spancross’ and ‘Tamnut 74’ during the 1970s from a cross between A. hypogaea and its tetraploid progenitor. However, introgression of useful genes from diploids has been difficult due to sterility barriers resulting from genomic and ploidy differences. To utilize diploids in section Arachis, direct hybrids have been made between A. hypogaea and diploid species, the chromosome number doubled to the hexaploid level, and then tetraploids recovered with resistances to nematodes, leaf spots, rust, and numerous insect pests. ‘Bailey’, a widely grown Virginia-type peanut, was released from these materials, and other cultivars are gown in Asia and South America. Alternatively, hybrids between diploid A and B genome species have been made, the chromosome number doubled, and cultivars released with nematode resistance derived from Arachis species. Introgression from Arachis species to A. hypogaea appears to be in large blocks rather than as single genes, and new genotyping strategies should enhance utilization of wild peanut genetic resources.

The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.

The first plant genome to be sequenced was the model plant Arabidopsis thaliana in 2000. Since then, over 140 plant species have had their genomes sequenced ( www.ncbi.nlm.nih.gov/genome/browse ). Most of the plants chosen fit specific criteria such as being model organisms or economically important, having small genome size, being diploids, access to genetic and physical maps, transcriptome, and other genomic tools, and also, a large research community. Peanut ( Arachis hypogaea L.) is an allotetraploid, with a large genome (3.2 Mb), commercially important in the United States and of paramount significance for the livelihoods of people in developing countries. The peanut research community gathered around the sequencing of the peanut genome with the clear objective of aiding peanut breeding, to expedite the production of elite cultivars and help ensure global food security and safety. In this chapter we first describe the history of the mobilization of the international peanut research community to plan and execute the sequencing of the peanut genome. Later, we describe the biology of the genome of peanut and its wild ancestral species and how their genomes have been essential for the understanding of the peanut genome.

The peanut, Arachis hypogaea L., is a native South American legume. Macrofossil and starch grain data show peanuts moved into the Zana Valley in Northern Peru 8500 years ago, presumably from the eastern side of the Andes Mountains, although the hulls found there do not have similar characteristics to modern domestic peanuts. At the time of the discovery of the American and European expansion into the New World, this cultivated species was known and grown widely throughout the tropical and subtropical areas of this hemisphere. The early Spanish and Portuguese explorers found the Indians cultivating the peanut in several of the West Indian Islands, in Mexico, on the northeast and east coasts of Brazil, in the warm land of the Rio de la Plata basin (Argentina, Paraguay, Bolivia, extreme southwest Brazil), and extensively in Peru. From these regions the peanut was disseminated to Europe, to the coasts of Africa, Asia, and the Pacific Islands. Eventually, the peanut traveled to the colonial seaboard of the present southeastern United States, but the time and place of its introduction was not documented.

Peanut, also known as groundnut (Arachis hypogaea L.), is a native new world crop. Arachis species originated in South America and are found in tropical and subtropical areas. Eighty-one species have been named (Krapovickas and Gregory, 1994; Valls and Simpson, 2005; Valls et al., 2013), including the domesticated peanut, A. hypogaea L. Species have evolved in highly diverse habitats and both annual and perennial types exist. New species are being discovered in areas that previously were very difficult to reach because of poor roads and transportation. It is likely that the genus originated in the highlands in the southwestern Mato Grosso do Sul region of Brazil close to Gran Pantanal where the most ancient species of the genus (Arachis guaranitica Chodat. and Hassl. and Arachis tuberosa Bong. Ex Benth.) are found (Gregory et al., 1980; Simpson and Faries, 2001). Subsequently, as the planalto continued to be uplifted coupled with water flow, the genus spread into the drier lowlands of South America (Gregory and Gregory, 1979; Stalker and Simpson, 1995; Simpson et al., 2001). The genus likely originated in tropical wetland areas and subsequently adapted for survival in dry environments. Species in the genus Arachis are widely distributed in South America from Northeast Brazil to southern Uruguay and from the Andean lowlands in the west to the eastern Atlantic coast, and the distribution is continuous across this region (Valls et al., 1985). Species grow in deep friable sand to thick, gummy clay and on schist rocks with virtually no soil, suggesting that species have adapted to highly diverse and harsh environments (Simpson et al., 2001). Fruiting below ground likely protected the seeds from predators and the many root adaptations (e.g., rhizomes, tuberous roots) likely helped species to adapt to new habitats. Conversely, the geocarpic fruit impeded rapid spread into new environments. Krapovickas and Gregory (1994) indicated that the most defining morphological features of the genus are underground plant parts, including the fruits, rhizomatous structures, root systems, and hypocotyls. The center of origin for the cultivated species A. hypogaea is believed to be southern Bolivia to northwestern Argentina based on the occurrence of the two progenitor species Arachis duranensis and Arachis ipaënsis, and archaeological evidence gathered in this region (Hammons, 1982; Stalker and Simpson, 1995). Simpson et al. (2001) also suggested that the eastern slopes of Cordillera may be a possible area for origin of A. hypogaea because of the favorable environment for peanut growth. Advances in the peanut genome sequence and the availability of new genomic tools will help clarify the origin and evolution of the cultivated and wild species of the genus Arachis. Wild peanut species were important as sources of food in pre-Columbian times and several taxa are still widely used as forages or for their aesthetic value as a ground cover. Arachis glabrata and Arachis pintoi are utilized for grazing and Arachis repens is used as a ground cover in residential areas and roadsides in tropical regions (Mathews et al., 2000; Hernandez-Garay et al., 2004). Two wild species (Arachis villosulicarpa Hoehne and Arachis stenosperma Krapov. and W.C. Gregory) were cultivated by indigenous people in Brazil for food and medicinal use, albeit on a limited scale (Gregory et al., 1973; Simpson et al., 2001), but only A. hypogaea is economically important today as a human food source. Importantly, many Arachis species have extremely high levels of disease and insect resistances that are not present in cultivated peanut. Fil: Stalker, H. Thomas. North Carolina State University; Estados Unidos Fil: Tallury, Shyamalrau P.. Clemson University, Florence; Estados Unidos Fil: Seijo, José Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; Argentina Fil: Leal Bertioli, Soraya C.M.. Embrapa Agroindustrial Tropical - CNPAT; Brasil

Rma, a dominant root-knot nematode resistance gene introduced into tetraploid peanut (Arachis hypogaea) from a synthetic allotetraploid donor (TxAG-6), has been widely deployed in modern cultivars. The genomic location and borders of the alien chromosome segment introgressed from TxAG-6 into NemaTAM (a BC7-derived introgression line) and other modern cultivars carrying Rma have not been genetically mapped, and resistance gene candidates (RGCs) have not been identified for Rma. Our study focused on densely populating the alien introgression with codominant DNA markers, identifying and mapping the borders of the alien introgression carried by NemaTAM, and identifying RGCs for Rma. Altogether, 2,847 simple sequence repeat (SSR) and 380 single strand conformational polymorphism (SSCP) markers were screened for linkage to Rma-247 of the SSCP markers targeted 202 nucleotide binding site (NBS) leucine-rich repeat (LRR) and other resistance (R) gene homologs (75 were identified by mining a peanut EST database). SSR, NBS-LRR, and Ser/Thr receptor-like protein loci within the alien introgression co-segregated with Rma in an F4 population (Gregory × Tifguard) and were tightly linked and spanned 3.4 cM in an F5 population (NemaTAM × GP-NC-WS-14). By comparative mapping in the A-genome progenitor of peanut (A. duranensis), Rma was discovered to have been introduced on an interstitial alien chromosome segment spanning one-third to one-half of chromosome 9A. Numerous codominant DNA markers were identified for finer mapping of Rma, shortening the alien introgression harboring Rma by marker-assisted selection, and introducing novel root-knot nematode R-genes into peanut by targeting syntenic segments on chromosomes 9A and 9B in wild diploid donors.

Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.

On December 14 to 15, 2004, some 50 legume researchers and funding agency representatives (the latter as observers) met in Santa Fe, New Mexico, to develop a plan for cross-legume genomics research. This conference was one of the outcomes of the Legume Crops Genome Initiative (LCGI), an organization

Peanut seeds contain high amounts of oil and protein as well as some useful bioactive phytochemicals which can contribute to human health. The U.S. peanut mini-core collection is an important genetic resource for improving seed quality and developing new cultivars. Variability of seed chemical composition within the mini-core was evaluated from freshly harvested seeds for two years. Oil, fatty acid composition, and flavonoid/resveratrol content were quantified by NMR, GC, and HPLC, respectively. Significant variability was detected in seed chemical composition among accessions and botanical varieties. Accessions were further genotyped with a functional SNP marker from the FAD2A gene using real-time PCR and classified into three genotypes with significantly different O/L ratios: wild type (G/G with a low O/L ratio1.7), heterozygote (G/A with O/L ratio1.4 but1.7), and mutant (A/A with a high O/L ratio1.7). The results from real-time PCR genotyping and GC fatty acid analysis were consistent. Accessions with high amounts of oil, quercetin, high seed weight, and O/L ratio were identified. The results from this study may be useful not only for peanut breeders, food processors, and product consumers to select suitable accessions or cultivars but also for curators to potentially expand the mini-core collection.

Embryo abortion is a barrier to interspecific hybridization between cultivated and wild species of Arachis L., and in vitro culture of embryos prior to abortion is potentially useful for overcoming this problem. In Arachis, the peg tips encase the embryos as they move from above to below ground. The objectives of this research were to enhance the in vitro techniques to rescue selfed embryos of Arachis species and to apply this technique to obtain hybrid plants. Arachis hypogaea L. and four diploid wild species—A. glandulifera Stalker, A. duranensis Krapov. and W.C. Gregory, A. batizocoi Krapov. and W.C. Gregory, and A. valida Krapov. and W.C. Gregory—which have different degrees of compatibility with A. hypogaea were used. Ten-day-old peg tips were cultured on the combined MS and B5 media with 1-naphthaleneacetic acid (NAA), gibherellic acid (GA3), and and 6-benzylaminopurine (BAP) for 90 d. In vitro-developed ovules, embryos, or seeds were subcultured to regenerate plants. The results indicated that A. hypogaea had higher frequencies of pod and seed production than the wild species. Arachis glandulifera produced more pods and seeds than the other three wild species, and no significant difference in pod and seed production was found among A. duranensis, A. valida, and A. batizocoi. Selfed plants were recovered from all live species. In vitro development of hybrid embryos to the cotyledonary stage was observed in all eight interspecific crosses among A. hypogaea and the four Arachis dipioids. Mature hybrid plants were recovered from seven of eight combinations. This is in contrast to plants recovered from five of eight hybrid combinations (including reciprocals) when pods were left on the plant. Arachis glandulifera × A. hypogaea hybrids which previously had been attempted, but not obtained, were recovered through peg tip culture followed by somatic embryogenesis. This study demonstrated that Arachis hybrid proembryos can be rescued through peg tip culture.

Nuclear restriction fragment length polymorphism (RFLP) analysis was used to determine the wild diploid Arachis species that hybridized to form tetraploid domesticated peanut. Results using 20 previously mapped cDNA clones strongly indicated A. duranensis as the progenitor of the A genome of domesticated peanut and A ipaensis as the B genome parent A large amount of RFLP variability was found among the various accessions of A duranensis, and accessions most similar to the A genome of cultivated peanut were identified. Chloroplast DNA RFLP analysis determined that A duranensis was the female parent of the original hybridization event Domesticated peanut is known to have one genome with a distinctly smaller pair of chromosomes ("A"), and one genome that lacks this pair. Cytogenetic analysis demonstrated that A duranensis has a pair of "A" chromosomes, and A. ipaensis does not The cytogenetic evidence is thus consistent with the RFLP evidence concerning the identity of the progenitors RFLP and cytogenetic evidence indicate a single origin for domesticated peanut in Northern Argentina or Southern Bolivia, followed by diversification under the influence of cultivation

Background Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea. Results More than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago. Conclusions The first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into A. hypogaea from A. cardenasii.

Peanut (Arachis hypogaea L.) is one of the most important oilseed and nutritional crops in the world. To efficiently utilize the germplasm collection, a peanut mini-core containing 112 accessions was established in the United States. To determine the population structure and its impact on marker-trait association, this mini-core collection was assessed by genotyping 94 accessions with 81 SSR markers and two functional SNP markers from fatty acid desaturase 2 (FAD2). Seed quality traits (including oil content, fatty acid composition, flavonoids, and resveratrol) were obtained through nuclear magnetic resonance (NMR), gas chromatography (GC), and high-performance liquid chromatography (HPLC) analysis. Genetic diversity and population structure analysis identified four major subpopulations that are related to four botanical varieties. Model comparison with different levels of population structure and kinship control was conducted for each trait and association analyses with the selected models verified that the functional SNP from the FAD2A gene is significantly associated with oleic acid (C18:1), linoleic acid (C18:2), and oleic-to-linoleic (O/L) ratio across this diverse collection. Even though the allele distribution of FAD2A was structured among the four subpopulations, the effect of FAD2A gene remained significant after controlling population structure and had a likelihood-ratio-based R ( 2 ) (R ( LR ) ( 2 ) ) value of 0.05 (oleic acid), 0.09 (linoleic acid), and 0.07 (O/L ratio) because the FAD2A alleles were not completely fixed within subpopulations. Our genetic analysis demonstrated that this peanut mini-core panel is suitable for association mapping. Phenotypic characterization for seed quality traits and association testing of the functional SNP from FAD2A gene provided information for further breeding and genetic research.

Improvement of agronomic and quality factors in Arachis hypogaea L. through interspecific hybridization with wild Arachis species is restricted because of reproductive barriers including genetic incompatibility. A description of embryogenesis and embryo abortion in reciprocal crosses between wild and cultivated Arachis species should clarify some of these reproductive barriers. This study documents embryogenesis in the diploids A. duranensis (K 7988) and A. stenosperma (HLK 410) in reciprocal crosses with A. hypogaea cv NC 6. A significant parental effect was observed among crosses. When NC 6 was used as the female parent in crosses with both diploid species, embryos developed at a near normal rate, while embryos in the reciprocal crosses showed retarded rates. Differences in embryo developmental morphology were not observed between the two wild species. When A. duranensis was used as a female parent, however, embryos aborted at a higher frequency. In contrast, A. stenosperma had delayed fertilization, bu...

The wild species germplasm resources of Arachis are potentially valuable for improving disease and insect resistance in A. hypogaea L. Improving cultivars through interspecific hybridization is restricted because of reproductive barriers and/or genetic incompatibility with many Arachis spp. A description of reproductive efficiency in reciprocal crosses between wild and cultivated Arachis species is needed to clarify potentials for germplasm utilization. This study documents reproductive efficiency using the diploid species A. duranensis (K 7988) and A. stenosperma (HLK 410) in reciprocal crosses with A. hypogaea cv. NC 6. A significant parental effect was observed among crosses and NC 6 was more successful when used as the female parent. Differences in total reproductive efficiency were not observed between the two wild diploid species. However, when A. duranensis was used as a female parent embryos aborted at a high frequency. In contrast, the reduced efficiency observed with A. stenosperma was due to lower fertilization. As attempts are made to utilize the genetic resources of Arachis, different approaches will be needed to overcome reproductive barriers which restrict introgression of potentially desirable traits.

Peanut germ plasm consists of the cultivated allotetraploid species Arachis hypogaea L. and a large number of wild species, which are nearly all diploids. Our previous work indicated a very low level of genetic variability in American cultivars, as assayed by restriction fragment length polymorphism (RFLP) analysis. Since American cultivars might represent a narrow genetic base, we expanded our study to include unadapted germ-plasm lines from the various South American centers of origin, Africa, and China, where considerable morphological and physiological variability has been reported to exist. Wild species of section Arachis were included in the evaluations since they show a high degree of variation when assayed by RFLPs. Three methods were used to assay for RFLP variation: (i) conventional RFLP analysis using random genomic clones from peanut and cDNA clones from peanut and alfalfa (Medicago sativa); (ii) polymerase chain reaction (PCR) amplification of random primer sequences; (iii) four-cutter analysis of PCR-amplified fragments. In all cases a very low level of variability was found in cultivated peanut, while abundant variability was present among wild diploid species. The results are discussed in terms of peanut evolution and significance to peanut breeding.Key words: polymerase chain reaction, Arachis hypogaea, restriction fragment length polymorphism.

Cultivated peanut (Arachis hypogaea L.) provides a significant source of oil and protein for large segments of the population, particularly in the less developed regions of Asia, Africa, and South America. In the United States, peanut is considered a high-value cash crop of regional importance, with production concentrated in the Southeast region of the country along with parts of Texas, Oklahoma, North Carolina and Virginia. Domestically, peanuts are grown primarily for use in the snack-food, peanut butter and confection industries, but also serve as an excellent source of mono-unsaturated cooking oil, as well as a source of meal for livestock.

Background Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. Results A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B-genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A- and B-genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution. Conclusions Our findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut.