Genomic research can provide new tools and resources to revolutionize crop genetic improvement and production [1]. However, genomic research in peanut (Arachis hypogaea L.) is far behind that in other crops such as maize, soybean, wheat, sorghum, and potato due to the shortage of essential genome infrastructure, tools, and resources [2]. As a consequence, peanut has lagged behind other crops on the use of molecular genetic technology for cultivar development. The early technologies (isozyme, RFLP (Restriction Fragment Length Polymorphism), AFLP (Amplified Fragment Length Polymorphism), RAPD (Random Amplified Polymorphic DNA), and SCAR (Sequence Characterized Amplified Region)) showed extremely low levels of polymorphism in A. hypogaea [3-11]. Those early struggles have been documented in several excellent reviews [2,12-14]. Recent advances in molecular genetic technology have allowed researchers to detect more frequent genetic polymorphism. These efforts have resulted in the construction of moderate density genetic maps for A. hypogaea [15-19] populated primarily with SSR (simple sequence repeat or microsatellite) markers that contrast with other PCR-based markers in their largely co-dominant vs. dominant (AFLP, RAPD, and SCAR) nature. Many of these SSR markers were developed from peanut ESTs (expressed sequence tags). Because of genome size and complexity, many plant EST libraries have been sequenced as an alternative to whole genome sequences, including peanut. EST data sets were foundational for functional genomics during the period when only a few plant genomes were sequenced and before the development of the second generation of high throughput sequencing technology. ESTs have been especially important resources for major crops or economically significant plants with large genomes (such as peanut) to enable gene discovery, gene expression analysis and molecular marker development.

The NCBI EST database contains 225,264 ESTs from peanut as of November 2011 [20]. There are 150,922 for A. hypogaea (including 745 for subsp. fastigiata), 35,291 for A. duranensis, 32,787 for A. ipaensis, and 6264 for A. stenosperma. Many of the A. hypogaea ESTs have been combined with short-read sequences to create a first generation transcriptome assembly (NCBI BioProject PRJNA49471). Before the completion of peanut whole genome sequence, sequencing large numbers of ESTs can create a formidable resource for studies in both biodiversity and gene-discovery. Sequence analysis tools have extended the scope of EST utility into the fields of proteomics, marker development and genome annotation. Although EST collections certainly are not intended to substitute for a whole genome sequence, the EST resource forms the core foundation for various genome-wide experiments, particularly for microarray gene expression study [21,22], marker development and genetic map construction [17], which will assist assembly of the whole genome. The ESTs will continue to be actively sequenced to fill knowledge gaps and complement the whole genome sequence.

In spite of the discovery of thousands of microsatellite-containing EST and genomic sequences from which markers have been developed [23], only ∼10–20% detect multiple alleles among tetraploid peanut genotypes [24-27], although somewhat higher levels of polymorphism have been observed in several studies [28-32]. In spite of considerable molecular tool expansion for A. hypogaea over the past decade, low polymorphism resulting from a genetic bottleneck due to polyploidization [33] continues to limit the number of markers that can be mapped in populations from intraspecific biparental crosses. The discovery of SNP (Single Nucleotide Polymorphism) markers will further enhance the molecular toolkit for peanut, although high-throughput SNP genotyping in the tetraploid will be challenging [23].

From a cultivar development standpoint, however, these advances in technology have enabled the identification of molecular markers associated with quantitative trait loci (QTLs) for several economically significant traits. Recent research has resulted in the discovery of molecular markers associated with resistance to foliar diseases, rust and late leaf spot [18,34-36], resistance to Cylindrocladium black rot and early leaf spot [14], nematode resistance [37-40], resistance to TSWV [17], resistance to the aphid vector of groundnut rosette disease [41], drought tolerance [15,42], yield parameters [43], high oleic acid [44,45], and seed biochemical traits [46]. Many of these QTLs are not major, i.e., they account for <10% of the phenotypic variation explained. Major QTLs identified for rust and late leaf spot in at least one germplasm source may be of wild species origin [18,36,47] as is the source of nematode resistance [40,48]. Many small effect QTLs were mapped in a population segregating for drought tolerance and its surrogate traits such as transpiration efficiency, specific leaf area, or dry weight and the percent of phenotypic variation explained was often low (<10%) [15,42]. Two additional populations confirmed that no major QTLs for drought tolerance could be identified [19]. The need to pyramid a large number of minor QTLs for drought tolerance may predetermine the most efficient breeding strategy to integrate with marker-assisted selection [49]. For example, marker-assisted backcrossing can efficiently combine only a few genes for foreground (trait-associated donor alleles) selection while conducting background selection using markers spanning the genome in order to rapidly recover the recurrent parent genotype plus the genes/alleles of interest. Foreground selection becomes more costly as the number of minor QTLs increases because population sizes increase dramatically. Up to now, neither background nor genome-wide selection has been practiced in peanut and must await the development of high-throughput, economical assays for large numbers of markers. For other traits such as high oleic acid or rust resistance, identification of major QTLs have or will enable efficient marker-assisted backcrossing [50].

Molecular breeding in peanut trails that of many crops [51,52] in part due to a lack of investment, but also because of low levels of molecular polymorphism among cultivated varieties. While polymorphism is abundant in diploid wild species, it is sparse in tetraploid peanut due to the genetic bottleneck imposed by its relatively recent origin [33]. Genomic research might also be used to enhance the amount of genetic diversity available for application in conventional breeding. The development of transgenic peanut, and the creation of TILLING populations and synthetic allotetraploids are three approaches that are being explored to create new sources of genetic diversity in peanut.

The first successful example of marker assisted selection (MAS) was the introgression of nematode resistance through an amphidiploid pathway into cultivated peanut [48], and the subsequent development of a nematode resistant cultivar, NemaTAM [94]. Although this cultivar has near immunity to the peanut root-knot nematode, it is not suitable for cultivation in the Southeastern U.S. due to extreme susceptibility to tomato spotted wilt tospovirus (TSWV) [95]. A goal of our peanut breeding program was to develop a cultivar with resistance to both TSWV and the peanut root-knot nematode. We chose to pursue this objective using phenotypic selection because the early markers were expensive, low throughput, and produced a significant amount of inaccurate data. Using a conventional breeding approach we produced ‘Tifguard’, the first peanut cultivar with high levels of resistance to both the peanut root-knot nematode and TSWV [95].

The next goal of the breeding program was to combine the high oleic fatty acid trait with resistance to both the peanut root-knot nematode and TSWV. Due to recent advances in molecular marker technology we decided to pursue this goal using a backcross breeding program accelerated by MAS. Research by Chu et al. [39] and Nagy et al. [40] resulted in the development of molecular markers for nematode resistance that can be used in high throughput systems and are more amenable for large breeding populations. Chu et al. [44,45] developed molecular markers for both genes which control the high oleic fatty acid trait in peanut. To achieve our breeding goal, Tifguard was used as the recurrent female parent and two high oleic cultivars were used as donor parents for the high O/L trait. ‘Tifguard High O/L’ was generated through three rounds of backcrossing using as the pollen donors BC_nF₁ progenies selected with molecular markers for these two traits. The high O/L trait is recessive but the use of a co-dominant molecular marker allowed backcrossing with heterozygous lines. Selfed BC₃F₂ plants yielded marker-homozygous individuals identified as Tifguard High O/L. Use of this MAS backcross breeding procedure compressed the hybridization and selection phases of the cultivar development process to less than 3 years [50], allowing for more rapid initiation of preliminary yield trials.

It is anticipated that more peanut cultivars developed using molecular technology will be released in the near future. Recent research has resulted in the development of several molecular markers or QTLs that should be useful for peanut cultivar development. Stalker et al. [96] presented a table with 14 references documenting molecular markers associated with traits in peanut, and efforts are ongoing to use the molecular markers associated with the QTL for leaf rust to incorporate leaf rust resistance into three elite cultivars at ICRISAT, India [23].

Efforts to shepherd initiatives for increased research on peanut genomics at the 2001 U.S. Legume Crops Genomics Workshop and at subsequent meetings of the International Peanut Genome Consortium have been described by Stalker et al. [96] and Feng et al. [20]. Recent updates are posted on http://www.peanutbioscience.com. These efforts have resulted in quantum leaps of knowledge about the peanut genome, and have facilitated ongoing marker assisted breeding programs. These efforts have also stimulated the development of molecular genetic tools and RIL populations that should result in additional quantum leaps of knowledge. In addition, these efforts have laid the foundation for plans to sequence the peanut genome in the near future. This should result in the development of additional molecular tools that will greatly advance peanut cultivar development.