H. Thomas Stalker

Legumes as a Model Plant Family. Genomics for Food and Feed Report of the Cross-Legume Advances through Genomics Conference

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

The genome sequences of Arachis duranensis and Arachis ipaensis , the diploid ancestors of cultivated peanut

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 peanuts 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 peanuts 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.

Population structure and marker–trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection

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 R2 (RLR2) 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.

A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

BackgroundCultivated 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.ResultsMore 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.ConclusionsThe 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.

Oil, fatty acid, flavonoid, and resveratrol content variability and FAD2A functional SNP genotypes in the U.S. peanut mini-core collection.

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 ratio <1.7), heterozygote (G/A with O/L ratio >1.4 but <1.7), and mutant (A/A with a high O/L ratio >1.7). 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.

Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

BackgroundCultivated 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.ResultsA 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.ConclusionsOur 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.

Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

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

Embryogenesis in Reciprocal Crosses of Arachis Hypogaea Cv NC 6 with A. duranensis and A. stenosperma

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, but initial embryo development was much faster and by day 5 had attained the same level of development as A. duranensis. These observations illustrate that as attempts are made to utilize the genetic resources of Arachis, different approaches will be needed to overcome the multiplicity of reproductive barriers that restrict introgression of potentially desirable traits to cultivated peanuts.

RFLP map of peanut

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.

Biology, Speciation, and Utilization of Peanut Species

Abstract Peanut, also known as groundnut (Arachis hypogaea L.), is a native new world crop. The Arachis species originated in South America and are found in tropical and subtropical areas. Eighty-one species have been named 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. 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. The center of origin for A. hypogaea is believed to be southern Bolivia to northwestern Argentina based on the occurrence of the two progenitor species Arachis duranensis and Arachis ipaensis, and archaeological evidence gathered in this region. 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. Two wild species (Arachis villosulicarpa and Arachis stenosperma) were cultivated by indigenous people in Brazil for food and medicinal use, albeit on a limited scale, 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.