title: A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut.
abstract: 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.
authors.affiliation: Institute of Plant Breeding, Genetics and Genomics, University of Georgia,111 Riverbend Rd, Athens, GA 30605, USA.
authors.forename: Ervin D
authors.initials: ED
authors.lastname: Nagy
authors.forename: Yufang
authors.initials: Y
authors.lastname: Guo
authors.forename: Shunxue
authors.initials: S
authors.lastname: Tang
authors.forename: John E
authors.initials: JE
authors.lastname: Bowers
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Okashah
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Taylor
authors.forename: Dong
authors.initials: D
authors.lastname: Zhang
authors.forename: Sameer
authors.initials: S
authors.lastname: Khanal
authors.forename: Adam F
authors.initials: AF
authors.lastname: Heesacker
authors.forename: Nelly
authors.initials: N
authors.lastname: Khalilian
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.forename: Noelia
authors.initials: N
authors.lastname: Carrasquilla-Garcia
authors.forename: R Varma
authors.initials: RV
authors.lastname: Penmetsa
authors.forename: Douglas
authors.initials: D
authors.lastname: Cook
authors.forename: H Thomas
authors.initials: HT
authors.lastname: Stalker
authors.forename: Niels
authors.initials: N
authors.lastname: Nielsen
authors.forename: Peggy
authors.initials: P
authors.lastname: Ozias-Akins
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Knapp
mesh_terms: D010367:Arachis / Q000235:genetics*; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013045:Species Specificity; D026801:Synteny / Q000235:genetics
chemical_list: D005819:Genetic Markers