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.

Figure 1

Genetic relationships among A- and B-genome Arachis species. Clustering of A- (A. duranensis and A. stenosperma) and B- (A. ipaensis and A. batizocoi) genome species according to analysis of data from SSR markers. The two parents used for mapping are indicated by arrows.

Figure 2

High-density linkage map of Arachis duranensis including 1,724 markers. SNP and SSR markers are prefixed by ‘SNP’ and ‘GM’, respectively, resistance gene candidate markers are prefixed by ‘RGC’ and ‘GS’. Twenty-four previously published markers (underlined) were selected from an interspecific map between A. duranensis and A. stenosperma[36] to establish synteny between the current and former linkage groups. The original linkage group assignments are given in the marker names separated by the pound (#) sign. Loci with significant segregation distortion (p = 0.05) are labeled with an asterisk. Graphs to the right of the linkage groups represent recombination frequencies. Each data point represents genetic distances between adjacent markers averaged for a window of 20 markers.

Figure 3

Synteny between diploid A-genome peanut (A. duranensis, 2n =20) and Glycine max (2n= 40). Arrows indicate clusters of genes in common between the two genomes. For plotting the data on the Y axis, the peanut genome for each chromosome is proportional in size to the total map size in centimorgans. For the X axis, the unit of measure is scaled to bp within the chromosomal assemblies of the respective genomes. The plot was obtained with a visual basic program that plotted the x‐y coordinates of each hit. The total number of matches for each pair wise comparison is listed at the upper left corner.