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

Abstract

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.

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

“…Placement was arbitrary within blocks with the same centiMorgan value. Scaffold orientation and placement were refined according to the conventional maps using, in order of priority, the tetraploid AB-genome map, the diploid F 2 A-genome Nagy map 22 (for the A. duranensis assembly), the diploid B-genome map 24 (for the A. ipaensis assembly) (Supplementary Data Set 2) and finally the tetraploid AB-genome Shirasawa map 17 . Markers were located on the scaffolds using BLAST and ePCR (electronic PCR) with high similarity parameters (taking the top hits only, with placement by BLAST (e value < 1 × 10 −10 ) given preference over ePCR where both were available).…”

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…BeadChip (Akond et al, 2013) • SoySNP50K array (Song et al, 2013) • 384 SNP GoldenGate assay (Hyten et al, 2008 (Varshney et al, 2012a) • 292 lines • 20 (crossing parentals of recombinant inbred lines, introgression lines, MAGIC and NAM population; Kumar et al, 2016) • 60K Axiom®Cajanus SNP array (Saxena et al, 2017 and unpublished) (Gupta et al, 2017) • 35 (parental genotypes of mapping populations; Thudi et al, 2016a) • 129 released varieties (Thudi et al, 2016b) • 300 lines (ICRISAT, unpublished) • 3000 lines (ICRISAT, unpublished) • GoldenGate assays based on VeraCode technology (Roorkiwal et al, 2013) • 60K Axiom®Cicer SNP array (Roorkiwal et al, 2017 (Chen et al, 2016) • 11 genotypes including synthetics and their diploid parents (Chen et al, 2016) • 41 diverse genotypes (30 tetraploids and 11 diploids) (Clevenger et al, 2017;Pandey et al, 2017a) • 58K Axiom®Arachis SNP array (Pandey et al, 2017a) •1536 SNP GoldenGate assay (Nagy et al, 2012) Common bean • 80.57% of Phaseolus vulgaris var G19833 genome (587 Mb); 26 279 protein coding genes (Schmutz et al, 2014) • 17 varieties • BARCBean6K_1, BARCBean6K_2 chips, BARCBean6K_3 SNP chips (Song et al, 2013 (Deulvot et al, 2010) • Combines custom-made growth vessels and new image analysis algorithms to non-destructively monitor RSA development over space (2D) and time • Allows information on soil properties (e.g. moisture)…”

The Value of Diploid Peanut Relatives for Breeding and Genomics

“…Analyses of species outside section Arachis have been infrequent. Stalker (1985) reported that the two diploid section Erectoides species A. rigonii 3 A. paraguariensis hybrids had many univalents and Krapovickas and Gregory (1994) (Lu and Pickersgill, 1993;Stalker et al, 1994), seed storage proteins (Singh et al, 1991;Bianchi-Hall et al, 1993;Liang et al, 2006), Restriction Fragment Length Polymorphisms (RFLPs) Paik-Ro et al, 1992), Amplified Fragment Length Polymorphisms (AFLPs) (Milla-Lewis et al, 2005b); Simple Sequence Repeats (SSRs) (Hopkins et al, 1999;He et al, 2005;Hong et al, 2010;Guo et al, 2012;Nagy et al, 2012). Randomly Amplified Polymorphic DNA (RAPDS) (Halward et al, 1992;Lanham et al, 1992;Hilu and Stalker, 1995), and in situ hybridization (Raina and Mukai, 1999;Seijo et al, 2004).…”

“…However, they have had limited use in peanut due to the difficulties of their implementation in polyploid plants, and in Arachis it will require separation of A and B-genome sequences. A SNP-based map of diploid Arachis was developed by Nagy et al (2012) wherein a high-density genetic map of the A genome was developed from an intra-species cross within A. duranensis, and 598 SSRs, 37 single-stranded DNA conformation polymorphism (SSCP) markers, and 1,054 SNPs were mapped. SNP-based markers have not yet been extensively used on the tetraploid Arachis, but they are expected to greatly accelerate genetic mapping and marker-assisted selection when genotyping-by-sequencing (Elshire et al, 2011) can be routinely implemented.…”