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

Abstract

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.

Utilizing Wild Species for Peanut Improvement

“…Simpson, and A. correntina (Burkart) Krapov. Multiple translocations have been observed in A. duranensis and A. batizocoi (Stalker et al, 1991aGuo et al, 2012), which indicates that species are continuing to evolve. The chromosomes of B-genome species are karyologically more diverse than those with an A genome (Fernandez and Krapovickas, 1994;Seijo et al, 2004).…”

“…By crossing two accessions of A. batizocoi, a denser map was developed by Guo et al (2012). Fiftyone common markers were present between the A and B genomes, which indicated synteny between the two genomes.…”

Integrated Consensus Map of Cultivated Peanut and Wild Relatives Reveals Structures of the A and B Genomes of Arachis and Divergence of the Legume Genomes

“…Recently, intraspecific maps for A-genome diploid ( A. duranensis ) and B-genome diploid ( Arachi batizocoi ) have been developed with 1724 and 449 marker loci, respectively, including single nucleotide polymorphisms and expressed sequence tag-simple sequence repeats (EST-SSRs) markers. 21,22 …”

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).…”

“…Fifty-one common markers presented evidence of the high synteny of the B and the A genomes. Guo et al (2012) created a more dense map by crossing two accessions of A. batizocoi. They compared high density A and B genome maps and observed a large amount of synteny between the A and B genomes, but also several inversions and translocations.…”