Genetic relationships among seven sections of genus Arachis studied by using SSR markers

Abstract

Background: The genus Arachis, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2n = 2x = 20) and the tetraploid species (2n = 2x = 40) are found in sections Arachis, Extranervosae and Rhizomatosae. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of Arachis by using simple sequence repeat (SSR) markers developed from Arachis hypogaea genomic library and gene sequences from related genera of Arachis.

Results: The average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (A. duranensis) and the B-genome accession ICG 8206 (A. ipaënsis) were found most closely related to A. hypogaea.

Conclusion: A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut.

Figure 1

Dendrogram of wild and cultivated Arachis accessions based on SSR polymorphism. Cluster analysis was performed using the neighbor-joining method. Bootstrap values obtained from 1000 replicate analyses higher than 80% are indicated on nodes. The names of accessions and taxonomical information are given next to their branches starting with the accession number followed by an abbreviated form of species name followed by respective genomes and sections (Abbreviated species names: bene: benensis; card: cardenasii; diog: diogoi; dura: duranensis; kemp: kempff-mercadoi; sten: stenosperma; kuhl: kuhlmannii; deco: decora; palu: palustris; corr: correntina; vali: valida; hoeh: hoehnei; majo: major; sylv: sylvestris; ipae: ipaënsis; hypo: hypogaea; mont: monticola; magn: magna; glan: glandulifera; pint: pintoi; appr: appressipila; kret: kretschmeri; mati: matiensis; rigo: rigonii; subc: subcoriacea; chiq: chiquitana; mati: matiensis; bati: batizocoi; herm: hermannii; para: paraguariensis; sphy: stenophylla; vill: villosa; pusi: pusilla; dard: dardani; vall: vallsii; tris: triseminata). (Abbreviated section names: Arac: Arachis; Caul: Caulorrhizae; Hete: Heteranthae; Proc: Procumbentes; Erec: Erectoides; Tris: Triseminatae; Extr: Extranervosae)

Figure 2

Dendrogram of seven sections of Arachis. Allelic data based on 32 SSR markers was used to develop dendrogram. The numbers on the nodes indicate bootstrap values for grouping based on 1000 bootstrap replicates.

Figure 3

Approximate geographical locations of A and B-genome accessions. A few AA-genome and BB-genome species accessions showing the least genetic distance to Arachis hypogaea accessions and originated from South America have been shown in the figure. Name of species, genome designation and genetic distance (D) of respective accessions with A. hypogaea have been shown in parentheses.