Development of a karyotype associated with the genome map and its applications in identification and characterization of chromosomes in peanut

Background Chromosomal structural variants are important materials for crop breeding and genetic research. Oligo fluorescence in situ hybridization (oligo FISH) is a useful tool for the identification of chromosomal structural variants. Results We developed 114 new repetitive oligos based on genome-wide tandem repeats (TRs) using genomic reference sequences of the cultivar Tifrunner and the diploid species Arachis ipaensis by bioinformatics and FISH. These oligo probes were positioned and classified into 28 types. Signals produced by representative probes from eight types were in the secondary constriction, middle arm, and terminal regions; signals of four probe types were on the B subgenome; and one probe being able to produce signals on only one pair of chromosomes could be used to recognize a special genome or chromosomes of peanut. Based on new and previous oligo probes, we developed a cocktail Multiplex #3 including FAM modified TIF-439, TIF-185-1, TIF-134-3, TIF-165-3, and TAMRA modified Ipa-1162, Ipa-1137, DP-1, and DP-5, which combined with the total genomic DNA of A. duranensis and A. ipaensis probes, and 45S rDNA and 5S rDNA probes to establish a karyotype associated with the genome map of peanut and identify 14 chromosomal structural variants. Conclusions The new oligo probes are useful and convenient for distinguishing peanut chromosomes or specific segments of peanut chromosomes. Comparisons of oligo sites in the karyotype and chromosome plots of electronic location revealed the characteristics of repeated sequences, and showed that the assembly of repeated sequence in peanut genomic reference sequence was incomplete. We therefor demonstrated the great potentials of the new oligo probes in facilitating chromosome identification and characterization, and provided novel materials for further study and genetic improvement of peanut.