PMID- 33610178 OWN - NLM STAT- MEDLINE DCOM- 20210504 LR - 20210504 IS - 1471-2229 (Electronic) IS - 1471-2229 (Linking) VI - 21 IP - 1 DP - 2021 Feb 20 TI - Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut. PG - 107 LID - 10.1186/s12870-021-02875-0 [doi] LID - 107 AB - BACKGROUND: Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. RESULTS: A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. CONCLUSIONS: The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions. FAU - Fu, Liuyang AU - Fu L AD - School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China. AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. FAU - Wang, Qian AU - Wang Q AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. FAU - Li, Lina AU - Li L AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. FAU - Lang, Tao AU - Lang T AD - Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China. FAU - Guo, Junjia AU - Guo J AD - School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China. AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. FAU - Wang, Siyu AU - Wang S AD - School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China. AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. FAU - Sun, Ziqi AU - Sun Z AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. FAU - Han, Suoyi AU - Han S AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. FAU - Huang, Bingyan AU - Huang B AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. FAU - Dong, Wenzhao AU - Dong W AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. FAU - Zhang, Xinyou AU - Zhang X AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. haasz@126.com. FAU - Du, Pei AU - Du P AD - Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China. dupei2005@163.com. LA - eng GR - 2020JQ03/Distinguished Young Scholars from Henan Academy of Agricultural Sciences/ GR - 2020CY07/Scientific and Technological Development from Henan Academy of Agricultural Sciences/ GR - 31801397/National Natural Science Foundation of China/ GR - CARS-13/China Agriculture Research System/ PT - Journal Article DEP - 20210220 PL - England TA - BMC Plant Biol JT - BMC plant biology JID - 100967807 RN - 0 (Oligonucleotide Probes) SB - IM MH - Arachis/*genetics MH - *Chromosome Mapping MH - Chromosomes, Plant/*genetics MH - Crops, Agricultural/*genetics MH - Genetic Variation MH - *Genome, Plant MH - Genotype MH - *Karyotype MH - Oligonucleotide Probes MH - Repetitive Sequences, Nucleic Acid/*genetics PMC - PMC7896385 OTO - NOTNLM OT - Chromosomal variants OT - FISH OT - Karyotype OT - Oligos OT - Peanut OT - Reference sequence OT - TRs COIS- The authors declare that they have no competing interests. EDAT- 2021/02/22 06:00 MHDA- 2021/05/05 06:00 PMCR- 2021/02/20 CRDT- 2021/02/21 20:23 PHST- 2020/06/23 00:00 [received] PHST- 2021/02/04 00:00 [accepted] PHST- 2021/02/21 20:23 [entrez] PHST- 2021/02/22 06:00 [pubmed] PHST- 2021/05/05 06:00 [medline] PHST- 2021/02/20 00:00 [pmc-release] AID - 10.1186/s12870-021-02875-0 [pii] AID - 2875 [pii] AID - 10.1186/s12870-021-02875-0 [doi] PST - epublish SO - BMC Plant Biol. 2021 Feb 20;21(1):107. doi: 10.1186/s12870-021-02875-0.