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Fu L, Wang Q, Li L, Lang T, Guo J, Wang S, Sun Z, Han S, Huang B, Dong W, Zhang X, Du P. Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut. BMC Plant Biol 2021; 21:107. [PMID: 33610178 PMCID: PMC7896385 DOI: 10.1186/s12870-021-02875-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
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.
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Affiliation(s)
- Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- 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
| | - Qian Wang
- 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
| | - Lina Li
- 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
| | - Tao Lang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Junjia Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- 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
| | - Siyu Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- 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
| | - Ziqi Sun
- 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
| | - Suoyi Han
- 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
| | - Bingyan Huang
- 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
| | - Wenzhao Dong
- 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
| | - Xinyou Zhang
- 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.
| | - Pei Du
- 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.
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Li SJ, Yu SS, Luo HY, Li X, Rao B, Wang Y, Li ZZ, Liu G, Zou LP, Zhang JS, Feng C, Liu J, Liu JW, Hu N, Chen XQ, Yu SY, Li K, He MW, Yu XG, Wang J, Guo SL, Chen ZY, Zhang L, Ma L. Two de novo variations identified by massively parallel sequencing in 13 Chinese families with children diagnosed with autism spectrum disorder. Clin Chim Acta 2018; 479:144-147. [PMID: 29366832 DOI: 10.1016/j.cca.2018.01.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 01/09/2023]
Abstract
Autism spectrum disorder (ASD) is a genetically heterogeneous neurodevelopmental disorder characterized by impairments in social interaction and communication, and by restricted and repetitive behaviors. The genetic architecture of ASD has been elucidated, including chromosomal rearrangements, de novo or inherited rare variants, and copy number variants. However, the genetic mechanism of Chinese families with ASD children is explored rarely. To identify genetic pathogenesis, we performed massively parallel sequencing on 13 Chinese ASD trio families, and found two de novo variations. The novel de novo splice alteration c.664 + 2T > G in the DEAF1 gene and the novel de novo missense mutation c.95 C > T in the AADAT gene associated with ASD may be important clues for exploring the etiology of this disorder.
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Affiliation(s)
- Shi-Jun Li
- Department of Medical Instruments, Chinese PLA General Hospital, Beijing 100853, China.
| | | | | | - Xin Li
- BGI-shenzhen, Shenzhen 518083, China
| | - Bin Rao
- BGI-shenzhen, Shenzhen 518083, China
| | - Yi Wang
- Department of Stomatology, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhen-Zhen Li
- Department of Medical Instruments, Chinese PLA General Hospital, Beijing 100853, China
| | - Gang Liu
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Li-Ping Zou
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Ji-Shui Zhang
- Department of Neurology, Beijing Children's Hospital of Capital Medical University, Beijing 100045, China
| | - Chen Feng
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Jing Liu
- Institute of Geriatric Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Jian-Wei Liu
- Institute of Geriatric Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Nan Hu
- Department of Rehabilitation Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiao-Qiao Chen
- Department of Neurology, Beijing Children's Hospital of Capital Medical University, Beijing 100045, China
| | - Sheng-Yuan Yu
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Ke Li
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Mian-Wang He
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Xin-Guang Yu
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Jun Wang
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Sheng-Li Guo
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhi-Ye Chen
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Lei Zhang
- Department of Medical Information, Chinese PLA General Hospital, Beijing 100853, China
| | - Lin Ma
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
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