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Wang L, Feng Y, Wang Y, Zhang J, Chen Q, Liu Z, Liu C, He W, Wang H, Yang S, Zhang Y, Luo Y, Tang H, Wang X. Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH. Int J Mol Sci 2022; 23:ijms232113213. [PMID: 36361999 PMCID: PMC9653872 DOI: 10.3390/ijms232113213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
A precise, rapid and straightforward approach to chromosome identification is fundamental for cytogenetics studies. However, the identification of individual chromosomes was not previously possible for Chinese cherry or other Prunus species due to the small size and similar morphology of their chromosomes. To address this issue, we designed a pool of oligonucleotides distributed across specific pseudochromosome regions of Chinese cherry. This oligonucleotide pool was amplified through multiplex PCR with specific internal primers to produce probes that could recognize specific chromosomes. External primers modified with red and green fluorescence tags could produce unique signal barcoding patterns to identify each chromosome concomitantly. The same oligonucleotide pool could also discriminate all chromosomes in other Prunus species. Additionally, the 5S/45S rDNA probes and the oligo pool were applied in two sequential rounds of fluorescence in situ hybridization (FISH) localized to chromosomes and showed different distribution patterns among Prunus species. At the same time, comparative karyotype analysis revealed high conservation among P. pseudocerasus, P. avium, and P. persica. Together, these findings establish this oligonucleotide pool as the most effective tool for chromosome identification and the analysis of genome organization and evolution in the genus Prunus.
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Affiliation(s)
- Lei Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Feng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenshan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Congli Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 410100, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Shaofeng Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu 611130, China
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Sun J, Su D, Ma R, Chen L, Cao Q, Li Z, Han Y. Chromosome painting reveals genomic structure of three polyploid species of Ipomoea. Genome 2022; 65:331-339. [PMID: 35254885 DOI: 10.1139/gen-2021-0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cultivated sweetpotato (Ipomoea batatas (L.) Lam.) from the family Convolvulaceae is a hexaploid species with 2n = 6x = 90, and has been controversial regarding its nature as an autopolyploid arising within a species or allopolyploid forming between species. Here, we developed oligonucleotide-based painting probes for two chromosomes of I.nil, a model diploid Ipomoea species. Using these probes, we revealed pairing behavior of homoeologous chromosomes in I. batatas and its two possible polyploid ancestral species, tetraploid I. tabascana (2n = 4x = 60) and hexaploid I. trifida (2n = 6x = 90). Chromosome painting analysis revealed a high percentage of quadrivalent formation in zygotene-pachytene cells of I. tabascana, which supported that I. tabascana was an autotetraploid likely derived by doubling of structurally similar and homologous genomes rather than a hybrid between I. batatas and I. trifida (2x). The high frequency of hexavalent/bivalent and tetravalent pairing was observed in I. trifida (6x) and I. batatas. However, the percentage of hexavalent pairing in I. trifida (6x) was far higher than that in I. batatas. Thus, present results tended to support that I. trifida (6x) was an autohexaploid, while I. batatas was more likely to be a segmental allohexaploid.
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Affiliation(s)
- Jianying Sun
- Jiangsu Normal University, 12675, Xuzhou, Jiangsu, China;
| | - Dan Su
- Jiangsu Normal University, 12675, Xuzhou, Jiangsu, China;
| | - Rengang Ma
- Jiangsu Normal University, 12675, Xuzhou, Jiangsu, China;
| | - Lei Chen
- Jiangsu Normal University, 12675, Xuzhou, Jiangsu, China;
| | - Qinghe Cao
- Chinese Academy of Agricultural Sciences, 12661, xuzhou, Jiangsu, China;
| | - Zongyun Li
- Jiangsu Normal University, 12675, Xuzhou, Jiangsu, China;
| | - Yonghua Han
- Jiangsu Normal University, 12675, Xuzhou, Jiangsu, China;
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Su D, Chen L, Sun J, Zhang L, Gao R, Li Q, Han Y, Li Z. Comparative Chromosomal Localization of 45S and 5S rDNA Sites in 76 Purple-Fleshed Sweet Potato Cultivars. PLANTS 2020; 9:plants9070865. [PMID: 32650507 PMCID: PMC7412053 DOI: 10.3390/plants9070865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022]
Abstract
In recent years, the purple-fleshed sweet potato has attracted more attention because of its high nutritional value. The cytogenetics of this crop is relatively unexplored, limiting our knowledge on its genetic diversity. Therefore, we conducted cytogenetic analysis of 76 purple-fleshed sweet potato cultivars to analyze the chromosome structure and distribution of 45S and 5S rDNA. We noted that only 62 cultivars had 90 chromosomes, and the others were aneuploid with 88, 89, 91, or 92 chromosomes. The number of 45S rDNA in the 76 cultivars varied from 16 to 21; these sites showed different signal sizes and intensities and were localized at the chromosomal termini or satellite. The number of 5S rDNA was relatively stable; 74 cultivars showed six sites located at the chromosomal sub-terminal or near the centromere. Only the ‘Quanzishu 96’ and ‘Yuzixiang 10’ showed seven and five 5S rDNA sites, respectively. Additionally, both parent cultivars of ‘Quanzishu 96’ showed 18 45S and six 5S rDNA sites. Overall, our results indicate a moderate diversity in the distribution pattern of rDNAs. Our findings provide comprehensive cytogenetic information for the identification of sweet potato chromosomes, which can be useful for developing a high-quality germplasm resource.
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Affiliation(s)
- Dan Su
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Lei Chen
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Jianying Sun
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Luyue Zhang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Runfei Gao
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences, Xuzhou 221100, China; (R.G.); (Q.L.)
| | - Qiang Li
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences, Xuzhou 221100, China; (R.G.); (Q.L.)
| | - Yonghua Han
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
- Correspondence: (Y.H.); (Z.L.); Tel.: +86-0516-8350-0083 (Y.H. & Z.L.)
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
- Correspondence: (Y.H.); (Z.L.); Tel.: +86-0516-8350-0083 (Y.H. & Z.L.)
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Deng H, Tang G, Xu N, Gao Z, Lin L, Liang D, Xia H, Deng Q, Wang J, Cai Z, Liang G, Lv X. Integrated Karyotypes of Diploid and Tetraploid Carrizo Citrange ( Citrus sinensis L. Osbeck × Poncirus trifoliata L. Raf.) as Determined by Sequential Multicolor Fluorescence in situ Hybridization With Tandemly Repeated DNA Sequences. FRONTIERS IN PLANT SCIENCE 2020; 11:569. [PMID: 32536930 PMCID: PMC7267054 DOI: 10.3389/fpls.2020.00569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/16/2020] [Indexed: 05/20/2023]
Abstract
Carrizo citrange [Citrus sinensis (L.) Osbeck × Poncirus trifoliata (L.) Raf., CC] is one of the most widely used rootstocks in citriculture worldwide, but its cytogenetic study has been hampered by its inherent small size, morphological similarity to mitotic chromosomes, and lack of accessible cytological landmarks. In our previous study, a spontaneously occurring tetraploid CC seedling was discovered. The main goals of this study were to elucidate the chromosome constitution and construct the karyotypes of diploid CC rootstock and its corresponding spontaneously occurring tetraploid. To accomplish these, the chromosomal characteristics were investigated by sequential multicolor fluorescence in situ hybridization (FISH) with eight properly labeled repetitive DNA sequences, including a centromere-like repeat, four satellite repeats, two rDNAs, and an oligonucleotide of telomeric (TTTAGGG) n repeat. The results nicely demonstrated that these repetitive DNAs are reliable cytogenetic markers that collectively facilitate simultaneous and unequivocal identification of homologous chromosome pairs. Based on chromosome size and morphology together with FISH patterns of repetitive DNAs, an integrated karyotype of CC rootstock was constructed, consisting of 2n = 2x = 12m (1sat) + 6sm with karyotype asymmetry degree being divided into 2B category. Cytogenetically speaking, the variable and asymmetric distribution patterns of these repetitive DNAs were fully confirmed the hybrid nature of CC rootstock. In addition, comparative distribution patterns and chromosomal localizations of these repetitive DNAs convincingly showed that this tetraploid CC material arose from somatic chromosome doubling of diploid CC rootstock. This study revealed, for the first time, the integrated karyotype and chromosomal characteristics of this important citrus rootstock as well as its spontaneously occurring tetraploid plant. Furthermore, this study is a good prospective model for study species with morphologically indistinguishable small chromosomes.
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Affiliation(s)
- Honghong Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Guohao Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Nuo Xu
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Zhijian Gao
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Dong Liang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Hui Xia
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Qunxian Deng
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Jin Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Zexi Cai
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- *Correspondence: Guolu Liang,
| | - Xiulan Lv
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
- Xiulan Lv,
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