Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing
Abstract Background Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in effi...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-12-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-023-04650-9 |
| _version_ | 1797398061437157376 |
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| author | Kanglu Zhao Yanbo Bai Qingyu Zhang Zhen Zhao Yao Cao Lu Yang Ni Wang Junxiong Xu Bo Wang Lei Wu Xiufeng Gong Tuanrong Lin Yufeng Wang Wei Wang Xingkui Cai Yuhe Yin Zhiyong Xiong |
| author_facet | Kanglu Zhao Yanbo Bai Qingyu Zhang Zhen Zhao Yao Cao Lu Yang Ni Wang Junxiong Xu Bo Wang Lei Wu Xiufeng Gong Tuanrong Lin Yufeng Wang Wei Wang Xingkui Cai Yuhe Yin Zhiyong Xiong |
| author_sort | Kanglu Zhao |
| collection | DOAJ |
| description | Abstract Background Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples. Results In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data. Conclusions This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding. |
| first_indexed | 2024-03-09T01:19:17Z |
| format | Article |
| id | doaj.art-2941f39f8cc54ad0b420212dd160dbcf |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-09T01:19:17Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-2941f39f8cc54ad0b420212dd160dbcf2023-12-10T12:13:17ZengBMCBMC Plant Biology1471-22292023-12-0123111010.1186/s12870-023-04650-9Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencingKanglu Zhao0Yanbo Bai1Qingyu Zhang2Zhen Zhao3Yao Cao4Lu Yang5Ni Wang6Junxiong Xu7Bo Wang8Lei Wu9Xiufeng Gong10Tuanrong Lin11Yufeng Wang12Wei Wang13Xingkui Cai14Yuhe Yin15Zhiyong Xiong16Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityInstitute of Ulanqab Agricultural and Forestry Sciences, Inner MongoliaInstitute of Ulanqab Agricultural and Forestry Sciences, Inner MongoliaInstitute of Ulanqab Agricultural and Forestry Sciences, Inner MongoliaKey Laboratory of Horticultural Plant Biology, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural UniversityInstitute of Ulanqab Agricultural and Forestry Sciences, Inner MongoliaKey Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia UniversityAbstract Background Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples. Results In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data. Conclusions This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.https://doi.org/10.1186/s12870-023-04650-9KaryotypeAneuploidPolyploidWhole-genome resequencingFISH |
| spellingShingle | Kanglu Zhao Yanbo Bai Qingyu Zhang Zhen Zhao Yao Cao Lu Yang Ni Wang Junxiong Xu Bo Wang Lei Wu Xiufeng Gong Tuanrong Lin Yufeng Wang Wei Wang Xingkui Cai Yuhe Yin Zhiyong Xiong Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing BMC Plant Biology Karyotype Aneuploid Polyploid Whole-genome resequencing FISH |
| title | Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing |
| title_full | Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing |
| title_fullStr | Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing |
| title_full_unstemmed | Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing |
| title_short | Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing |
| title_sort | karyotyping of aneuploid and polyploid plants from low coverage whole genome resequencing |
| topic | Karyotype Aneuploid Polyploid Whole-genome resequencing FISH |
| url | https://doi.org/10.1186/s12870-023-04650-9 |
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