Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara
Abstract Background Domestication from wild rice species to cultivated rice is a key milestone, which involved changes of many specific traits and the variations of the genetic systems. Among the AA-genome wild rice species, O. rufipogon and O. nivara, have many favorable genes and thought to be pro...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2023-09-01
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| Series: | Rice |
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| Online Access: | https://doi.org/10.1186/s12284-023-00655-y |
| _version_ | 1827708327367278592 |
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| author | Zhangqiang Wang Zisheng Guo Tuo Zou Zhe Zhang Jianan Zhang Ping He Ruifeng Song Ziqiang Liu Haitao Zhu Guiquan Zhang Xuelin Fu |
| author_facet | Zhangqiang Wang Zisheng Guo Tuo Zou Zhe Zhang Jianan Zhang Ping He Ruifeng Song Ziqiang Liu Haitao Zhu Guiquan Zhang Xuelin Fu |
| author_sort | Zhangqiang Wang |
| collection | DOAJ |
| description | Abstract Background Domestication from wild rice species to cultivated rice is a key milestone, which involved changes of many specific traits and the variations of the genetic systems. Among the AA-genome wild rice species, O. rufipogon and O. nivara, have many favorable genes and thought to be progenitors of O. sativa. Results In the present study, by using O. rufipogon and O. nivara as donors, the single segment substitution lines (SSSLs) have been developed in the background of the elite indica cultivar, HJX74. In the SSSLs population, 11 genes for 5 domestication traits, including tiller angle, spreading panicle, awn, seed shattering, and red pericarp, were identified and mapped on 5 chromosomes through substitution mapping. Herein, allelic variations of 7 genes were found through sequence alignment with the known genes, that is, TA7-RUF was allelic to PROG1, TA8-RUF was allelic to TIG1, SPR4-NIV was allelic to OsLG1, AN4-RUF was allelic to An-1, SH4-NIV was allelic to SH4, and both RC7-RUF and RC7-NIV were allelic to Rc. Meanwhile, 4 genes, TA11-NIV, SPR3-NIV, AN3-NIV, and AN4-NIV, were considered as the novel genes identified in these SSSLs, because of none known genes for the related domestication traits found in the chromosomal locations of them. Conclusion The results indicated that the SSSLs would be precious germplasm resources for gene mining and utilization from wild rice species, and it laid the foundation for further analyses of the novel domestication genes to better understand the genetic basis in regulating the traits variation during domestication. |
| first_indexed | 2024-03-10T17:02:09Z |
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| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-03-10T17:02:09Z |
| publishDate | 2023-09-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-b1b5bbf0dbbe402d9f263088469045cf2023-11-20T10:55:50ZengSpringerOpenRice1939-84251939-84332023-09-0116111710.1186/s12284-023-00655-ySubstitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivaraZhangqiang Wang0Zisheng Guo1Tuo Zou2Zhe Zhang3Jianan Zhang4Ping He5Ruifeng Song6Ziqiang Liu7Haitao Zhu8Guiquan Zhang9Xuelin Fu10Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityCollege of Life Sciences, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural UniversityAbstract Background Domestication from wild rice species to cultivated rice is a key milestone, which involved changes of many specific traits and the variations of the genetic systems. Among the AA-genome wild rice species, O. rufipogon and O. nivara, have many favorable genes and thought to be progenitors of O. sativa. Results In the present study, by using O. rufipogon and O. nivara as donors, the single segment substitution lines (SSSLs) have been developed in the background of the elite indica cultivar, HJX74. In the SSSLs population, 11 genes for 5 domestication traits, including tiller angle, spreading panicle, awn, seed shattering, and red pericarp, were identified and mapped on 5 chromosomes through substitution mapping. Herein, allelic variations of 7 genes were found through sequence alignment with the known genes, that is, TA7-RUF was allelic to PROG1, TA8-RUF was allelic to TIG1, SPR4-NIV was allelic to OsLG1, AN4-RUF was allelic to An-1, SH4-NIV was allelic to SH4, and both RC7-RUF and RC7-NIV were allelic to Rc. Meanwhile, 4 genes, TA11-NIV, SPR3-NIV, AN3-NIV, and AN4-NIV, were considered as the novel genes identified in these SSSLs, because of none known genes for the related domestication traits found in the chromosomal locations of them. Conclusion The results indicated that the SSSLs would be precious germplasm resources for gene mining and utilization from wild rice species, and it laid the foundation for further analyses of the novel domestication genes to better understand the genetic basis in regulating the traits variation during domestication.https://doi.org/10.1186/s12284-023-00655-ySingle segment substitution linesDomestication geneSubstitution mappingAllelic variationO. rufipogonO. nivara |
| spellingShingle | Zhangqiang Wang Zisheng Guo Tuo Zou Zhe Zhang Jianan Zhang Ping He Ruifeng Song Ziqiang Liu Haitao Zhu Guiquan Zhang Xuelin Fu Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara Rice Single segment substitution lines Domestication gene Substitution mapping Allelic variation O. rufipogon O. nivara |
| title | Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara |
| title_full | Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara |
| title_fullStr | Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara |
| title_full_unstemmed | Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara |
| title_short | Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara |
| title_sort | substitution mapping and allelic variations of the domestication genes from o rufipogon and o nivara |
| topic | Single segment substitution lines Domestication gene Substitution mapping Allelic variation O. rufipogon O. nivara |
| url | https://doi.org/10.1186/s12284-023-00655-y |
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