Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions
Abstract Background Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing bi...
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| Format: | Article |
| Language: | English |
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SpringerOpen
2018-05-01
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| Series: | Rice |
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| Online Access: | http://link.springer.com/article/10.1186/s12284-018-0224-3 |
| _version_ | 1811196558264238080 |
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| author | Naoki Yamamoto Richard Garcia Tomohiro Suzuki Celymar Angela Solis Yuichi Tada Ramaiah Venuprasad Ajay Kohli |
| author_facet | Naoki Yamamoto Richard Garcia Tomohiro Suzuki Celymar Angela Solis Yuichi Tada Ramaiah Venuprasad Ajay Kohli |
| author_sort | Naoki Yamamoto |
| collection | DOAJ |
| description | Abstract Background Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties. However, the molecular basis of the traits in NU varieties is largely unknown. Results Whole genome re-sequencing was performed of four NU lines (3, 4, 5, and 7) and for the parental Oryza sativa WAB56–104 and Oryza glaberrima CG14. The k-mer analysis predicted large genomes for the four NU lines, most likely inherited from WAB56–104. Approximately 3.1, 0.10, and 0.40 million single nucleotide polymorphisms, multi nucleotide polymorphisms, and short insertions/deletions were mined between the parental lines, respectively. Integrated analysis with another four NU lines (1, 2, 8, and 9) showed that the ratios of the donor CG14 allelic sites in the NU lines ranged from 1.3 to 9.8%. High resolution graphical genotype indicated genome-level similarities and common genetic events during the breeding process: five xyloglucan fucosyltransferase from O. glaberrima were introgressed in common. Segregation of genic segments revealed potential causal genes for some agronomic traits including grain shattering, awnness, susceptibility to bacterial leaf bright, and salt tolerance. Analysis of unmapped sequences against the reference cultivar Nipponbare indicated existence of unique genes for pathogen and abiotic stress resistance in the NU varieties. Conclusions The results provide understanding of NU genomes for rice improvement for Africa reinforcing local capacity for food security and insights into molecular events in breeding of interspecific hybrid crops. |
| first_indexed | 2024-04-12T01:00:52Z |
| format | Article |
| id | doaj.art-26ad9a64de9e4e1980ec25989ce19e6e |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-04-12T01:00:52Z |
| publishDate | 2018-05-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-26ad9a64de9e4e1980ec25989ce19e6e2022-12-22T03:54:27ZengSpringerOpenRice1939-84251939-84332018-05-0111111610.1186/s12284-018-0224-3Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositionsNaoki Yamamoto0Richard Garcia1Tomohiro Suzuki2Celymar Angela Solis3Yuichi Tada4Ramaiah Venuprasad5Ajay Kohli6International Rice Research InstituteInternational Rice Research InstituteUtsunomiya UniversityInternational Rice Research InstituteTokyo University of TechnologyAfrica Rice CenterInternational Rice Research InstituteAbstract Background Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties. However, the molecular basis of the traits in NU varieties is largely unknown. Results Whole genome re-sequencing was performed of four NU lines (3, 4, 5, and 7) and for the parental Oryza sativa WAB56–104 and Oryza glaberrima CG14. The k-mer analysis predicted large genomes for the four NU lines, most likely inherited from WAB56–104. Approximately 3.1, 0.10, and 0.40 million single nucleotide polymorphisms, multi nucleotide polymorphisms, and short insertions/deletions were mined between the parental lines, respectively. Integrated analysis with another four NU lines (1, 2, 8, and 9) showed that the ratios of the donor CG14 allelic sites in the NU lines ranged from 1.3 to 9.8%. High resolution graphical genotype indicated genome-level similarities and common genetic events during the breeding process: five xyloglucan fucosyltransferase from O. glaberrima were introgressed in common. Segregation of genic segments revealed potential causal genes for some agronomic traits including grain shattering, awnness, susceptibility to bacterial leaf bright, and salt tolerance. Analysis of unmapped sequences against the reference cultivar Nipponbare indicated existence of unique genes for pathogen and abiotic stress resistance in the NU varieties. Conclusions The results provide understanding of NU genomes for rice improvement for Africa reinforcing local capacity for food security and insights into molecular events in breeding of interspecific hybrid crops.http://link.springer.com/article/10.1186/s12284-018-0224-3Genome structureOryza glaberrimaRicePolymorphismUpland NERICAWAB56–104 |
| spellingShingle | Naoki Yamamoto Richard Garcia Tomohiro Suzuki Celymar Angela Solis Yuichi Tada Ramaiah Venuprasad Ajay Kohli Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions Rice Genome structure Oryza glaberrima Rice Polymorphism Upland NERICA WAB56–104 |
| title | Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions |
| title_full | Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions |
| title_fullStr | Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions |
| title_full_unstemmed | Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions |
| title_short | Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions |
| title_sort | comparative whole genome re sequencing analysis in upland new rice for africa insights into the breeding history and respective genome compositions |
| topic | Genome structure Oryza glaberrima Rice Polymorphism Upland NERICA WAB56–104 |
| url | http://link.springer.com/article/10.1186/s12284-018-0224-3 |
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