Analysis of evolutionary relationships provides new clues to the origins of weedy rice
Abstract Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR)...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2020-01-01
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| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.5948 |
| _version_ | 1818913858384822272 |
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| author | Bing Han Xiaoding Ma Di Cui Yanjie Wang Leiyue Geng Guilan Cao Hui Zhang Hee‐Jong Koh Longzhi Han |
| author_facet | Bing Han Xiaoding Ma Di Cui Yanjie Wang Leiyue Geng Guilan Cao Hui Zhang Hee‐Jong Koh Longzhi Han |
| author_sort | Bing Han |
| collection | DOAJ |
| description | Abstract Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (He = 0.8386) and can be divided into two groups (japonica‐type and indica‐type). The japonica‐type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica‐types from Jiangsu province (JS) also clustered with the indica‐type landraces from JS province. Comparative transcriptome analysis of WR‚ IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty‐two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding. |
| first_indexed | 2024-12-19T23:37:10Z |
| format | Article |
| id | doaj.art-b05cab57c5b647ee84c10abd7864a66b |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-12-19T23:37:10Z |
| publishDate | 2020-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-b05cab57c5b647ee84c10abd7864a66b2022-12-21T20:01:34ZengWileyEcology and Evolution2045-77582020-01-0110289190010.1002/ece3.5948Analysis of evolutionary relationships provides new clues to the origins of weedy riceBing Han0Xiaoding Ma1Di Cui2Yanjie Wang3Leiyue Geng4Guilan Cao5Hui Zhang6Hee‐Jong Koh7Longzhi Han8Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing ChinaInstitute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing ChinaInstitute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing ChinaInstitute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing ChinaInstitute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing ChinaInstitute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing ChinaInstitute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing ChinaDepartment of Plant Science, Plant Genomics and Breeding Institute of Agriculture and Life Science Seoul National University Seoul KoreaInstitute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing ChinaAbstract Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (He = 0.8386) and can be divided into two groups (japonica‐type and indica‐type). The japonica‐type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica‐types from Jiangsu province (JS) also clustered with the indica‐type landraces from JS province. Comparative transcriptome analysis of WR‚ IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty‐two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding.https://doi.org/10.1002/ece3.5948comparative transcriptome analysisgenetic diversityhaplotype analysisweedy rice |
| spellingShingle | Bing Han Xiaoding Ma Di Cui Yanjie Wang Leiyue Geng Guilan Cao Hui Zhang Hee‐Jong Koh Longzhi Han Analysis of evolutionary relationships provides new clues to the origins of weedy rice Ecology and Evolution comparative transcriptome analysis genetic diversity haplotype analysis weedy rice |
| title | Analysis of evolutionary relationships provides new clues to the origins of weedy rice |
| title_full | Analysis of evolutionary relationships provides new clues to the origins of weedy rice |
| title_fullStr | Analysis of evolutionary relationships provides new clues to the origins of weedy rice |
| title_full_unstemmed | Analysis of evolutionary relationships provides new clues to the origins of weedy rice |
| title_short | Analysis of evolutionary relationships provides new clues to the origins of weedy rice |
| title_sort | analysis of evolutionary relationships provides new clues to the origins of weedy rice |
| topic | comparative transcriptome analysis genetic diversity haplotype analysis weedy rice |
| url | https://doi.org/10.1002/ece3.5948 |
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