Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China
- 1.1k Downloads
Whole-genome re-sequencing of weedy rice from southern China reveals that weedy rice can originate from hybridization of domesticated indica and japonica rice.
Weedy rice (Oryza sativa f. spontanea Rosh.), which harbors phenotypes of both wild and domesticated rice, has become one of the most notorious weeds in rice fields worldwide. While its formation is poorly understood, massive amounts of rice genomic data may provide new insights into this issue. In this study, we determined genomes of three weedy rice samples from the lower Yangtze region, China, and investigated their phylogenetics, population structure and chromosomal admixture patterns. The phylogenetic tree and principle component analysis based on 46,005 SNPs with 126 other Oryza accessions suggested that the three weedy rice accessions were intermediate between japonica and indica rice. An ancestry inference study further demonstrated that weedy rice had two dominant genomic components (temperate japonica and indica). This strongly suggests that weedy rice originated from indica-japonica hybridization. Furthermore, 22,443 novel fixed single nucleotide polymorphisms were detected in the weedy genomes and could have been generated after indica-japonica hybridization for environmental adaptation.
KeywordsWeedy rice (Oryza sativa f. spontanea Rosh.) Whole-genome re-sequencing Population structure Hybridization origin
We thank Xunbin Guo and Junsen Jiao for collecting the weedy rice samples. This work was financially supported in part by grants from the China Agriculture Research System (CARS-01-02A) and the Natural Science Foundation of China (31171863).
Conflict of interest
We declare that we have no financial or personal relationships with other people or organizations that may have inappropriately influenced our work, and there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in or the review of the manuscript.
This manuscript has not been published previously and there is no prior interaction with Planta. We confirm that there are no known conflicts of interest associated with the publication. The manuscript has been read and approved by all of the authors.
- Allston RFW (1846) The rice plant. DeBow’s Rev I:320–356 (Available online from U. Michigan)Google Scholar
- Baki BB, Chin DV, Mortimer M (eds) (2000) Wild and weedy rice in rice ecosystems in Asia—a review, Los Baños. International Rice Research Institute, Philippines 118Google Scholar
- Bres-Patry C, Bangratz M, Ghesquiere A (2001) Genetic diversity and population dynamics of weedy rice in Camargue area. Genet Sel Evol 33:S425–S440Google Scholar
- Chen W, Xu Z, Zhang L, Zhang W, Ma D (2007) Theories and practices of breeding japonica rice for super high yield. Sci Agric Sin 40:869–874 (in Chinese)Google Scholar
- Cingolani P, Platts A, le Wang L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso–2; iso–3. Fly 6:80–92PubMedCentralPubMedCrossRefGoogle Scholar
- Ding Y (1983) Classification of Chinese culture rice. Anthology of Ding Ying’s paper in rice. Agricultural Publishing Company, Beijing (in Chinese)Google Scholar
- Gu XY, Foley ME, Horvath DP, Anderson JV, Feng JH, Zhang LH, Mowry CR, Ye H, Suttle JC, Kadowaki K, Chen ZX (2011) Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy red rice. Genetics 189:1515–1524PubMedCentralPubMedCrossRefGoogle Scholar
- Harlan J (1992) Crops and Man. American Society of Agronomy, Crop Science Society of America, Madison, pp 117–130Google Scholar
- Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–501PubMedCrossRefGoogle Scholar
- Liang DY, Qiang S (2011) Current situation and control strategy of weedy rice in China. China PlantProt 31:21–24 (in Chinese)Google Scholar
- Mortimer M, Pandey S, Piggin C (2000) Weedy rice: approaches to ecological appraisal and implications for research priorities. In: Baki BB, Chin DV, Mortimer M (eds.) Proceedings of wild and weedy rice in rice ecosystems in Asia—a review. Limited proceedings no. 2, International Rice Research Institute, Los Baños, pp 97–105Google Scholar
- Noldin JA, Chandler JM, McCauley GN (1999) Red rice (Oryza sativa) biology. I. Characterization of red rice ecotypes. Weed Technol 13:12–18Google Scholar
- Tang LH, Morishima H (1996) Genetic characteristics and origin of weedy rice. In: Origin and differentiation of Chinese cultivated rice. China Agricultural University Press, Beijing, pp 211–2180Google Scholar
- Wang J, Yang J, Yang JH, Chen ZD, Fan FJ, Zhu JY, Zhong WG (2012) Genetic similarity and origin of weedy rice in Yangzhong region of Jiangsu province. Jiangsu J Agric Sci 28:748–753 (in Chinese with English abstract)Google Scholar
- Xiong HB, Xu HY, Xu Q, Zhu Q, Gan SX, Feng DD, Zhang XL, Xie XD, Zhang H, Li J, Han YL, Wen JC, Li DX, Shi YM, Wei XH, Chen LJ (2012) Origin and evolution of weedy rice revealed by inter-subspecific and inter-varietal hybridizations in rice. Mol Plant Breed 10:131–139 (in Chinese with English abstract)Google Scholar
- Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30:105–111CrossRefGoogle Scholar
- Yu Y, Tang T, Qian Q, Wang Y, Yan M, Zeng D, Han B, Wu CI, Shi S, Li J (2008) Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication. Plant Cell 20:2946–2959PubMedCentralPubMedCrossRefGoogle Scholar