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Plant Diversity and Resources

Journal of Systematics and Evolution

Volume 55 Issue 2, Pages 149C157.

Published Online: 4 Jan. 2017

DOI: 10.1111/jse.12230

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Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution

Dong-Yuan Song1, Zhe Wang1, Zhuo-Jun Song1, Cheng-Chuan Zhou1, Peng-Hao Xu1, Jie Yang2, Ji Yang1, and Bao-Rong Lu1*

1Ministry of Education, Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai 200438, China

2Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement/Jiangsu High Quality Rice R&D Center, Nanjing 210014, China

Keywords: adaptive evolution; change of farming practice; genome sequence; human influence; novel mutant; weed


Substantial genetic variation is found in weedy rice (Oryza sativa f. spontanea Roshev.) populations from different rice-planting regions with the change of farming styles. To determine the association of such genetic variation with rice farming changes is critical for understanding the adaptive evolution of weedy rice. We studied weedy-rice specific novel single nucleotide polymorphisms (SNPs) by genome-wide comparison between DNA sequences of weedy and cultivated rice, in addition to polymerase chain reaction fingerprinting at 22 selected novel SNP loci in weedy rice populations. A great number of novel SNPs were identified across the weedy rice genome. High frequencies of the novel SNPs were determined at the 22 selected loci, although with considerable variation among weedy rice populations in different rice-planting regions. The highest frequency (∼57%) of novel SNPs was identified in weedy rice populations from Jiangsu that experienced the most dramatic changes in rice farming styles, including the shift from transplanting to direct seeding, and from indica to japonica varieties. The lowest frequency (∼29%) was detected in weedy rice populations from Northeast China, where rice farming has undergone relatively less change. The association between frequencies of novel SNPs in weedy rice populations and the extent of changes in rice farming styles suggests the critical role of adaptive mutation and accumulation of the mutation influenced by human activities in the rapid evolution of weedy rice.


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