Diachronic analysis of genetic diversity in rice landraces under on-farm conservation in Yunnan, China
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Diachronic analysis showed no significant changes in the level of genetic diversity occurred over the past 27 years’ domestication, which indicated genetic diversity was successfully maintained under on-farm conservation.
Rice (Oryza sativa L.) is one of the earliest domesticated crop species. Its genetic diversity has been declining as a result of natural and artificial selection. In this study, we performed the first analysis of the levels and patterns of nucleotide variation in rice genomes under on-farm conservation in Yunnan during a 27-year period of domestication. We performed large-scale sequencing of 600 rice accessions with high diversity, which were collected in 1980 and 2007, using ten unlinked nuclear loci. Diachronic analysis showed no significant changes in the level of genetic diversity occurring over the past 27 years’ domestication, which indicated genetic diversity was successfully maintained under on-farm conservation. Population structure revealed that the rice landraces could be grouped into two subpopulations, namely the indica and japonica groups. Interestingly, the alternate distribution of indica and japonica rice landraces could be found in each ecological zone. The results of AMOVA showed that on-farm conservation provides opportunities for continued differentiation and variation of landraces. Therefore, dynamic conservation measures such as on-farm conservation (which is a backup, complementary strategy to ex situ conservation) should be encouraged and enhanced, especially in crop genetic diversity centers. The results of this study offered accurate insights into short-term evolutionary processes and provided a scientific basis for on-farm management practices.
KeywordsGenetic Differentiation Artificial Selection Ecological Zone Rice Accession Rice Landrace
We thank the Chinese National Germplasm Bank for providing the landrace rice seeds. This work was supported by the National Key Technology Research and Development Program of China (2013BAD01B02-2, 2013BAD01B0101-02), Science and Technology Innovation Program of CAAS, the platform of National Crop Germplasm Resources, the Project of 973 (2010CB125904-5), the Protective Program of Crop Germplasm of China (NB2013-2130135-25-01), International Cooperation Project from National Institute of Crop Science, RDA (PJ008685).
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Conflict of interest statement
- Bellon MR, Pham JL, Jackson MT (1997) Genetic conservation: a role for rice farmers. In: Hawkes JG (ed) Plant conservation: the in situ approach. Chapman and Hall, IPGRI, LondonGoogle Scholar
- Brown AHD (2000) The genetic structure of crop landraces and the challenge to conserve them in situ on farms. In: Brush SB (ed) Genes in the fields: on–farm conservation of crop diversity. International Plant Genetic Resources Institute (IPGRI), Rome, International Development Research Centre (IDRC), Ottawa and Lewis Publishers, Boca Raton, pp 29–48Google Scholar
- Dai LY, Ye CR, Xu FR et al (1999) Genetic analysis on cold tolerance characteristics of Yunnan rice landrace (Oryza sativa L.) Kunmingxiaobaigu. Chin J Rice Sci 13:73–76Google Scholar
- Dong SB, Lu BR, Wang YY et al (2010) Preliminary studies on the within-varietal genetic diversity and its maintenance of traditional rice from Yunnan. J Yunnan Agric Univ 25:1–9Google Scholar
- Hall TA (1999) Bioedit: a user–friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
- Harlan JR (1975) Crops and man. American Society of Agronomy, MadisonGoogle Scholar
- Liu XZ, Zhao MF, He YQ et al (2007) Breeding and blast resistance identification of Lijiangxintuanheigu nearnisogenic pyramid lines. Acta Agron Sin 33:20–24Google Scholar
- Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
- Sirabanchongkran A, Yimyam N, Boonma W et al (2004) Varietal turnover and seed exchange: implications for conservation of rice genetic diversity on-farm. Int Rice Res Notes 29(2):18–19Google Scholar
- Shang JJ, Tao Y, Chen XW et al (2009) Identification of a new rice blast resistance gene, Pid3, by genomewide comparison of paired nucleotide-binding site–leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. Genetics 182:1303–1311CrossRefPubMedPubMedCentralGoogle Scholar
- Xu FR, Tang CF, Yu TQ et al (2010b) Diversity of paddy rice varieties from Yuanyang Hani’s terraced fields in Yunnan, China. Acta Ecologica Sinica 30:3346–3357Google Scholar
- Xu FR, Dong C, Yang WY et al (2011) Comparison of genetic diversity of rice landraces planted in two periods in Hani’s terraced fields in Yuanyang County, Yunnan province, China using microsatellite markers. Chin J Rice Sci 25:38l–386Google Scholar
- Zhou YH (1988) Regionalization of rice cropping in Yunnan. In: Min SK, Wu XZ (eds) Regionalization of rice cropping in China. Zhejiang Science, and Technology Pubublication, Hangzhou, pp 104–108Google Scholar
- Zhu YY, Chen HR, Fan JH et al (2003) The use of rice variety diversity for rice blast control. Sci Agric Sin 36:521–527Google Scholar
- Zhang HL, Sun JL, Wang MX et al (2006) Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR. Genome 50:72–83Google Scholar