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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.

Abstract

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.

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Acknowledgments

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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Authors and Affiliations

  1. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Germplasm Resources and Utilization, The National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, No.12 Zhongguancun Nandajie, Beijing, 100081, China

    Di Cui, Jinmei Li, Xiaoding Ma, Guilan Cao, Yongli Qiao & Longzhi Han

  2. Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No.9 Xueyunlu, Kunming, 650205, Yunnan, China

    Cuifeng Tang, Xinxiang A, Tengqiong Yu, Enlai Zhang, Furong Xu & Luyuan Dai

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  1. Di Cui
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Correspondence to Longzhi Han.

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Communicated by M. Thomson.

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122_2015_2617_MOESM1_ESM.pdf

Supplementary Fig. 1 Schematic diagrams of ten nuclear loci and locations of the regions sequenced. Exons are shown as open boxes, and exon numbers are labeled with capital roman numbers. Thin lines between open boxes refer to introns. Locations of primers for each fragment are sketched above the diagrams. (PDF 151 kb)

Supplementary Fig. 2 Regression between the number of haplotypes and latitude in 1980 (a) and 2007 (b). (PDF 84 kb)

Supplementary Fig. 3 The statistic ⊿K value for each given k in 1980 (a) and 2007 (b). (PDF 12 kb)

122_2015_2617_MOESM4_ESM.pdf

Supplementary Table 1 List of the materials sampled in the study, origin and subpopulation. Code No.: Official numbers of the accessions conserved in the Chinese National Germplasm Bank. (PDF 639 kb)

Supplementary Table 2 Descriptions of five ecological zones in Yunnan. (PDF 93 kb)

Supplementary Table 3 Summary of SSR markers and the primer sequences. (PDF 25 kb)

Supplementary Table 4 Summary of the genes sequenced and the primer sequences used in this study. (PDF 97 kb)

122_2015_2617_MOESM8_ESM.pdf

Supplementary Table 5 Summary of haplotype richness for rice accessions in each ecological zone from 1980 and 2007. (PDF 103 kb)

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Cui, D., Li, J., Tang, C. et al. Diachronic analysis of genetic diversity in rice landraces under on-farm conservation in Yunnan, China. Theor Appl Genet 129, 155–168 (2016). https://doi.org/10.1007/s00122-015-2617-7

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