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Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.)

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Abstract

Single nucleotide polymorphisms (SNPs) are the most abundant DNA markers in plant genomes. In this study, based on 54,465 SNPs between the genomes of two Indica varieties, Minghui 63 (MH63) and Zhenshan 97 (ZS97) and additional 20,705 SNPs between the MH63 and Nipponbare genomes, we identified and confirmed 1,633 well-distributed SNPs by PCR and Sanger sequencing. From these, a set of 372 SNPs were further selected to analyze the patterns of genetic diversity in 300 representative rice inbred lines from 22 rice growing countries worldwide. Using this set of SNPs, we were able to uncover the well-known Indica–Japonica subspecific differentiation and geographic differentiations within Indica and Japonica. Furthermore, our SNP results revealed some common and contrasting patterns of the haplotype diversity along different rice chromosomes in the Indica and Japonica accessions, which suggest different evolutionary forces possibly acting in specific regions of the rice genome during domestication and evolution of rice. Our results demonstrated that this set of SNPs can be used as anchor SNPs for large scale genotyping in rice molecular breeding research involving Indica–Japonica and Indica–Indica crosses.

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Acknowledgments

We are grateful to Drs. Qifa Zhang and Weibo Xie for sharing the SNP information between MH63 and ZS97 before their publication. We thank Hao Chen, Li Wang, Qiushi Huang, and Tiantian Zhu for their assistances in SNP verification. We appreciate Dr. Judy Lee’s help for manuscript editing. This work was supported by grants from the Bill and Melinda Gates foundation (51587-5), the Ministry of Science and Technology of China (2009DFB30030 and 2010AA101806), the Ministry of Agriculture of China (2008ZX08012-005, 2009ZX08012-021B, 2011-G2B and 2006-G51) and the Generation Challenge Program (#12) of CGIAR.

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Authors and Affiliations

  1. Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, 100871, Beijing, China

    Haodong Chen, Hang He, Yanjiao Zou, Wei Chen, Renbo Yu, Xia Liu, Yang Yang, Liu-Min Fan, Yi Li & Xing Wang Deng

  2. Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 100081, Beijing, China

    Yong-Ming Gao, Jian-Long Xu & Zhi-Kang Li

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  1. Haodong Chen
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  2. Hang He
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  3. Yanjiao Zou
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  4. Wei Chen
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  10. Liu-Min Fan
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  11. Yi Li
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  12. Zhi-Kang Li
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  13. Xing Wang Deng
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Corresponding authors

Correspondence to Zhi-Kang Li or Xing Wang Deng.

Additional information

Communicated by M. Wissuwa.

H. Chen, H. He and Y. Zou contributed equally to this work.

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Table S1 (XLS 81 kb)

Table S2 (XLS 28 kb)

Table S3 (XLS 28 kb)

Table S4 (XLS 88 kb)

Table S5 (XLS 153 kb)

Fig. S1 (JPG 2916 kb)

122_2011_1633_MOESM7_ESM.tiff

Fig. S2 Three separate clusters of the 300 parental rice lines of the international rice molecular breeding network revealed by a representative SNP (TIFF 278 kb)

Fig. S3 (JPG 1617 kb)

122_2011_1633_MOESM9_ESM.emf

Fig. S4 Classification of the 300 parental rice lines of the international rice molecular breeding network revealed by a neighbor-joining tree based on 258 SNP data (EMF 617 kb)

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Chen, H., He, H., Zou, Y. et al. Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.). Theor Appl Genet 123, 869–879 (2011). https://doi.org/10.1007/s00122-011-1633-5

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