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Correlation between allele sizes of microsatellites and phenotypic variations in rice landraces

  • Research Article
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Frontiers of Agriculture in China

Abstract

Yunnan is one of the largest centers of genetic diversity in the world. Allele size of microsatellites associated with phenotypic traits of rice landraces in Yunnan, Southwest China, was investigated based on 20 SSR markers and 23 phenotypic traits, as well as eight mineral elements in brown rice within the core collection of 629 accessions; and there was a significant correlation for 182 (r = 0.083* − 0.438**) of 620 pairs among these markers and traits, as well as elements. Surprisingly, there was a significant correlation for 94 of 180 pairs between the allele size of microsatellites and grain traits, and 48 of 160 pairs between allele size of microsatellites and panicle traits. In these rice landraces, 309 alleles were detected, with an average of 15.5 alleles per marker, ranging from 5 (RM60) to 40 (RM257). There was a significant correlation between the allele size of 20 SSR markers and some phenotypic traits, such as the significant correlation of 17 (r = −0.085* − 0.438**) pairs between the allele size of RM224 and 23 phenotypic traits, as well as eight elements. The allele size of microsatellites was more associated with grain or panicle traits than that of plant traits or element contents in brown rice. Grain length/width ratio and 1–2 internode length, as indica-japonica classification traits, in which two traits were closely associated with the allele size of 14 SSR markers ranging from 0.089* to −0.438**. Therefore, allele size of SSRs was associated with phenotypic traits (especially in grain traits), as well as elemental contents in brown rice.

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Authors and Affiliations

  1. Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China

    Yawen Zeng, Shuming Yang, Juan Du & Xiaoying Pu

  2. Key Lab of Crop Genomics and Genetic Improvement of Ministry of Agriculture, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China

    Hongliang Zhang & Zichao Li

  3. Supervision and Testing Center for Farm Products Quality, Ministry of Agriculture of the People’s Republic of China, Kunming, 650223, China

    Luxiang Wang & Jiafu Liu

  4. Yunnan Agricultural University, Kunming, 650201, China

    Fenghui Xiao

Authors
  1. Yawen Zeng
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  2. Hongliang Zhang
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  3. Shuming Yang
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  4. Juan Du
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  5. Xiaoying Pu
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  6. Luxiang Wang
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  7. Jiafu Liu
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  8. Fenghui Xiao
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  9. Zichao Li
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Corresponding authors

Correspondence to Yawen Zeng or Zichao Li.

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These authors contributed equally to this work.

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Zeng, Y., Zhang, H., Yang, S. et al. Correlation between allele sizes of microsatellites and phenotypic variations in rice landraces. Front. Agric. China 3, 130–139 (2009). https://doi.org/10.1007/s11703-009-0033-y

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  • DOI: https://doi.org/10.1007/s11703-009-0033-y

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