Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice

Abstract

Awn is one of the most important domesticated traits in rice (Oryza sativa). Understanding the genetic basis of awn length is important for grain harvest and production, because long awn length is disadvantageous for both grain harvest and milling. We investigated the awn length of 529 rice cultivars and performed a Genomewide association studies (GWAS) in the indica and japonica subpopulations, and the whole population. In total, we found 17 loci associated with awn length. Of these loci, seven were linked to previously reported quantitative trait loci, and one was linked to the awn gene An-1. Nine novel loci were repeatedly identified in different environments. One of the nine associations was identified in both the whole and japonica populations. Special interest was the detection of the most significant association SNP, sf0136352825, which was less than 95 kb from the seed shattering gene qSH1. These results may provide potentially favourable haplotypes for molecular breeding in rice.

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Acknowledgements

This work was supported by grants from the National Science Foundation of China (31300991, 91335201), the National Special Programme for Research of Transgenic Plants of China (2014ZX0800936B) and the 863 programme on the functional genomics of stress resistance and nutrient utility in rice (2012 AA10A303).

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Correspondence to XUFENG BAI.

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Magwa R. A., Zhao H., Yao W., Xie W., Yang L., Xing Y. and Bai X. 2016 Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice. J. Genet. 95, xx–xx

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MAGWA, R.A., ZHAO, H., YAO, W. et al. Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice. J Genet 95, 639–646 (2016). https://doi.org/10.1007/s12041-016-0679-1

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Keywords

  • awn length
  • genomewide association analysis
  • single-nucleotide polymorphism
  • genetic linkage.